hapi-fhir/pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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6_4 mergeback (#4547) * 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' * Remove checkstyle * Verison bump * Move migrations * semicolon --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: 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: Ken Stevens <ken@smilecdr.com>
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<!-- the version info -->
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<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>7.7.5-SNAPSHOT</version>
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<name>HAPI-FHIR</name>
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<description>An open-source implementation of the FHIR specification in Java.</description>
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<url>https://hapifhir.io</url>
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<organization>
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<name>Smile CDR, Inc.</name>
<url>https://smilecdr.com</url>
</organization>
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<inceptionYear>2014</inceptionYear>
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<issueManagement>
<system>GitHub</system>
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<url>https://github.com/hapifhir/hapi-fhir/issues/</url>
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</issueManagement>
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<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
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<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
<site>
<id>git.server</id>
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<url>scm:git:git@github.com:hapifhir/hapi-fhir.git</url>
</site>
</distributionManagement>
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<scm>
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<connection>scm:git:git@github.com:hapifhir/hapi-fhir.git</connection>
<url>scm:git:git@github.com:hapifhir/hapi-fhir.git</url>
<developerConnection>scm:git:git@github.com:hapifhir/hapi-fhir.git</developerConnection>
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</scm>
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<repositories>
<repository>
<id>oss-snapshot</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>false</enabled>
</releases>
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</repository>
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</repositories>
<modules>
<module>hapi-fhir-checkstyle</module>
<module>hapi-fhir-bom</module>
<module>hapi-deployable-pom</module>
<module>hapi-fhir-base</module>
<module>hapi-fhir-docs</module>
<module>hapi-fhir-test-utilities</module>
<module>hapi-fhir-jpaserver-test-utilities</module>
<module>hapi-fhir-jpaserver-test-dstu2</module>
<module>hapi-fhir-jpaserver-test-dstu3</module>
<module>hapi-fhir-jpaserver-test-r4</module>
<module>hapi-fhir-jpaserver-test-r4b</module>
<module>hapi-fhir-jpaserver-test-r5</module>
<module>hapi-fhir-jpaserver-elastic-test-utilities</module>
<module>hapi-tinder-plugin</module>
<module>hapi-tinder-test</module>
<module>hapi-fhir-client</module>
<module>hapi-fhir-server</module>
<module>hapi-fhir-server-mdm</module>
<module>hapi-fhir-server-openapi</module>
<module>hapi-fhir-converter</module>
<module>hapi-fhir-validation</module>
<module>hapi-fhir-structures-dstu2</module>
<module>hapi-fhir-structures-hl7org-dstu2</module>
<module>hapi-fhir-validation-resources-dstu2</module>
<module>hapi-fhir-structures-dstu2.1</module>
<module>hapi-fhir-validation-resources-dstu2.1</module>
<module>hapi-fhir-structures-dstu3</module>
<module>hapi-fhir-validation-resources-dstu3</module>
<module>hapi-fhir-structures-r4</module>
<module>hapi-fhir-validation-resources-r4</module>
<module>hapi-fhir-structures-r4b</module>
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>
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<module>hapi-fhir-validation-resources-r4b</module>
<module>hapi-fhir-structures-r5</module>
<module>hapi-fhir-validation-resources-r5</module>
<module>hapi-fhir-jpa</module>
<module>hapi-fhir-serviceloaders</module>
<module>hapi-fhir-storage</module>
<module>hapi-fhir-storage-batch2</module>
<module>hapi-fhir-storage-batch2-test-utilities</module>
<module>hapi-fhir-storage-batch2-jobs</module>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
<module>hapi-fhir-storage-cr</module>
<module>hapi-fhir-storage-mdm</module>
<module>hapi-fhir-storage-test-utilities</module>
