2020-05-22 15:03:20 -04:00
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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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2014-05-05 08:57:43 -04:00
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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2015-02-03 17:53:22 -05:00
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<artifactId>hapi-deployable-pom</artifactId>
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2024-11-07 16:10:58 -05:00
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<version>7.7.2-SNAPSHOT</version>
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2023-04-02 11:50:20 -04:00
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2015-02-03 17:53:22 -05:00
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2014-05-05 08:57:43 -04:00
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</parent>
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2014-10-30 13:57:29 -04:00
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2014-05-05 08:57:43 -04:00
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<artifactId>hapi-fhir-jpaserver-base</artifactId>
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<packaging>jar</packaging>
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<name>HAPI FHIR JPA Server</name>
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<dependencies>
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2017-10-26 06:02:12 -04:00
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<dependency>
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2020-11-27 19:49:06 -05:00
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<groupId>com.fasterxml.woodstox</groupId>
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<artifactId>woodstox-core</artifactId>
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2020-05-22 15:03:20 -04:00
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</dependency>
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2017-10-26 06:02:12 -04:00
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2016-05-17 09:05:37 -04:00
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-csv</artifactId>
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</dependency>
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2014-05-05 08:57:43 -04:00
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<dependency>
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2020-02-28 16:09:16 -05:00
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<groupId>co.elastic.apm</groupId>
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<artifactId>apm-agent-api</artifactId>
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</dependency>
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2014-05-05 08:57:43 -04:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-base</artifactId>
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2017-01-29 13:22:28 -05:00
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<version>${project.version}</version>
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2014-07-21 09:24:38 -04:00
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<exclusions>
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<exclusion>
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<artifactId>commons-logging</artifactId>
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<groupId>commons-logging</groupId>
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</exclusion>
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</exclusions>
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2014-05-05 08:57:43 -04:00
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</dependency>
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2014-10-16 17:19:27 -04:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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2017-08-13 14:39:47 -04:00
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<artifactId>hapi-fhir-client</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-server</artifactId>
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<version>${project.version}</version>
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</dependency>
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2020-05-22 15:03:20 -04:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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2020-12-17 10:12:53 -05:00
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<artifactId>hapi-fhir-server-mdm</artifactId>
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2020-05-22 15:03:20 -04:00
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<version>${project.version}</version>
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</dependency>
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2022-11-08 22:18:36 -05:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-storage</artifactId>
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<version>${project.version}</version>
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</dependency>
|
2018-11-30 17:19:16 -05:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
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<version>${project.version}</version>
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</dependency>
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2021-09-21 11:36:08 -04:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-sql-migrate</artifactId>
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<version>${project.version}</version>
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</dependency>
|
2018-11-30 17:19:16 -05:00
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|
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<dependency>
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|
<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-jpaserver-model</artifactId>
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<version>${project.version}</version>
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</dependency>
|
2017-08-13 14:39:47 -04:00
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|
|
<dependency>
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|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
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|
|
<artifactId>hapi-fhir-validation</artifactId>
|
2017-01-29 13:22:28 -05:00
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|
<version>${project.version}</version>
|
2014-10-16 17:19:27 -04:00
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|
|
</dependency>
|
2014-12-21 18:13:37 -05:00
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|
<dependency>
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|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2015-02-06 15:50:29 -05:00
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|
|
<artifactId>hapi-fhir-structures-dstu2</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2014-12-21 18:13:37 -05:00
|
|
|
</dependency>
|
2015-11-29 11:43:09 -05:00
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|
|
<dependency>
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|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2016-02-01 08:55:58 -05:00
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|
|
<artifactId>hapi-fhir-structures-dstu3</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2015-11-29 11:43:09 -05:00
|
|
|
</dependency>
|
2017-08-13 14:39:47 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-r4</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2022-10-20 16:57:06 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-r4b</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2019-08-06 17:30:31 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-r5</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2015-07-10 16:05:40 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2015-08-31 08:20:24 -04:00
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2015-09-03 14:36:37 -04:00
|
|
|
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2015-07-10 16:05:40 -04:00
|
|
|
</dependency>
|
2015-11-29 11:43:09 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2016-02-01 08:55:58 -05:00
|
|
|
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2015-11-29 11:43:09 -05:00
|
|
|
</dependency>
|
2017-08-13 14:39:47 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
Bulk export reducer step fix mergeback (#4606)
* 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
* License
* fix batch2 reduction step (#4499)
* fix bug where FINALIZE jobs are not cancellable
* moved reduction step to message hander
* moving reduction step to queue
* addingchangelog
* cleaning up
* review fixes
* review fix'
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* Scheduled batch 2 bulk export job and binary delete (#4492)
* First commit: Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.
