hapi-fhir/hapi-fhir-storage-batch2/pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
<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>
Messages submitted to the subscription pipeline are lost when submission fails. (#4733) * One more fix for #4467 * Enabling massIngestionMode causes incomplete resource deletion (#4476) * Adding initial test. * Adding fix and subsequent test. * Adding changelog. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Provide the capability to request that the name of the subscription matching channel be unqualified (#4464) * Adding initial test. * Adding initial solution implementation. * Adding change log and code clean up. * addressing comments from 1st code review. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Change visibility of migration method (#4471) * change migration visibility * add empty migration method for 640 --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484) * First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests. * Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog. * Remove erroneous TODOs and tweak the validation logic. * Enhance unit tests and fix changelog. * Reindex batch job fails when processing deleted resources. (#4482) * adding changelog. * Providing solution and adding changelog. * Adding new test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cleaning up checkstyle files (#4470) * cleaning up checkstyle files * One more fix for #4467 (#4469) * added exlusions for files at base project level so checkstyle doesn't error out * duplicate error code from merge * changing lifecycle goal for all module checkstyle check * moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code * wip * trying to figure out why pipeline cannot copy files * removing modules that don't actually need to be built. * I messed up the version --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Bump core to 5.6.881 (#4496) * Bump core to 5.6.881-SNAPSHOT * Work on fixing tests * Work on fixing tests 2 * Bump to core release --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> * Issue 4486 mdm inconsistent possible match score values (#4487) * Extract method for readability * Save always normalized score values in POSSIBLE_MATCH links. * Avoid setting properties to null values. Adjust test. * Simplify fix * Fix test. Add RangeTestHelper. --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Revert "cleaning up checkstyle files (#4470)" This reverts commit efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * initial test implementation/changes and solution wiring. * adding support for jpa/mongo abstraction. * refact completed. need to start implementing scheduling of subscription re-submission with the scheduler service. * post release, merging in master. * wip: commit before merging in branch master. * wip: resuming work on the issue. * wip: before merging in master. * wip: partial implementation of mongo support. * wip: more work to support partial implementation on mongo. * Test implementation * providing method getMessageKeyOrDefault(); * providing changelog * preping codereview. * wip: passing tests * wip: finally solving the Meta issue. * wip: adjusting interfaces * Adding IT and * IT test; fixing rollback issue. * removing non required logging * fixing merge conflict * Preparing for code review. * Preparing for code review. * Compiling code after merging in master. * Fixing checkstyle failure. * Modifications towards getting all tests to pass. * addressing comments from code review. * compiling code after switching target merge branch to rel_pub_2023_05 * compiling code after switching target merge branch to rel_6_6 * Addressing comments made in design meeting. wip. * Addressing comments made in design meeting. finally completed. and last 2 comments addressed. * removing non required override * reverting changes as they are not required. * Modified test and implementation. * implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only. * fix tests by modifying the matchingInterceptor to call pointcut when processing * fixing more tests. * WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue * fixing circular dependency * Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor. * bumping version 6.7.7-SNAPSHOT * bumping HAPI version to 6.7.7-SNAPSHOT * fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline. * passing all tests. * unbumping to 6.7.7 * compiling after merging in master. * creating a custom hapi version * providing an synchronous subscription matcher interceptor for testing. * updating pom version to generate artifacts. * fixing tests, WIP/0 * fixing tests, WIP/1 * fixing tests, WIP/2 * Matching entity annotation with migration task declarations. * Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage. * Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage. * Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc]. * Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again. * Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction. * bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline. * bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline. * Formatter changes. * add generic * add generic * Addressing code review comments. * Adding file asynch_subscription_610.md to docs/upgrades * changing poms to 6.9.2-SNAPSHOT before merging in master. * compiling after merging in master. * Lowering logging level to debug. * Bumping to 6.9.3-SNAPSHOT * Bumping hapi version to 6.9.4-SNAPSHOT * Adding update documentation. * Modifying update file following review. --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-08-28 12:47:53 -04:00
