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* 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>
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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>
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* 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>
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Co-authored-by: Ken Stevens <khstevens@gmail.com>
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* 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>
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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
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* 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>
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* 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>
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* 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>
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* 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
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* 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…- Loading branch information
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Jun 14, 2023
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