* Refine solution and add a concrete unit test but still work to do.
* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.
* Unit tests complete. New Msg code for new IJobPersistence.fetchInstances() method. Cleanup TODOs and add others.
* Finish final touches on implementation.
* Add changelog.
* Various cleanup.
* Code review feedback.
* Small tweak to changelog.
* Last code review tweak.
* Address more code review comments.
* Reverse changes to consider work chunks. Add a constant for write-to-binary.
* Change bulk import test for valueUri type (#4503)
* change tests
* suggested test change
* CVE resolutions (#4513)
* Bump Postgres for CVE
* Bump jetty
* Verison bump
* Remove comments
* Revrt bump
* Add check in scanner (#4518)
* 4516 create hapi fhir cli command to clear stale lock entries (#4517)
* Initial implementation
* better tests
* Add changelog and docs
* Forgotten files
* Code review comments
* Fix checkstyle
* Unable to Expunge CodeSystem (#4507)
* changes for GL-3943
* changes for GL-3943
---------
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
* New line::
* Update to documentation regarding narrative generation; (#4521)
Providing changelog;
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* changed what score is set for mdmlinks that created new golden resource (#4514)
* changed what score is set for mdmlinks that created new golden resource
* fix test
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* REVERT: change to operationoutcome.html
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* added change log
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fix build (#4530)
* Making narrative_generation.md reference an html snippet (#4531)
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)
* fix + test
* minor fix
* Addressing suggestion
* Minor changes
* 4441 rel 6 4 bad references creation bug (#4519)
* adding a test
* fail in the case of ref enforce on type and on write and autocreate are all true
* update to code
* removing a line
* cleanup
* removing check on urn
* changing just to trigger a build
* adding a comment to the pom
* updating test for better information
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fixed channel import null pointer exception from null header (#4534)
* retryCount 0 on null header + test + changelog
* suggested changes
* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)
This reverts commit 53252b8d153f97f4a66a7d20751913911a71f098.
* Better error handling for when channel type is not supported (#4538)
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Avoid logging message payloads that contain sensitive data (#4537)
Don't log payloads - they may contain sensitive data.
* Bulk Export Bug With Many Resources and Low Max File Size (#4506)
* failing test
* fix + changelog
* tweak
* add method to IJobPersistence to use a Stream
* tweak
* tweak
* decrease test time
* clean up
* code review comments
* version bump
* Increase timeout limit to match BulkExportUseCaseTest
* shorten test
* maintenance pass
* add logging
* Revert "add logging"
This reverts commit b0453fd9538d6858e6bd212f402d4b04c6306136.
* Revert "maintenance pass"
This reverts commit bbc7418d519260c4b9827546a0bf822db1c78b1b.
* test
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* shorten tests
* logging
* move test location
* fixes a regression caused my change in hapi-fhir
* timeout
* Revert "fixes a regression caused my change in hapi-fhir"
This reverts commit 4b58013149836eededc568d295c5baf8fb3df989.
* testing
* Revert "testing"
This reverts commit aafc95c2f36bf89ae935c6c342017ec300fe4289.
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* bump ver
* License updates'
* Downgrade dep'
* Updating version to: 6.4.1 post release.
* Add javadocs and sources to our serviceloaders
* Reset version
* Change parent
* Remove bumped version
* License fixes, new parent
* Updating version to: 6.4.1 post release.
