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* 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>
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