Sync 6.2.2 #41

shubhamparikh927 · 2023-01-06T09:20:10Z

Synced with opensource v6.2.2
Tested the changes locally by running docker locally.

…sLocal()

Subscription tests fail ...

5.6.0 upgrade

the Ubuntu runner base image already includes Helm 3.7.0

* master: Update application.yaml Bumped version of Spring Boot in order to fix same issue as jmix-projects/jmix-security#90 Upgraded to 5.6.0 Subscription tests fail ... Added OpenAPI / Swagger option simplified helm chart build ARM-compatible images bumped dependencies to latest only push build images to DockerHub Adds ability to change HAPI FHIR JPA server's port with the environment variable server.port Adds ability to control the number of executor threads through environment variables server.tomcat.max-threads and server.tomcat.min-spare-threads. There is not a breaking change and does not affect the function of the JPA server unless these environment variables are set. Adds ability to use delete-expunge operations to the JPA Starter Server. # Conflicts: # pom.xml # src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java # src/main/java/ca/uhn/fhir/jpa/starter/Application.java # src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java # src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java # src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java # src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java # src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java # src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java

registering ValueSetOperationProvider

Https support for es

updated helm chart to use image v5.6.0

* PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io>

hankwallace

A few comments on things that are different between our fork and the upstream.

docker-compose.yml

README.md

src/main/resources/application.yaml

docker-compose.yml

* Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as jmix-projects/jmix-security#90 * Update application.yaml See hapifhir#292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (hapifhir#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](pgjdbc/pgjdbc@REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](hapifhir#318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (hapifhir#319) * Updated docker image according to discussion on hapifhir#305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (hapifhir#324) * added reindexProvider to Config (hapifhir#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (hapifhir#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (hapifhir#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (hapifhir#345) * add support for ms sql server (hapifhir#347) * Fix comments in Demo that lead to 404 (hapifhir#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (hapifhir#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (hapifhir#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (hapifhir#355) * Add: of-type modifier option in application.yaml (hapifhir#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (hapifhir#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (hapifhir#377) * updated helm chart to use latest v6.0.1 version of the image (hapifhir#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. hapifhir/hapi-fhir#3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (hapifhir#391) Closes hapifhir#387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (hapifhir#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (hapifhir#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (hapifhir#426) * added back lost config entry: allowed_bundle_types (hapifhir#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: hapifhir#430 * Proper close DB connection after dialect was resolved (hapifhir#435) * removed duplicated and wrong subscription code (hapifhir#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (hapifhir#444) * revering to H2 (hapifhir#449) * Tracking Hapi 6.2-PRE releases (hapifhir#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (hapifhir#451) * fixes for support of R4B / 6.2.0 (hapifhir#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (hapifhir#458) * Bumped version (hapifhir#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as jmix-projects/jmix-security#90 * Update application.yaml See hapifhir#292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (hapifhir#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](pgjdbc/pgjdbc@REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](hapifhir#318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (hapifhir#319) * Updated docker image according to discussion on hapifhir#305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (hapifhir#324) * added reindexProvider to Config (hapifhir#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (hapifhir#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (hapifhir#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (hapifhir#345) * add support for ms sql server (hapifhir#347) * Fix comments in Demo that lead to 404 (hapifhir#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (hapifhir#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (hapifhir#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (hapifhir#355) * Add: of-type modifier option in application.yaml (hapifhir#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (hapifhir#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (hapifhir#377) * updated helm chart to use latest v6.0.1 version of the image (hapifhir#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * sync change with version 6.2.2 * sync deployment.yaml * added newline in dockerfile * added new line EOF * Updated code to use non tmp directory * removed duplicate files * Updated code as per PR suggestion * Updated code as suggested on pr Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: Arbaaz Muslim <arbaaz.muslim@freenome.com> Co-authored-by: Thomas Papke <web@thopap.de> Co-authored-by: rti <rti@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Kai-W <kai.westerkamp@web.de> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> Co-authored-by: Vadim Dribinsky <dimon37@users.noreply.github.com> Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io>

* registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi pro…

* updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * 6.4.0 (#47) * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentica…

* registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated …

* updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * 6.4.0 (#47) * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentica…

* Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as jmix-projects/jmix-security#90 * Update application.yaml See hapifhir#292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (hapifhir#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](pgjdbc/pgjdbc@REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](hapifhir#318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (hapifhir#319) * Updated docker image according to discussion on hapifhir#305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (hapifhir#324) * added reindexProvider to Config (hapifhir#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (hapifhir#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (hapifhir#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (hapifhir#345) * add support for ms sql server (hapifhir#347) * Fix comments in Demo that lead to 404 (hapifhir#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (hapifhir#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (hapifhir#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (hapifhir#355) * Add: of-type modifier option in application.yaml (hapifhir#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (hapifhir#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (hapifhir#377) * updated helm chart to use latest v6.0.1 version of the image (hapifhir#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. hapifhir/hapi-fhir#3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (hapifhir#391) Closes hapifhir#387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (hapifhir#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (hapifhir#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (hapifhir#426) * added back lost config entry: allowed_bundle_types (hapifhir#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: hapifhir#430 * Proper close DB connection after dialect was resolved (hapifhir#435) * removed duplicated and wrong subscription code (hapifhir#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (hapifhir#444) * revering to H2 (hapifhir#449) * Tracking Hapi 6.2-PRE releases (hapifhir#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (hapifhir#451) * fixes for support of R4B / 6.2.0 (hapifhir#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (hapifhir#458) * Bumped version (hapifhir#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as jmix-projects/jmix-security#90 * Update application.yaml See hapifhir#292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (hapifhir#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](pgjdbc/pgjdbc@REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](hapifhir#318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (hapifhir#319) * Updated docker image according to discussion on hapifhir#305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (hapifhir#324) * added reindexProvider to Config (hapifhir#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (hapifhir#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (hapifhir#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (hapifhir#345) * add support for ms sql server (hapifhir#347) * Fix comments in Demo that lead to 404 (hapifhir#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (hapifhir#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (hapifhir#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (hapifhir#355) * Add: of-type modifier option in application.yaml (hapifhir#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (hapifhir#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (hapifhir#377) * updated helm chart to use latest v6.0.1 version of the image (hapifhir#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](mysql/mysql-connector-j@8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix hapifhir#122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * sync change with version 6.2.2 * sync deployment.yaml * added newline in dockerfile * added new line EOF * Updated code to use non tmp directory * removed duplicate files * Updated code as per PR suggestion * Updated code as suggested on pr Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: Arbaaz Muslim <arbaaz.muslim@freenome.com> Co-authored-by: Thomas Papke <web@thopap.de> Co-authored-by: rti <rti@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Kai-W <kai.westerkamp@web.de> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> Co-authored-by: Vadim Dribinsky <dimon37@users.noreply.github.com> Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io>

* updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * 6.4.0 (#47) * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi pro… * removed duplicate variable --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: Arbaaz Muslim <arbaaz.muslim@freenome.com> Co-authored-by: Thomas Papke <web@thopap.de> Co-authored-by: rti <rti@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Kai-W <kai.westerkamp@web.de> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Luke deGruchy <luke.de…

* updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * 6.4.0 (#47) * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi pro… * removed duplicate variable * Logging changes (#50) * Updated the logging when auth fail to show in warn level * added newline * updated dockerfile to use root user before creating directory * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * 6.4.0 (#47) * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](htt…

* Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Spelling error in Application.yaml Fix spelling error in comments section * configuration option to not reload IG resources that are already loaded * Update docker-compose sample with small application.properties When running from Docker Hub, it is not convenient to have to copy the full application.yaml as a starting point. Based on Spring's property initialization order, it's possible to mount a small version of application.yaml in the config folder in the run directory. * Removed explicit inclusion of snakeyaml and allow spring-boot-starter-actuator to pull it in as a needed dependency. * Simplify using an interceptor with Docker Now it is possible to mount a folder with extra classes that are loaded by HAPI. This makes it easy to load an interceptor JAR while using the standard Docker image. The README explains how to use it. Spring by default uses the WarLauncher. Now the ENTRYPOINT uses the PropertiesLauncher, configured in such a way that it is compatible with the WarLauncher, but adding the folder /app/extra-classes to the loader.path. * Update pom.xml Update to 6.4.1 * Update pom.xml * Update pom.xml * 497 - Fix typo on property setter. * Create smoke-tests.yml * Update smoke-tests.yml Don't do integration tests. Start server Run smoke tests Stop Server * Rename plain_server.rest to plain_server.http * Update smoke-tests.yml Skip maven tests Wait longer for server * Update smoke-tests.yml Wait longer just in case Maybe don't kill the jetty server? * Use docker for HTTP client * Try fixing TTY issue * Sleep a little longer... * Additional param for linux localhost * Intentional failure * Restore reasonable sleep time * Bump HAPI to release 6.6.0 (#539) * Start tracking 6.5 * Use JpaStorageSettings and StorageSettings * Bump parent pom version + add deps for jaxb * Bump HAPI * Fix Subscription/Topic resource creation * fix subscription topic beans * Change to rel_6_6 hapi-fhir SNAPSHOT * Fix emailSender config * Split method calls by line. * Merge pull request #524 from hapifhir/do-20230509-smoke-test-ci Create smoke-tests.yml * Bump core to release 6.6.0 --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added consent rule to allow patch request * Updated method names * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * Removed client id validation from oauth token * fixed indentation * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oau…

* Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * updated dockerfile to use root user before creating directory * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Updated hapi-fhir dependency version to 6.2.5 (#44) * Spelling error in Application.yaml Fix spelling error in comments section * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * 6.4.0 (#47) * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes to the helm chart * updated helm chart to use version 6.1.0 of the image * added appProperties.getInline_resource_storage_below_size() (#420) * added appProperties.getInline_resource_storage_below_size() * indentations * Feat/restructuring (#422) * Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean * Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library * Disabled default validation enabled * Extract IG loading (#426) * added back lost config entry: allowed_bundle_types (#427) * added back lost config entry * disabled entry * Bump snakeyaml from 1.30 to 1.31 Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * fix: configuration of cors Refs: #430 * Proper close DB connection after dialect was resolved (#435) * removed duplicated and wrong subscription code (#440) * fixed SubscriptionDebugLogInterceptor adding logic * switch to postgres db (#444) * revering to H2 (#449) * Tracking Hapi 6.2-PRE releases (#408) * Tracking branch for 6.1 pre-releases. * Update to 6.1.0-PRE3-SNAPSHOT * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Adjust enumeration renaming * Repoint FHIR 6.2.0-PRE1-SNAPSHOT * Add missing Bean to starter configuration * Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT * Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod. * Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT * Update dep * Bump version fix failures * Remove dead import * Fix up * remove batch refs Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Added hibernate.dialect for Postgress to Readme (#451) * fixes for support of R4B / 6.2.0 (#455) * upping hapi version to 6.2.1 * Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458) * Bumped version (#462) * allow interceptors to be registered via properties * Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465) * Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT. This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api). * Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors. * Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none. Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true * Set allow-bean-definition-overriding: true on test application.yaml as well. * Remove lines in ExampleServerR4BIT that causes an implementation guide version error. * Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding. Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2. * Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors. Also, remove explici logger disabling code in Application.java. * Restore Application.java as well as both application.yaml files to the same as master. * Feature/static files (#456) * Added mapping * Added documentation * Remove old junit4 usage. * Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT. This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476) This reverts commit 9a513cd1845723c630565ac2b124d74e56491006. * Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479) * First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes. Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none"); * Feature/index default (#475) * Added default * Refactored the default resolution * Updated Helm chart to use hapi fhir image 6.2.2 (#472) * Implement a new solution: Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions. It's the addition of the rollback for slf4j-api that seems to restore logging. * Fix tests for websocket * Update pipeline to run integration tests. * Initial IPS + Cql to Cr migration * Allow Enabling IPS via config * typo * CQL to CR * HAPI FHIR bump * docs: Updated README.md. Discontinue mysql * removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4 * docs: Fix postgresql typo in docker-compose * docs: Explicitly set hibnerate.search.enabled to false if database is postgresql * refactor: Separate unrelated settings and documentation * docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions * docs: Revert dislaimer in postgres * Bump Hapi * Fix Application error regarding multiple beans * Add optional explicit ip config for smoke tests * Revert "Add optional explicit ip config for smoke tests" This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe. * Dev (#45) * updated dockerfile to use root user before creating directory * Updated hapi-fhir dependency version to 6.2.5 (#44) * reverted dockerfile which was earlier modified to test build issue on jenkins * Added newline in Dockerfile * Changes how the capability statement is implemented (#46) * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * BT-140 set legacy sql builder based on hibernate to true * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added basic authentication * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * PT-669 Updated dockerfile to use user dir path for build * Sync 6.1.0 (#38) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * Tracking branch for 6.1 pre-releases. * add BinaryAccessProvider to BaseJpaRestfulServer * Update to 6.1.0-PRE3-SNAPSHOT * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Adjust for hapi-fhir namespace changes and version * Adjust version to include new hapi-fhir HSearch fast path feature * Bump hapi PRE * Update to PRE16 * Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation. Add commented out sample properties for lucene and elastic. Move batch.job.enabled property under spring: prefix to have it considered. * Bump to release * Add missing bean * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1687 Updated code to allow metadata request for server healthcheck (#7) Co-authored-by: Shubham Parikh * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-80 Updated code to allow header x-api-key * Updated docker compose file with required env variables * SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4) Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated code to read url pattern from environment. (#10) * BT-140 set legacy sql builder based on hibernate to true * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * code refactor * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentication * Code refactor * Added username/password check while checking is basic auth enabled * Added custom property file * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * Updated docker compose file with required env variables * Update docker-compose.yml Updated file as per suggestions * Added custom property file * SAP-1596 Updated custom property file to read values from env * SAP-1667 Added interceptor for authorization (#5) * SAP-1667 Added interceptor for authorization * SAP-1667 Removed unused space. * SAP-1667 Added newline at the end of the file. Co-authored-by: Shubham Parikh <> * DEV-769: Update from upstream branch (#9) * Adding environment variables to override hapi properties file settings * Only override existing hapi properties with env ones * Start Release branch for 5.1.0 * Add property for multitenancy * Get test passing * Add repo * Bump to current release * Rework the JPA server class a bit * Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though. * Adding .dockerignore file to improve the efficiency of docker builds * Added support for configurable client ID strategy * Bump mysql-connector-java from 8.0.11 to 8.0.16 Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16) Signed-off-by: dependabot[bot] <support@github.com> * Resolve some compile errors * Fix EMPI rules json * Have EmpiSettings actually return an EmpiSettings bean * Update readme * Remove dead space * Update property * Update README to include Docker info * Prepare for release * Merge master * Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless. * Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter * Update Dockerfile Added caching of maven dependency resolving * Fix #122 - EMPI error on startup when EMPI not enabled Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> * BT-96 Fixed spacing * BT-96 Removed unwanted filed * added rest security extension in metadata * code refactor * Update JpaRestfulServer.java * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added custom search narrowing filter * Updated code to get claim name from environment * Added rule builder to filter resources * code refactor * Added oauth support for task resource * Added verification of clientId from token * Added hibernate physical_naming_strategy to use proper table names. * updated code to use url mapping from environment * Removed client id validation from oauth token * fixed indentation * Updated fork with upstream * Removed unwanted files * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * removed unwanted imports and files merged during rebase 6.1.0 * Updated application-custom.yaml * commented allow-bean-definition-overriding * Sync application-custom.yaml * commented unused hibernate settings Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: jkv <jenskristianvilladsen@gmail.com> Co-authored-by: chgl <chgl@users.noreply.github.com> Co-authored-by: ppalacin <patrick.palacin@i-atros.com> Co-authored-by: Ally Shaban <allyshaban5@gmail.com> Co-authored-by: Vadim Peretokin <vperetokin@hey.com> Co-authored-by: Jaison B <jaisonb@gmail.com> Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <pa.f.werner@gmail.com> Co-authored-by: Håkan MacLean <hakan@maclean.se> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Joel Schneider (NMDP) <jschneid@nmdp.org> Co-authored-by: craig mcclendon <XcrigX@users.noreply.github.com> Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Alejandro Medina <janol77@users.noreply.github.com> Co-authored-by: Alejandro Medina <amedina@cens.cl> Co-authored-by: Dennis Verspuij <6680484+dennisverspuij@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@gmail.com> Co-authored-by: Ibrohim Kholilul Islam <ibrohimislam@users.noreply.github.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@heaptrace.com> Co-authored-by: Hank Wallace <hwallace@elimu.io> Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com> Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com> Co-authored-by: jvi <jvi@trifork.com> Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com> Co-authored-by: Shubham Parikh <sparikh@elimu.io> Co-authored-by: vpanhale <vsingh@elimu.io> * Updated docker file to use /user/app dir (#39) * PT-689 split url (#40) * PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io> * Sync 6.2.2 (#41) * Bump dep version * Remove javamail and replace with simple-java-mail * WIP * Remove print * Remove bean override * Bump version * Add broken test * Update for new style of container bean * Bump for new version * Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index * Disable default flyway processing * Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal() * Added OpenAPI / Swagger option * Upgraded to 5.6.0 Subscription tests fail ... * Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90 * Update application.yaml See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292 * documented use of Values.extraEnv * added options for specifying a PodDisruptionBudget * simplified chart release workflow the Ubuntu runner base image already includes Helm 3.7.0 * Support HTTPS * Use default application.yaml * registering ValueSetOperationProvider * Upgrade to 5.7.0-PRE4-SNAPSHOT for testing * Share elasticsearch configuration * Fixed compile issues * Fix misconfiguration modelConfig is part of DaoConfig and should not have a separate lifecycle. * Bump to 5.7.0-PRE8-SNAPSHOT * Typo fix in README * Add configuration flag to enable storing of resources in lucene index (#304) * Add configuration flag to enable storing of resources in lucene index * Fix build issue * Fix code review suggestions Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com> * Add ES native aggregation builder for lastN * Revert "Add ES native aggregation builder for lastN" This reverts commit 5312f78b956d4ad4863580035972263586d616c3. * bump version * Update for 5.7.x changes * Fix h2 dialect, replace mail dep * Bump postgresql from 42.2.23 to 42.2.25 Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * bump Hapi PRE version * Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider. * Version bump to 5.7.0 and a few other components now draw the version from parent * Update application.yaml Momentarily added `allow-circular-references: true` * bump to real version * Bump version * Remove search coord thread pool * Added instructions about removing Hibernate dialect To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue. * Bump HAPI-FHIR version * Move to newlines * fix to work with latest hapi-fhir * Feature/update docker support (#319) * Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305 * Added doc * Added corrections according to comments * Update Dockerfile * Update build-images.yaml Updated to default to distroless * add dao_scheduling_enabled configuration property (#324) * added reindexProvider to Config (#326) * Update application.yaml * Update application.yaml Roll back - mistake from my side * Bump hapi-fhir version to 'PRE5' (#329) * Add actuator * Bump to PRE8 * disable springboot actuator endpoints other than 'health' for security reasons (#338) Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com> * Bump to PRE9 * Update application.yaml (#345) * add support for ms sql server (#347) * Fix comments in Demo that lead to 404 (#348) Co-authored-by: dotasek <david.otasek@smilecdr.com> * updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346) * Update application.yaml Reverted to sane defaults * Bump to PRE10 * Updated to HAPI FHIR version 5.7.2 (#349) * Revert accidental default activation of experimental lucene indexing * Add disclaimer for advanced_lucene_indexing added warning to advanced_lucene_indexing: false property * Bump to hapi PRE11 * Expose Prometheus metrics (#355) * Add: of-type modifier option in application.yaml (#363) Co-authored-by: Alejandro Medina <amedina@cens.cl> * Fix applying supported_resource_types option with list that already includes SearchParameter (#365) * Bump pom and minimum java version * Bump ES version * hibernate search application properties updates. * make lastN test pass * Remove value set provider as it causes a boot failure without lucene * Fix reindex provider * Bump java version for test * Bump to pre-01 * fix build * Re-add valuesetoperation provider * Disable lucene by default * Re-add valueset operation provider * adding smoke test files * adding base documentation * wip * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <khstevens@gmail.com> * bumping to non-snapshot version (#377) * updated helm chart to use latest v6.0.1 version of the image (#382) * updated helm chart to use latest v6.0.1 version of the image * updated workflow to run against multiple k8s versions * add BinaryAccessProvider to BaseJpaRestfulServer * Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> * Applying fix from upstream for h2 Binaries This issue is already fixed upstream. Can be removed with next hapi version upgrade. https://github.com/hapifhir/hapi-fhir/pull/3676 * removed wrong and duplicated config entry `daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy` * Added OpenTelemetry Java Agent JAR to container image (#391) Closes #387 * changes to pom.xml to enable publishing * fixed directory of the .war in tomcat-based image * bulk data instrumentation included * bulk data instrumentation turned off by default * updated opentelemetry-java-instrumentation JAR to 1.16.0 * Better support for ARM java17 regular doesn't have ARM, java17-debian11 does * Updated Otel Java agent to 1.17.0 * Updated hapi-fhir to 6.1.0 * Minor Helm chart dependency updates and security improvements * Don't run maven CI on changes …