* Fix bad creation of versionenum
* Improve performance on bulk export
* Add changelog
* Start working on cleaned up reducer
* Clean up batch calls
* Work on issues
* Build fixes
* typedbundleprovider getallresources override (#4552)
* typedbundleprovider getallresources override
* added test to immunization tests that validates pagination does not result in null pointer if over default queryCount
* moved HapiFhirDal test to its own test class
* removed unused imports
* Update to use JpaStorageSettings
* adding changelog for issue 4551
* fix changelog spacing
* changelog type to fix
---------
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Add backport info
* Upgrade core to 5.6.97, make adjustments in hapi-fhir, and ensure that all tests pass (#4579)
* First commit: Create new branch from the release branch with changes from James' branch. This probably won't compile as the work is incomplete.
* Second round of changes from integrating James' branch.
* Mark most test failures with TODOs.
* Add whitespace
* Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation.
* Fix CreatePackageCommandTest to assert null instead of empty string. Comments on tests that fail due to the double-quote encoding problem.
* Downgrade to core 5.6.97.
* Fix another test and remove TODOs.
* Fix changelog.
* Clean up some erroneous changes and TODOs.
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Fix up dal test
* Address leftover code review feedback from the upgrade to core 5.6.97. (#4585)
* Exclude pinned core deps
* Force pin structs
* Add model changes to IBaseCoding and related changes (#4587)
* Add IbaseCoding changes, and tinder changes
* Fix up tag definition
* converter addition
* Fix unit test and add changelog.
* Add jira to changelog.
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Fix changelog
* Tidy metadata
* Test fixing
* Test fixes
* Work on progress
* Add changelog
* Build tweak
* Fixes
* Disable intermittently failing tests. (#4593)
* rename tests to IT
* Disable more intermittently failing tests (#4595)
* Disable more intermittently failing tests.
* Disable another intermittently failing tests.
* ITify
* Disable yet another intermittently failing tests. (#4596)
* disable
* disables
* Fixes
* disables
* Fix compile
* Test fixes
* Updating version to: 6.4.2 post release.
* Bump to 6.4.2-SNAPSHOT
* Fix compile
* fix version
* Address review comments
* Review comments
* Version bump
* Compile fix
* Test fixes
* Compile fixes
* One more compile fix
* Test fixes
* Version bump
* Resolve fixme
---------
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: 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: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.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: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-03-01 14:52:36 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-validation-resources-r4b</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
2019-08-06 17:30:31 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
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|
|
<artifactId>hapi-fhir-validation-resources-r5</artifactId>
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<version>${project.version}</version>
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</dependency>
|
2022-02-27 16:04:49 -05:00
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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|
<artifactId>hapi-fhir-storage-batch2</artifactId>
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|
<version>${project.version}</version>
|
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|
</dependency>
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
|
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|
|
<artifactId>hapi-fhir-storage-batch2-jobs</artifactId>
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|
|
<version>${project.version}</version>
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</dependency>
|
2022-03-18 08:39:12 -04:00
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-dbcp2</artifactId>