<module>hapi-fhir-jpaserver-model</module>
<module>hapi-fhir-jpaserver-searchparam</module>
<module>hapi-fhir-jpaserver-subscription</module>
<module>hapi-fhir-jaxrsserver-base</module>
<module>hapi-fhir-jpaserver-base</module>
<module>hapi-fhir-sql-migrate</module>
<module>hapi-fhir-jpaserver-ips</module>
<module>hapi-fhir-jpaserver-hfql</module>
<module>hapi-fhir-jpaserver-mdm</module>
<module>hapi-fhir-testpage-overlay</module>
<module>hapi-fhir-jpaserver-uhnfhirtest</module>
<module>hapi-fhir-client-okhttp</module>
<module>hapi-fhir-android</module>
<module>hapi-fhir-cli</module>
<module>hapi-fhir-dist</module>
<module>tests/hapi-fhir-base-test-jaxrsserver-kotlin</module>
<module>tests/hapi-fhir-base-test-mindeps-client</module>
<module>tests/hapi-fhir-base-test-mindeps-server</module>
<module>hapi-fhir-spring-boot</module>
<module>hapi-fhir-jacoco</module>
<module>hapi-fhir-server-cds-hooks</module>
</modules>
2014-02-17 17:58:32 -05:00
<dependencies>
Replace hamcrest with assertj (#5911) * optimize imports * optimize imports * Hamcrest replacement * Hamcrest replacement * Test failures * migrate hapi-fhir-base * docs * Few more cutovers * Full rewrite of all assert cases * Full rewrite of all assert cases * Partial cutover * assert library conversion * wip * fix imports * remove equalto * once-over again * minor cutover * wip * wip * wip * wip * wip * Remove hamcrest asserts replace with assertj * wip * Partial hamcrest rip-out * More hamcrest stripping * wip * Partial completion * spotless * it compiles now * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fix compile issues * fix compile issues * hapi-fhir now compiles * fix test * fix test * fix test * fix tests * fix tests * fix tests * fix test * fix test * fix tests * fix tests * fix tests * yay all tests pass now! * revert assertEquals change * revert assertEquals change * organize imports * organize imports * organize imports * post merge cleanup * organize imports * more cleanup * more cleanup * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * organize imports * organize imports * remove final hamcrest stuff * remove final hamcrest usages * remove final hamcrest usages * Revert "remove final hamcrest usages" This reverts commit eaf5107396af7c0fedbb8f1dce8b75133cc790eb. * fix compile issues from a hacky search/replace * compiles with fixmes * fix tests * fix test * fix test * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge test issues * fix test * fix test * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * all but mdm tests * final hamcrest removed from hapi-fhir yay! * revert mdm changes. it's too hard for now * revert cdr breaking change * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert changes that break cdr * merge master with compile errors * review feedback * review feedback * review feedback: revert bad regexp change * fix test * fix test * convert new hamcrest entries * convert new hamcrest entries --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-06-05 16:02:46 -04:00
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2021-10-14 16:37:13 -04:00
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<properties>
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6_4 mergeback (#4547) * 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' * Remove checkstyle * Verison bump * Move migrations * semicolon --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: 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: Ken Stevens <ken@smilecdr.com>
2023-02-13 16:23:25 -05:00
<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->
<maven.build.timestamp.format>yyyy-MM-dd'T'HH:mm:ss'Z'</maven.build.timestamp.format>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<!-- For site-deploy -->
<siteMainDirectory>${user.home}/sites/hapi-fhir</siteMainDirectory>
<scmPubCheckoutDirectory>${user.home}/sites/scm/hapi-fhir</scmPubCheckoutDirectory>
<!-- Dependency Versions -->
<activation_api_version>1.2.0</activation_api_version>
<apache_karaf_version>4.2.5</apache_karaf_version>
<aries_spifly_version>1.2</aries_spifly_version>
<caffeine_version>3.1.8</caffeine_version>
<checkstyle_version>10.17.0</checkstyle_version>
<maven_changes_version>2.12.1</maven_changes_version>
<commons_codec_version>1.15</commons_codec_version>
<commons_compress_version>1.26.0</commons_compress_version>
2023-12-29 11:43:47 -05:00
<!--
Note if you bump the version here - The commons-dbcp2 2.11.0 version
explicitly depends on commons-pool2 2.12.0, so we explicitly specify that
version below as well. If you bump this, make sure you're bumping the
pool2 version appropriately too.
