hapi-fhir/hapi-fhir-storage/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>
GM1 Mergeback (#5203) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
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<version>6.9.3-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-storage</artifactId>
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<packaging>jar</packaging>
<name>HAPI FHIR Storage api</name>
<description>This project provides services useful for fhir repository storage. Actual repository storage services
are not in this project, just the api and helper libraries.
</description>
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<dependencies>
<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-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${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>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId>
<version>${project.version}</version>
</dependency>
<!-- TODO KHS remove jpa stuff from here -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-model</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
<version>${project.version}</version>
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</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
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<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>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
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</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</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>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
</dependency>
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<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>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
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</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
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<!-- test dependencies -->
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<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>
<dependency>
<groupId>com.github.dnault</groupId>
<artifactId>xml-patch</artifactId>
</dependency>
<dependency>
<groupId>io.dogote</groupId>
<artifactId>json-patch</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
</dependency>
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</dependencies>
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<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>