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<exclusions>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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</exclusions>
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|
|
</dependency>
|
2022-11-08 22:18:36 -05:00
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|
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<dependency>
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|
<groupId>net.ttddyy</groupId>
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|
<artifactId>datasource-proxy</artifactId>
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</dependency>
|
2022-03-18 08:39:12 -04:00
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|
2014-05-29 19:00:16 -04:00
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<dependency>
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<groupId>ch.qos.logback</groupId>
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<artifactId>logback-classic</artifactId>
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<scope>test</scope>
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</dependency>
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2019-08-20 09:14:21 -04:00
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<dependency>
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<groupId>org.awaitility</groupId>
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<artifactId>awaitility</artifactId>
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<scope>test</scope>
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</dependency>
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2015-10-29 15:38:19 -04:00
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|
<dependency>
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|
<groupId>org.javassist</groupId>
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|
<artifactId>javassist</artifactId>
|
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</dependency>
|
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2022-02-22 09:48:57 -05:00
|
|
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<!-- GraphQL -->
|
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|
|
<dependency>
|
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|
|
<groupId>com.graphql-java</groupId>
|
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|
|
<artifactId>graphql-java</artifactId>
|
|
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</dependency>
|
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|
|
|
2020-10-26 05:24:26 -04:00
|
|
|
<!-- SQL Builder -->
|
|
|
|
<dependency>
|
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|
|
<groupId>com.healthmarketscience.sqlbuilder</groupId>
|
|
|
|
<artifactId>sqlbuilder</artifactId>
|
|
|
|
</dependency>
|
|
|
|
|
|
|
|
|
2017-09-21 08:33:20 -04:00
|
|
|
<!-- Jackson -->
|
|
|
|
<dependency>
|
|
|
|
<groupId>com.fasterxml.jackson.core</groupId>
|
|
|
|
<artifactId>jackson-annotations</artifactId>
|
|
|
|
</dependency>
|
2019-04-24 14:10:21 -04:00
|
|
|
<dependency>
|
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|
|
<groupId>com.fasterxml.jackson.core</groupId>
|
|
|
|
<artifactId>jackson-databind</artifactId>
|
|
|
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</dependency>
|
2020-06-10 05:30:20 -04:00
|
|
|
<dependency>
|
2021-12-02 13:01:50 -05:00
|
|
|
<groupId>org.springdoc</groupId>
|
2023-12-03 11:15:37 -05:00
|
|
|
<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
|
2020-06-10 05:30:20 -04:00
|
|
|
</dependency>
|
2017-09-21 08:33:20 -04:00
|
|
|
|
2017-09-16 15:03:22 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.thymeleaf</groupId>
|
|
|
|
<artifactId>thymeleaf</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.thymeleaf</groupId>
|
2023-12-03 11:15:37 -05:00
|
|
|
<artifactId>thymeleaf-spring6</artifactId>
|
2017-09-16 15:03:22 -04:00
|
|
|
</dependency>
|
|
|
|
|
2017-10-15 11:27:30 -04:00
|
|
|
<!-- For UCUM: TODO we should replace this with org.fhir UCUM -->
|
2014-07-21 09:24:38 -04:00
|
|
|
<dependency>
|
2014-10-30 13:57:29 -04:00
|
|
|