<version>6.9.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-storage-batch2</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR JPA Server - Batch2 Task Processor</name>
<description>Batch2 is a framework for managing and executing long running "batch" jobs</description>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpa</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
6.6.0 Mergeback (#4924) * Force Verify tests * fix ITs (#4809) * fix RestHookTestR5IT * fix intermittent --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix migrator error on Oracle (#4814) * Fix Oracle SQL error * Add changelog * Update clinical reasoning version (#4816) * Update clinical reasoning version * Update version * Update version * Clean-up and more wireup of evaluationSettings * Add changelog --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> * Opening the care-gaps endpoint for GET. (#4823) Co-authored-by: Chalma Maadaadi <chalma@alphora.com> * added version to mdm golden resource tag (#4820) Co-authored-by: Long Ma <long@smilecdr.com> * Update the changelog for 4697 to be more descriptive (#4827) * Update the changelog for 4697 to be more descriptive * Futher tweaks of the changelog * Fixes a bug with tags. (#4813) * Test, fix * Drop constraint, add migration * Add changelog * Fix userSelected null vs false * Fix merge * Fix up checkstyle whining * One more failure * Fix test * wip * changelog clarity Co-authored-by: James Agnew <jamesagnew@gmail.com> * change index --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * fix migration issue (#4830) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Create correct version enum * Remove superfluous migration * fixing test (#4835) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * email subscription, throw NullPointerException (#4790) * fix bug * Favoring constructor initialization to autowiring. * enhancing test. * Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module. * Passing all tests. * adding changelog. * Bumping version to 6.5.20-SNAPSHOT * addressing code review comment. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Add docs for CR operations (#4855) * Add docs for CR operations * Correct changelog and javadoc for $package * Add documentation for $apply parameters * Add additional documentation for $package * Cleanup * Cleanup * Cleanup * Address review comments * Add documentation for $care-gaps operation. (#4862) * Add documentation for -gaps. * addressing the comments. --------- Co-authored-by: Chalma Maadaadi <chalma@alphora.com> * 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854) * added failing test * implemented the solution * changed test name * added change log * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml Co-authored-by: James Agnew <jamesagnew@gmail.com> --------- Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * fixing patient everything operator (#4845) * fixing patient everything operator * review fix --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * fix link * Move image file * Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871) * Add failing unit test. * Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value. * Add changelog. * added warn message and test (#4848) * added warn message and test * code review fixes --------- Co-authored-by: Long Ma <long@smilecdr.com> * Issue 4804 full table scan on mpi link during mdm clear (#4805) * version bump for next release (#4793) * version bump * Bump to correctnumber * Version Enum and folder * Remove interim from list * wip * Fix operation on nested type-choices in FhirPatch implementation (#4783) * Fix operation on nested type-choices in FhirPatch implementation * Add credit for #4783 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * #4468 fix previous link offset no cache pagination (#4489) * #4468 Add test reproducing the issue * #4468 Fix previous link for no cache offset pagination * #4468 Use unchecked URI parsing * Credit for #4489 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Changelog and data generating test * Add MdmLink index * Avoid double link deletion * Use ThreadLocal safely --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859) * Add failing unit test. * Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step. This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress. * Add final. * Add changelog. * disable wars (#4877) Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4868 fix paging hapi (#4870) * fixing some offset and adding a test * fixing the offset paging * Removing duplicate --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> * 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876) * Add failing test * Add failing test * Fix and changelog * Pass content type parameter * Back to auto wiring the context * Invoke interceptor only when getting blobId, not also when storing it * Avoid breaking implementers * Address review comment * Add new exception Msg code * Fix broken test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix batch job (bulk export) processed record count (#4879) * Remove racy stats recalc. * Throw 404 when requesting $export of non-existent Group or Patient (#4890) * Remove default implementation intended only for interim backwards compatibility (#4894) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Rule apply patient export (#4893) * Test, fix, and changelog * Better partition resolution * Add checks based on rule applier * Fix ordering failure due to hash set * Allow empty auth interceptor * Fix up operation type on invocation * Add more tests, make hack implementation for patient instance level operation * Tighten test name * Changelog * Default method * remove dead method * Remove dead autowire --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve pom changes (#4898) Co-authored-by: Long Ma <long@smilecdr.com> * backport subscription topic bean cleanup (#4904) * 4891 bulk export do not recurse unasked for resources (#4895) * updating tests * fixing bulk export to not fetch resources not requested * cleanup * cleanup * more warning suppressing * adding error code * blah * fix test * review fixes --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * lowers log level to remove bootup noise (#4908) * CVE rel 6 6 (#4907) * cve pom changes * bump javax.el to jakarta.el --------- Co-authored-by: Long Ma <long@smilecdr.com> * Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906) * Initial failing test * Avoid applying binary blob id prefix multiple times * Remove recently introduced method not needed anymore --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Enhance LogbackCaptureTestExtension (#4869) * repro bug with test, fix bug * ken informed me he resolved this bug on master, so i'm switching to use his solution * disable wars * review feedback * review feedback * review feedback again --------- Co-authored-by: josie <josie.vandewetering@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> * Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887) * Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources * Canonicalizers now correctly handle search parameters for custom resources * created changelog * Modification based on comments: - remove Resource from target field when there are custom resource types - fixed changelog typo - removed unnecessary variable providesMembershipInCompartments * Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources * Fixed typo and removed commented code * re-ordered init methods * Update changelog Co-authored-by: Tadgh <garygrantgraham@gmail.com> * modifications following first code review. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * License * Remove _lastUpdated filtering of _revincludes. (#4899) Remove _lastUpdated filtering of _revincludes. * 4910-dm-migration-error-for-oracle-19c (#4916) * Remove all_constraints references which break in oracle 19c * Add changelog --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * 4873 empty fhirid causes missing resource (#4874) * add check for empty fhirid string and add test * add test for populateid * changelog * version bump * version bump * reverse version bump * Back to 6.5.21-SNAPSHOT. --------- Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Fix include canonical url performance (#4919) Use hash_identity for canonical join * License * Version bump * Fix failure in test * Licenses * Review comments for pipeline * Dead entry * other typo --------- Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com> Co-authored-by: josie <josie.vandewetering@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-05-20 23:38:35 -04:00
<artifactId>jakarta.el</artifactId>
</dependency>
<!-- test -->
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
Ks 20220916 remove flyway (#4040) * removed flyway, started coding persistence * started wiring up new dao service * replace jpa with sqlbuilder * down to 16 failed tests * remove outOfOrder test. We no longer support validating order. * Removed noFlyway mode. It is no longer a thing. * merge migrator * down to 1 failing test * cleanup * removed unused noflyway cli arguments * cleanup * cleanup * cleanup * cleanup * create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot. This allows us to add a bunch of behaviour to that as a first-order thing * fix test * fix test * improve migration table detection to use the catalogue * Msg.code() * cleanup * save version in same format as flyway * cleanup * add migration result to migration result class * failed migrations stay in the table and don't really affect anything. * change log * docs * ugh Flyway requires lower-case column names * integration test fixes * log * fix oracle issue * lowercase tablenames for postgres. fussy fussy! * Revert "lowercase tablenames for postgres. fussy fussy!" This reverts commit 92c9cb263b90cff2190cc327fab051dc3bb2f83f. * revert to capital table names. surround table name by quotes for Postgres. * added log message before executing find all query * changed log message from info to debug * javadoc * pom cleanup * review feedback * Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * review feedback * review feedback. Use prepared statement. * Change installedOn insert from timestamp to date * Change installedOn column type from timestamp to date * bump hapi version * fix poms * fix poms and cdr compile * add exclusions to clean up build Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2022-10-03 22:40:09 -04:00
<version>${project.version}</version>
<scope>compile</scope>
</dependency>
</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>