tadgh and others added 30 commits August 27, 2021 13:34

Bump dep version

395a87e

Remove javamail and replace with simple-java-mail

5038b5b

WIP

6e876c1

Remove print

a8a98c3

Remove bean override

e263646

Bump version

6e2836b

Add broken test

f3ea680

Update for new style of container bean

e41c186

Bump for new version

370d68a

Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index

ac75421

Disable default flyway processing

3272b8c

Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsA…

097db16

…sLocal()

Added OpenAPI / Swagger option

ea3f10e

Upgraded to 5.6.0

16559ea

Subscription tests fail ...

Bumped version of Spring Boot in order to fix same issue as jmix-proj…

9645087

…ects/jmix-security#90

Merge pull request hapifhir#291 from hapifhir/5.6.0-upgrade

a58ef1c

5.6.0 upgrade

Update application.yaml

0203a36

See hapifhir#292

documented use of Values.extraEnv

e39d84e

added options for specifying a PodDisruptionBudget

304f779

simplified chart release workflow

8ce44c2

the Ubuntu runner base image already includes Helm 3.7.0

Support HTTPS

6092200

Use default application.yaml

ff8302a

registering ValueSetOperationProvider

e077091

Upgrade to 5.7.0-PRE4-SNAPSHOT for testing

8c6a1a7

Share elasticsearch configuration

bfa6ed1

Merge pull request hapifhir#295 from ashaban/master

18cf0fd

registering ValueSetOperationProvider

Merge pull request hapifhir#294 from ZuSe/https-support-for-es

7ece4c3

Https support for es

Merge pull request hapifhir#293 from chgl/updated-helm-chart

c89b0d4

updated helm chart to use image v5.6.0

Fixed compile issues

8568132

dimon37 and others added 7 commits January 4, 2023 17:46

PT-689 split url (#40)

4537fe8

* PT-689 splitting the URL of datasource * PT-689 splitting the URL of datasource * PT-689 adding an easier ability to switch to another DB server * PT-689 standardizing variable names Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io>

sync change with version 6.2.2

0cd0810

sync deployment.yaml

b91616f

added newline in dockerfile

c6c663f

added new line EOF

36d3283

Merge branch 'master' into sync-6.2.2

761f5ef

Updated code to use non tmp directory

47b036a

shubhamparikh927 requested a review from hankwallace January 6, 2023 12:19

removed duplicate files

07f5174

hankwallace requested changes Jan 13, 2023

View reviewed changes

Updated code as per PR suggestion

4bdd0a4

shubhamparikh927 requested a review from hankwallace January 16, 2023 14:44

hankwallace requested changes Jan 16, 2023

View reviewed changes

docker-compose.yml Outdated Show resolved Hide resolved

Updated code as suggested on pr

5ac9c44

shubhamparikh927 requested a review from hankwallace January 17, 2023 06:52

hankwallace approved these changes Jan 17, 2023

View reviewed changes

shubhamparikh927 merged commit 484b057 into master Jan 18, 2023

hankwallace deleted the sync-6.2.2 branch January 20, 2024 02:11

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