<groupId>org.jscience</groupId>
|
|
|
|
<artifactId>jscience</artifactId>
|
2019-05-09 12:51:13 -04:00
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
|
|
|
<groupId>org.javolution</groupId>
|
|
|
|
<artifactId>javolution</artifactId>
|
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
2014-07-21 09:24:38 -04:00
|
|
|
</dependency>
|
2016-09-17 16:55:21 -04:00
|
|
|
|
2021-03-02 13:18:43 -05:00
|
|
|
|
2016-09-17 16:55:21 -04:00
|
|
|
<!-- Patch Dependencies -->
|
|
|
|
<dependency>
|
2020-05-22 15:03:20 -04:00
|
|
|
<groupId>io.dogote</groupId>
|
|
|
|
<artifactId>json-patch</artifactId>
|
|
|
|
</dependency>
|
2016-09-17 16:55:21 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>com.github.dnault</groupId>
|
|
|
|
<artifactId>xml-patch</artifactId>
|
|
|
|
</dependency>
|
|
|
|
|
2018-05-03 18:34:29 -04:00
|
|
|
<!--
|
|
|
|
Dependencies that need to be added since JDK9
|
|
|
|
-->
|
2014-07-10 08:50:51 -04:00
|
|
|
<dependency>
|
2023-12-03 11:15:37 -05:00
|
|
|
<groupId>jakarta.servlet</groupId>
|
|
|
|
<artifactId>jakarta.servlet-api</artifactId>
|
2014-07-10 08:50:51 -04:00
|
|
|
<scope>provided</scope>
|
|
|
|
</dependency>
|
2014-10-30 13:57:29 -04:00
|
|
|
|
2014-05-05 08:57:43 -04:00
|
|
|
<!-- Spring -->
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-core</artifactId>
|
2014-07-21 09:24:38 -04:00
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
|
|
|
<artifactId>commons-logging</artifactId>
|
|
|
|
<groupId>commons-logging</groupId>
|
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
2014-05-05 08:57:43 -04:00
|
|
|
</dependency>
|
2015-09-24 07:01:04 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework.data</groupId>
|
|
|
|
<artifactId>spring-data-jpa</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
|
|
|
<artifactId>spring-aop</artifactId>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
2015-09-24 07:01:04 -04:00
|
|
|
</dependency>
|
2021-05-02 12:14:32 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework.data</groupId>
|
|
|
|
<artifactId>spring-data-commons</artifactId>
|
|
|
|
</dependency>
|
2015-09-26 08:49:06 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-messaging</artifactId>
|
|
|
|
</dependency>
|
2014-05-05 08:57:43 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-tx</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-context-support</artifactId>
|
|
|
|
</dependency>
|
2015-09-26 08:49:06 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-webmvc</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework</groupId>
|
|
|
|
<artifactId>spring-websocket</artifactId>
|
|
|
|
</dependency>
|
2014-08-05 10:46:46 -04:00
|
|
|
<dependency>
|
2014-10-30 13:57:29 -04:00
|
|
|
<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>
|
2014-08-05 10:46:46 -04:00
|
|
|
</dependency>
|
2019-09-30 09:30:39 -04:00
|
|
|
|
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>
2021-01-05 17:56:59 -05:00
|
|
|
<!-- Note that we need this dependency to send log4j logging requests to slf4j -->
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.apache.logging.log4j</groupId>
|
|
|
|
<artifactId>log4j-to-slf4j</artifactId>
|
|
|
|
</dependency>
|
2019-09-30 09:30:39 -04:00
|
|
|
<!-- Hibernate Search -->
|
2015-11-02 08:12:36 -05:00
|
|
|
<dependency>
|
2023-12-03 11:15:37 -05:00
|
|
|
<groupId>co.elastic.clients</groupId>
|
|
|
|
<artifactId>elasticsearch-java</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>
2021-01-05 17:56:59 -05:00
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
2023-12-03 11:15:37 -05:00
|
|
|
<groupId>jakarta.json</groupId>
|
|
|
|
<artifactId>jakarta.json-api</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>
2021-01-05 17:56:59 -05:00
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.hibernate.search</groupId>
|
|
|
|
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.hibernate.search</groupId>
|
|
|
|
<artifactId>hibernate-search-backend-lucene</artifactId>
|
2015-11-02 08:12:36 -05:00
|
|
|
</dependency>
|
2022-09-09 19:24:06 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.hibernate.search</groupId>
|
|
|
|
