hapi-fhir/hapi-fhir-jpaserver-model/pom.xml

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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
Rel 7 0 mb 2 (#5714) * pom bump to 7.0.0 (#5615) * pom bump to 7.0.0 * add version enum * fixed feb release name --------- Co-authored-by: Long Ma <long@smilecdr.com> * Check index existence on raw SQL creation (#5624) * Add conditional check on index existence before we try again * Add conditional check on index existence before we try again * Changelog * remit * remit * debug statements * 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622) * Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback. * Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations. * adding changelog and spotless. * Fixing typo. * Addressing comments from code review. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614) * Failing test * fix * changelog * Avoiding Exception being thrown on @EventListener invocation (#5628) * replaced EventListener annotation with @PreDestroy * adding changelog --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * simple fix (#5630) Co-authored-by: Long Ma <long@smilecdr.com> * Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625) * Incorrect version from versioned_references.auto_at_paths for conditional update - implementation * Oracle: Ensure migrated database still takes large resource text updates (#5629) * First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration. * First stab at agreed upon solution. * Fix error with 4001 by removing unnecessary annotation. * Spotless and TODO. * Remove annotation for good and set length to LONG32. * Fix copyright year. * Finalize changelog. * Remove migration changes. Fix unit test. * Fix compile error. * Log output. * Refactor resource history code into new ResourceHistoryCalculator. * Spotless. * Convert record to POJO. * Restore pre-17 switch statement. * Finalize new resource history calculator code and tests. * Spotless. * Remove logging. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml Apply code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review feedback. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638) * When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases. * Minor change to fix test * Rename changelog file * Remove TODOs as they're replaced by reported issue * Revert accidental change added with TODO removal * $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637) * $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation * Fix Measure group id null pointer exception (#5620) * Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id * add changelog --------- Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> * Rule evaluation: Allow Bundles with PATCH Parameters (#5641) * Remove parameters clause. * Finalize changelog. Add tests. Finalize implementation. * Undo changes to this test. * Revert all changes to FhirQueryRuleImplTest. Add new RuleImplOpTest. Ensure that proper nested Bundle is created for test and other fixes. * Tweak test. * Use real rule applier in test and remove all mocks. * Prevent batch2 job execution to stop for empty chunk when last job st… (#5635) * Prevent batch2 job execution to stop for empty chunk when last job step is a reduction. Add output to bulk export result even when empty. * Fix test * Unimportant change to force fresh build * Implement review suggestions --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Index review fixes (#5649) * Don't hold locks while adding indices during upgrade. * concurrent indexing is non-transactional in PG. * Fix conditional creates without leading '?' (#5646) * First commit with failing test. * More tests and logs. * More logs * Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(). * Simplify solution. Add more tests. * Changelog. * javadoc * Searching for Bundles with read all Bundles permission returns 403 (#5644) * failing test * another failing test case * fix * changelog * fix bug * spotless * cr * Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660) * Bump json-path * Pin parrson * Bump elastic * Bump spring version * Exclude JDBC * Serializing changes for sensitive data (#5655) * Add new senstiive data serializer * Add new senstiive data serializer * Add new senstiive data serializer * Remove dead comments * Change up the test * review comments * wip * Tighten tests and push annotation down * Tighten tests and push annotation down * Changelog * Add test * 7.0.1-SNAPSHOT bump * Error code * Add method used by CDR * add version enum * Fix test * Revert change to other safe version to stop problem with deprecated field * Rel 7 0 CVE (#5663) * Bump json-path * Pin parrson * Bump elastic * Bump spring version * Exclude JDBC * Descendent fix (#5669) * Fix "is-a" ValueSet expansion, add "descendent-of" support * Fixed tests in DSTU3 and R5 * Trigger new build * Revert "Trigger new build" This reverts commit 46c672b338db1f85c4f438344bfa828bfc723a37. * fix default partition setting on resource (#5617) * fix default partition setting on resource * changelog * Handle DEFAULT partition in rule checker. * Fix spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * pom bump, doc add, version enum add (#5616) Co-authored-by: Long Ma <long@smilecdr.com> * fix default partition setting on resource (#5618) * fix default partition setting on resource * Handle DEFAULT partition in rule checker. Co-authored-by: Ken Stevens <khstevens@gmail.com> * Add setting to make broker not use JacksonMessageConverter (#5611) * Add setting to make broker not use JacksonMessageConverter * Add changelog * Implement suggestions --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix version * add changelog, add attribution, remove accidental bring-overs * add changelog, add attribution, remove accidental bring-overs * Finish jira section --------- Co-authored-by: Ole Hedegaard <ohe@trifork.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * $poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681) * Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. * Fix NPE on -export-status operation with PatientIdPartitionInterceptor * 5654 measurescorer bug for denominator exception (#5677) * update measure bundles and tests for enforced populationId specification on Measure group resources * bump CR version to PRE17 * fix bug in versionEnumTest * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698) * Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. * Spotless fix * Address code review comments * version bump to 7.0.0 * pipeline fix * Update java home * Updating version to: 7.0.1 post release. * post mergeback cleanup * bump clinical-reasoning.version to pre17 * test fix * version bump to 7.1.5-snapshot --------- Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ole Hedegaard <ohe@trifork.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: markiantorno <markiantorno@gmail.com>
