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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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <[email protected]> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: michaelabuckley <[email protected]> Co-authored-by: juan.marchionatto <[email protected]> Co-authored-by: Tadgh <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <[email protected]> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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] <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Michael Buckley <[email protected]> Co-authored-by: jkv <[email protected]> Co-authored-by: chgl <[email protected]> Co-authored-by: ppalacin <[email protected]> Co-authored-by: Ally Shaban <[email protected]> Co-authored-by: Vadim Peretokin <[email protected]> Co-authored-by: Jaison B <[email protected]> Co-authored-by: Jaison B <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Werner <[email protected]> Co-authored-by: Håkan MacLean <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Joel Schneider (NMDP) <[email protected]> Co-authored-by: craig mcclendon <[email protected]> Co-authored-by: Craig McClendon <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: michaelabuckley <[email protected]> Co-authored-by: Alejandro Medina <[email protected]> Co-authored-by: Alejandro Medina <[email protected]> Co-authored-by: Dennis Verspuij <[email protected]> Co-authored-by: markiantorno <[email protected]> Co-authored-by: Ibrohim Kholilul Islam <[email protected]> Co-authored-by: Ibrohim Kholilul Islam <[email protected]> Co-authored-by: Kevin Dougan SmileCDR <[email protected]> Co-authored-by: juan.marchionatto <[email protected]> Co-authored-by: jmarchionatto <[email protected]> Co-authored-by: Shubham Parikh <[email protected]> Co-authored-by: Hank Wallace <[email protected]> Co-authored-by: Peter Micuch <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> Co-authored-by: Shubham Parikh <[email protected]> Co-authored-by: vpanhale <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <[email protected]> * Update src/test/smoketest/SMOKE_TEST.md Co-authored-by: Ken Stevens <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: michaelabuckley <[email protected]> Co-authored-by: juan.marchionatto <[email protected]> Co-authored-by: Tadgh <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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 <[email protected]> * 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] <[email protected]> * 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 <[email protected]> Co-authored-by: Vladimir Nemergut <[email protected]> Co-authored-by: jamesagnew <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: jvi <[email protected]> Co-authored-by: Sean McIlvenna <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> * Updated code to read url pattern from environment. (#10) * BT-96 Added OAuth support * BT-96 Fixed indentation * BT-96 Fixed spacing * BT-96 Removed unwanted filed * Changes in code as per PR suggestions * added rest security extension in metadata * Updated PR as per suggestions * Updated README.md file to run the app with custom property file & env variables * Updated PR as per suggestions * Added user role validation in Oauth * code refactor * Updated code for using single oauth user role * Updated code as per PR suggestions * Updated code as pr PR siggestions * Added suppoet of delete operation to admin only * Refactored code * Added custom search narrowing filter * Updated code to work with oauth disabled * Updated code to get claim name from environment * change claim name env varible to proper name * Updated code to use hard-coded claim name * Changed custom mapper claim name to patient from subject * Added rule builder to filter resources * code refactor * Update CustomAuthorizationInterceptor.java * updated code to support operations on bundle resources * Added consent rule to allow patch request * Added oauth support for task resource * Updated code to make refrence check generic method * Updated method names * Updated code as per PR suggestions * Update code as per PR suggestion * Updated code as per PR * Added verification of clientId from token * Added basic authentica…
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