<artifactId>hibernate-search-backend-elasticsearch-aws</artifactId>
|
|
|
|
</dependency>
|
2023-03-14 15:32:00 -04:00
|
|
|
<dependency>
|
2023-12-03 11:15:37 -05:00
|
|
|
<groupId>org.hibernate.orm</groupId>
|
2023-03-14 15:32:00 -04:00
|
|
|
<artifactId>hibernate-envers</artifactId>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.springframework.data</groupId>
|
|
|
|
<artifactId>spring-data-envers</artifactId>
|
|
|
|
</dependency>
|
2015-11-02 08:12:36 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.apache.lucene</groupId>
|
2024-01-14 14:15:08 -05:00
|
|
|
<artifactId>lucene-analysis-phonetic</artifactId>
|
2019-09-30 09:30:39 -04:00
|
|
|
</dependency>
|
2014-05-29 09:17:12 -04:00
|
|
|
<!-- Misc -->
|
|
|
|
<dependency>
|
2014-10-30 13:57:29 -04:00
|
|
|
<groupId>com.google.guava</groupId>
|
|
|
|
<artifactId>guava</artifactId>
|
2014-05-29 09:17:12 -04:00
|
|
|
</dependency>
|
2022-11-08 22:18:36 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>jakarta.annotation</groupId>
|
|
|
|
<artifactId>jakarta.annotation-api</artifactId>
|
|
|
|
</dependency>
|
2015-09-24 07:01:04 -04:00
|
|
|
|
2021-04-28 10:29:09 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-server-openapi</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
<scope>test</scope>
|
|
|
|
</dependency>
|
2021-04-25 15:40:50 -04:00
|
|
|
|
2021-04-28 10:29:09 -04:00
|
|
|
<dependency>
|
2022-11-09 14:47:23 -05:00
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-caching-caffeine</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>
|
2023-01-24 12:07:36 -05:00
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-test-utilities</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
<scope>test</scope>
|
2018-05-10 10:52:56 -04:00
|
|
|
</dependency>
|
2018-06-24 20:02:27 -04:00
|
|
|
|
2019-04-26 11:21:42 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.jetbrains</groupId>
|
|
|
|
<artifactId>annotations</artifactId>
|
|
|
|
</dependency>
|
2021-04-28 10:29:09 -04:00
|
|
|
<dependency>
|
|
|
|
<groupId>org.apache.jena</groupId>
|
|
|
|
<artifactId>jena-arq</artifactId>
|
2021-10-28 14:42:06 -04:00
|
|
|
<scope>compile</scope>
|
2022-11-08 22:18:36 -05:00
|
|
|
<exclusions>
|
|
|
|
<exclusion>
|
|
|
|
<groupId>javax.annotation</groupId>
|
|
|
|
<artifactId>javax.annotation-api</artifactId>
|
|
|
|
</exclusion>
|
|
|
|
</exclusions>
|
2021-10-28 14:42:06 -04:00
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>org.apache.jena</groupId>
|
|
|
|
<artifactId>jena-core</artifactId>
|
2021-04-28 10:29:09 -04:00
|
|
|
<scope>compile</scope>
|
|
|
|
</dependency>
|
2022-02-02 16:03:53 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>com.jayway.jsonpath</groupId>
|
|
|
|
<artifactId>json-path-assert</artifactId>
|
|
|
|
<scope>test</scope>
|
|
|
|
</dependency>
|
|
|
|
<dependency>
|
|
|
|
<groupId>com.jayway.jsonpath</groupId>
|
|
|
|
<artifactId>json-path</artifactId>
|
|
|
|
</dependency>
|
2021-04-28 10:29:09 -04:00
|
|
|
</dependencies>
|
2014-05-05 08:57:43 -04:00
|
|
|
|
|
|
|
<build>
|
|
|
|
<plugins>
|
2023-12-03 11:15:37 -05:00
|
|
|
<!-- Generate the Spring ContextCfg classes for loading JPA DAOs and RPs -->
|
2014-12-21 18:13:37 -05:00
|
|
|
<plugin>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-tinder-plugin</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2014-12-21 18:13:37 -05:00
|
|
|
<executions>
|
|
|
|
<execution>
|
2015-02-06 15:50:29 -05:00
|
|
|
<id>build_dstu2</id>
|
2014-12-21 18:13:37 -05:00
|
|
|
<goals>
|
|
|
|
<goal>generate-jparest-server</goal>
|
|
|
|
</goals>
|
|
|
|
<configuration>
|
2015-02-06 15:50:29 -05:00
|
|
|
<version>dstu2</version>
|
2015-10-16 08:57:07 -04:00
|
|
|
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
|
2015-02-06 15:50:29 -05:00
|
|
|
<packageBase>ca.uhn.fhir.jpa.rp.dstu2</packageBase>
|
2020-07-13 08:51:13 -04:00
|
|
|
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml
|
|
|
|
</targetResourceSpringBeansFile>
|
2019-09-17 16:01:35 -04:00
|
|
|
<baseResourceNames/>
|
2015-07-18 18:44:46 -04:00
|
|
|
<excludeResourceNames>
|
2015-10-29 15:38:19 -04:00
|
|
|