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<version>7.1.5-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jpaserver-model</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR JPA Model</name>
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<dependencies>
<!-- FHIR -->
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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</exclusions>
</dependency>
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<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpa</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
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<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>${project.version}</version>
</dependency>
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<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<groupId>org.hibernate.orm</groupId>
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<artifactId>hibernate-core</artifactId>
</dependency>
<dependency>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
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<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-mapper-orm</artifactId>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
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</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
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</dependency>
Introduce hibernate envers, use it only for MdmLink, disable it for now, add to MdmLink Dao and unit test revisions. (#4615) * First commit with new maven deps for envers and stubbed changelist. * Add repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class to BaseAppCtxPersistence. Comment it out in JpaConfig. Add constant for hibernate.integration.envers.enabled. Hard-code envers to false. App starts without error. Basic smoke testing for MpmLink update works. * Add mdmLink code to retrieve envers history and unit test it. * Initial code to handle envers from HapiFhirEnversRevision along with a custom extension of the revision/REVINFO entity. * Add changelist and tweak table/sequence/field names and clean up the HapiFhirJpaMigrationTasks method. * Fix some unit test failures and address TODOs. * Ensure hard-coded deactivation of envers is overridden by unit tests. * Remove commented-out code. * Address code review comments. * Remove sysout traces. * Tweaks to poms with comments explaining why I left the versions in the plugin dependencies. Get rid of a duplicate envers dependency. * Bump hapi-fhir version to 6.5.5-SNAPSHOT. * Disable intermittently failing test: PartitionedSubscriptionTriggeringR4Test.testCreateSubscriptionInPartitionAndResourceInDifferentPartition * Try disabling Batch2CoordinatorIT failing test and see if branch pipeline passes. * Add back hapi-fhir-validation-resources-r4b to hapi-fhir-jpaserver-base pom.xml. * Bump hapi-fhir to 6.5.6-SNAPSHOT. * Bump rest of hapi-fhir to 6.5.6-SNAPSHOT. * Fix compile error on Batch2CoordinatorIT. * Change revision ID column from integer to long in both the revision entity and the migration tasks. Fix a bug with the migration tasks having the wrong name for the timestamp column. * Fix interface in MongoDB to return Long for the revision ID instead of Int. Implement TINYINT for all supported database products. Keep TARGET_TYPE column at 40 instead of 100 for now since otherwise the schema migration test will fail. Also, don't try to rename the foreign key or the schema migration test will fail.
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<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>org.hibernate.orm</groupId>
Introduce hibernate envers, use it only for MdmLink, disable it for now, add to MdmLink Dao and unit test revisions. (#4615) * First commit with new maven deps for envers and stubbed changelist. * Add repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class to BaseAppCtxPersistence. Comment it out in JpaConfig. Add constant for hibernate.integration.envers.enabled. Hard-code envers to false. App starts without error. Basic smoke testing for MpmLink update works. * Add mdmLink code to retrieve envers history and unit test it. * Initial code to handle envers from HapiFhirEnversRevision along with a custom extension of the revision/REVINFO entity. * Add changelist and tweak table/sequence/field names and clean up the HapiFhirJpaMigrationTasks method. * Fix some unit test failures and address TODOs. * Ensure hard-coded deactivation of envers is overridden by unit tests. * Remove commented-out code. * Address code review comments. * Remove sysout traces. * Tweaks to poms with comments explaining why I left the versions in the plugin dependencies. Get rid of a duplicate envers dependency. * Bump hapi-fhir version to 6.5.5-SNAPSHOT. * Disable intermittently failing test: PartitionedSubscriptionTriggeringR4Test.testCreateSubscriptionInPartitionAndResourceInDifferentPartition * Try disabling Batch2CoordinatorIT failing test and see if branch pipeline passes. * Add back hapi-fhir-validation-resources-r4b to hapi-fhir-jpaserver-base pom.xml. * Bump hapi-fhir to 6.5.6-SNAPSHOT. * Bump rest of hapi-fhir to 6.5.6-SNAPSHOT. * Fix compile error on Batch2CoordinatorIT. * Change revision ID column from integer to long in both the revision entity and the migration tasks. Fix a bug with the migration tasks having the wrong name for the timestamp column. * Fix interface in MongoDB to return Long for the revision ID instead of Int. Implement TINYINT for all supported database products. Keep TARGET_TYPE column at 40 instead of 100 for now since otherwise the schema migration test will fail. Also, don't try to rename the foreign key or the schema migration test will fail.
2023-03-14 15:32:00 -04:00
<artifactId>hibernate-envers</artifactId>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-messaging</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<exclusions>
<exclusion>
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
</dependency>
<dependency>
<groupId>org.quartz-scheduler</groupId>
<artifactId>quartz</artifactId>
</dependency>
<!-- Caffeine -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-testing</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
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<!-- test dependencies -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<scope>test</scope>
</dependency>
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<dependency>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
</dependency>
2018-11-30 17:19:16 -05:00
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<configuration>
<skipDeploy>true</skipDeploy>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>