<!-- <excludeResourceName>OperationDefinition</excludeResourceName> <excludeResourceName>OperationOutcome</excludeResourceName> -->
|
2015-07-18 18:44:46 -04:00
|
|
|
</excludeResourceNames>
|
2014-12-21 18:13:37 -05:00
|
|
|
</configuration>
|
|
|
|
</execution>
|
2015-11-29 11:43:09 -05:00
|
|
|
<execution>
|
2016-02-01 08:55:58 -05:00
|
|
|
<id>build_dstu3</id>
|
2015-11-29 11:43:09 -05:00
|
|
|
<goals>
|
|
|
|
<goal>generate-jparest-server</goal>
|
|
|
|
</goals>
|
|
|
|
<configuration>
|
2016-02-01 08:55:58 -05:00
|
|
|
<version>dstu3</version>
|
2015-11-29 11:43:09 -05:00
|
|
|
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
|
2016-02-01 08:55:58 -05:00
|
|
|
<packageBase>ca.uhn.fhir.jpa.rp.dstu3</packageBase>
|
2020-07-13 08:51:13 -04:00
|
|
|
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu3.xml
|
|
|
|
</targetResourceSpringBeansFile>
|
2015-11-29 11:43:09 -05:00
|
|
|
<baseResourceNames></baseResourceNames>
|
|
|
|
<excludeResourceNames>
|
2017-08-13 14:39:47 -04:00
|
|
|
</excludeResourceNames>
|
|
|
|
</configuration>
|
|
|
|
</execution>
|
|
|
|
<execution>
|
|
|
|
<id>build_r4</id>
|
|
|
|
<goals>
|
|
|
|
<goal>generate-jparest-server</goal>
|
|
|
|
</goals>
|
|
|
|
<configuration>
|
|
|
|
<version>r4</version>
|
|
|
|
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
|
|
|
|
<packageBase>ca.uhn.fhir.jpa.rp.r4</packageBase>
|
2020-07-13 08:51:13 -04:00
|
|
|
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r4.xml
|
|
|
|
</targetResourceSpringBeansFile>
|
2017-08-13 14:39:47 -04:00
|
|
|
<baseResourceNames></baseResourceNames>
|
|
|
|
<excludeResourceNames>
|
2015-11-29 11:43:09 -05:00
|
|
|
</excludeResourceNames>
|
|
|
|
</configuration>
|
2022-10-20 16:57:06 -04:00
|
|
|
</execution>
|
|
|
|
<execution>
|
|
|
|
<id>build_r4b</id>
|
|
|
|
<goals>
|
|
|
|
<goal>generate-jparest-server</goal>
|
|
|
|
</goals>
|
|
|
|
<configuration>
|
|
|
|
<version>r4b</version>
|
|
|
|
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
|
|
|
|
<packageBase>ca.uhn.fhir.jpa.rp.r4b</packageBase>
|
|
|
|
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r4b.xml
|
|
|
|
</targetResourceSpringBeansFile>
|
|
|
|
<baseResourceNames></baseResourceNames>
|
|
|
|
<excludeResourceNames>
|
|
|
|
</excludeResourceNames>
|
|
|
|
</configuration>
|
2015-11-29 11:43:09 -05:00
|
|
|
</execution>
|
2019-08-06 17:30:31 -04:00
|
|
|
<execution>
|
|
|
|
<id>build_r5</id>
|
|
|
|
<goals>
|
|
|
|
<goal>generate-jparest-server</goal>
|
|
|
|
</goals>
|
|
|
|
<configuration>
|
|
|
|
<version>r5</version>
|
|
|
|
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
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|
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|
<packageBase>ca.uhn.fhir.jpa.rp.r5</packageBase>
|
2020-07-13 08:51:13 -04:00
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|
|
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r5.xml
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</targetResourceSpringBeansFile>
|
2019-08-06 17:30:31 -04:00
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|
|
<baseResourceNames></baseResourceNames>
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|
|
</configuration>
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|
|
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</execution>
|
2014-12-21 18:13:37 -05:00
|
|
|
</executions>
|
2017-08-13 14:39:47 -04:00
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|
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|
2014-12-21 18:13:37 -05:00
|
|
|
<dependencies>
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|
|
|
<dependency>
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|
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<groupId>ca.uhn.hapi.fhir</groupId>
|
2017-08-13 14:39:47 -04:00
|
|
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<artifactId>hapi-fhir-structures-dstu2</artifactId>
|
2017-01-29 13:22:28 -05:00
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|
|
<version>${project.version}</version>
|
2014-12-21 18:13:37 -05:00
|
|
|
</dependency>
|
|
|
|
<dependency>
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|
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|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2017-08-13 14:39:47 -04:00
|
|
|
<artifactId>hapi-fhir-structures-dstu3</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2014-12-21 18:13:37 -05:00
|
|
|
</dependency>
|
2015-11-29 11:43:09 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2017-08-13 14:39:47 -04:00
|
|
|
<artifactId>hapi-fhir-structures-r4</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2015-11-29 11:43:09 -05:00
|
|
|
</dependency>
|
2017-08-13 14:39:47 -04:00
|
|
|
|
2015-12-20 09:29:52 -05:00
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
2016-02-01 08:55:58 -05:00
|
|
|
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
|
2017-01-29 13:22:28 -05:00
|
|
|
<version>${project.version}</version>
|
2015-12-20 09:29:52 -05:00
|
|
|
</dependency>
|
2014-12-21 18:13:37 -05:00
|
|
|
</dependencies>
|
|
|
|
</plugin>
|
2023-12-03 11:15:37 -05:00
|
|
|
<!-- Generate the DDL schema files -->
|
|
|
|
<plugin>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-tinder-plugin</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
<executions>
|
|
|
|
<execution>
|
|
|
|
<goals>
|
|
|
|
<goal>generate-ddl</goal>
|
|
|
|
</goals>
|
|
|
|
</execution>
|
|
|
|
</executions>
|
|
|
|
<configuration>
|
|
|
|
<packageNames>
|
|
|
|
<packageName>ca.uhn.fhir.jpa.entity</packageName>
|
|
|
|
<packageName>ca.uhn.fhir.jpa.model.entity</packageName>
|
|
|
|
</packageNames>
|
|
|
|
<dialects>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirDerbyDialect</className>
|
|
|
|
<targetFileName>derby.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirMySQLDialect</className>
|
|
|
|
<targetFileName>mysql.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirMariaDBDialect</className>
|
|
|
|
<targetFileName>mariadb.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirOracleDialect</className>
|
|
|
|
<targetFileName>oracle.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirSQLServerDialect</className>
|
|
|
|
<targetFileName>sqlserver.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirCockroachDialect</className>
|
|
|
|
<targetFileName>cockroachdb.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect</className>
|
|
|
|
<targetFileName>h2.sql</targetFileName>
|
|
|
|
</dialect>
|
|
|
|
<dialect>
|
|
|
|
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect</className>
|
|
|
|
<targetFileName>postgres.sql</targetFileName>
|
2023-12-06 12:33:34 -05:00
|
|
|
<appendFile>classpath:ca/uhn/fhir/jpa/docs/database/hapifhirpostgres94-init01.sql</appendFile>
|
2023-12-03 11:15:37 -05:00
|
|
|
</dialect>
|
|
|
|
</dialects>
|
|
|
|
<outputDirectory>${project.build.directory}/classes/ca/uhn/hapi/fhir/jpa/docs/database</outputDirectory>
|
|
|
|
</configuration>
|
|
|
|
<dependencies>
|
|
|
|
<dependency>
|
|
|
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
|
|
|
<artifactId>hapi-fhir-jpaserver-model</artifactId>
|
|
|
|
<version>${project.version}</version>
|
|
|
|
</dependency>
|
|
|
|
</dependencies>
|
|
|
|
</plugin>
|
2017-02-04 16:31:18 -05:00
|
|
|
<plugin>
|
|
|
|
<groupId>org.codehaus.mojo</groupId>
|
|
|
|
<artifactId>build-helper-maven-plugin</artifactId>
|
|
|
|
<executions>
|
|
|
|
<execution>
|
|
|
|
<id>add-source</id>
|
|
|
|
<phase>generate-sources</phase>
|
|
|
|
<goals>
|
|
|
|
<goal>add-source</goal>
|
|
|
|
</goals>
|
|
|
|
<configuration>
|
|
|
|
<sources>
|
|
|
|
<source>target/generated-sources/tinder</source>
|
|
|
|
</sources>
|
|
|
|
</configuration>
|
|
|
|
</execution>
|
|
|
|
</executions>
|
|
|
|
</plugin>
|
2022-02-16 20:44:03 -05:00
|
|
|
</plugins>
|
2014-12-21 18:13:37 -05:00
|
|
|
<resources>
|
|
|
|
<resource>
|
2018-04-21 14:32:17 -04:00
|
|
|
<directory>${project.basedir}/src/main/resources</directory>
|
2014-12-21 18:13:37 -05:00
|
|
|
</resource>
|
|
|
|
<resource>
|
2018-04-21 14:32:17 -04:00
|
|
|
<directory>${project.basedir}/target/generated-resources/tinder</directory>
|
2014-12-21 18:13:37 -05:00
|
|
|
</resource>
|
|
|
|
</resources>
|
2014-05-05 08:57:43 -04:00
|
|
|
</build>
|
|
|
|
|
|
|
|
</project>
|