-->
<commons_dbcp2_version>2.11.0</commons_dbcp2_version>
<!-- Before Bumping: See note above about dbcp2 -->
<commons_pool2_version>2.12.0</commons_pool2_version>
<commons_text_version>1.10.0</commons_text_version>
<commons_io_version>2.11.0</commons_io_version>
<commons_lang3_version>3.14.0</commons_lang3_version>
<com_jamesmurty_utils_version>1.2</com_jamesmurty_utils_version>
<error_prone_core_version>2.23.0</error_prone_core_version>
<mockito_version>5.8.0</mockito_version>
<nullaway_version>0.7.9</nullaway_version>
<guava_version>33.2.1-jre</guava_version>
<gson_version>2.8.9</gson_version>
<jaxb_bundle_version>2.2.11_1</jaxb_bundle_version>
<jaxb_api_version>2.3.1</jaxb_api_version>
<jaxb_core_version>2.3.0.1</jaxb_core_version>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<jaxb_runtime_version>4.0.4</jaxb_runtime_version>
Rel 6 10 mb (#5441) * Allow cached search with consent active when safe (#5387) Allow the search cache when using consent if safe * Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376) * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation * Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * first fix * tests and preliminary fixes * wip, commit before switching to release branch. * adding capability to handle _lastUpdated in reverse search (_has) * adding changelog * applying spotless. * addressing code review comments. --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Br 20231019 add cr settings for cds hooks (#5394) * Add settings used in CR CDS Services. Remove config dependency on Spring Boot. * Add changelog * Use String.format rather than concat strings * spotless apply * Add javadoc * Upgrade notes for the forced-id change (#5400) Add upgrade notes for forced-id * Clean stale search results more aggressively. (#5396) Use bulk DMA statements when cleaning the search cache. The cleaner job now works as long as possible until a deadline based on the scheduling frequency. * bump version of clinical reasoning (#5406) * Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added * removed unused alias from SQL query of mdm-clear (#5416) * Issue 5418 support Boolean class return type in BaseInterceptorService (#5421) * Enable child classes to use Boolean class return type * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420) * If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix * Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423) This reverts commit 4e295a59fb143a2ba54bc44305474096e2acd578. Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> * Use new FHIR_ID column for sorting (#5405) * Sort `_id` using new FHIR_ID column. * Fix old tests that put client-assigned ids first. * Better indexing for sort * Bump core to 6.1.2.2 (#5425) * Bump core to 6.1.2.1 Patch release that uses https for primary org.hl7.fhir.core package server * Bump core to 6.1.2.2 * Make sure to return always a value for Boolean class return type. (#5424) Implement change in a non-disruptive way for overriders Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) Add a non-standard __pid SP. * Review changes for new _pid SP. (#5430) Change name to _pid to match our standard and add warning. * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432) * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition. * Fix spotless issue * CVEs for 6.10.0 (#5433) * Bump jetty * Bump okio-jvm * 8.2.0 mysql connector * Jena and elastic bumps * Fix test * 5412 post bundle on partition incorrect response.link shown (#5413) * Initial fix and unit test provided * spottless check * Made relevant changes to make solution version agnostic * relevant logic changes made * spotless changes made * New logic added to fix failing test cases * formatting * New logic to make the function more robust * spotless checks * Left a trailing slash in the tests * Made relevant test changes and changed logic * spotless changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml changing changelog Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Formatting requirements --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414) * first fix * - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber - refactored code to reduce repeated code - cleaned unnecessary comments and reformatted files * Changed myResourceModifiedMessagePersistenceSvc to be autowired * removed unused import * added error handling when inflating the message to email and message subscriber * reformatted code * Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc * Changes by gary * Reformatted file * fixed failed tests * implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File. * - implemented IT - fixed logical error - added changelog * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * resolve code review comments * reformatted files * fixed tests * Fix for failing IT test in jpaserver-starter (#5435) Co-authored-by: dotasek <dotasek.dev@gmail.com> * wip --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: dotasek <dotasek.dev@gmail.com>
2023-11-10 17:00:08 -05:00
<jena_version>4.9.0</jena_version>
<jersey_version>3.0.3</jersey_version>
<jetty_version>12.0.9</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<junit_version>5.10.1</junit_version>
<flexmark_version>0.64.8</flexmark_version>
<flyway_version>9.4.0</flyway_version>
<hibernate_version>6.4.1.Final</hibernate_version>
<logback_version>1.4.14</logback_version>
<!-- Update lucene version when you update hibernate-search version - These go together! -->
<hibernate_search_version>7.0.0.Final</hibernate_search_version>
<!-- Update lucene version when you update hibernate-search version - These go together! -->
<lucene_version>9.8.0</lucene_version>
<hamcrest_version>2.2</hamcrest_version>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<hibernate_validator_version>8.0.0.Final</hibernate_validator_version>
<httpcore_version>4.4.13</httpcore_version>
<httpclient_version>4.5.13</httpclient_version>
<jackson_version>2.17.1</jackson_version>
<jackson_databind_version>2.17.1</jackson_databind_version>
<maven_assembly_plugin_version>3.3.0</maven_assembly_plugin_version>
<maven_license_plugin_version>1.8</maven_license_plugin_version>
<okhttp_version>4.12.0</okhttp_version>
2024-10-03 08:32:37 -04:00
<otel_instrumentation.version>2.8.0</otel_instrumentation.version>
<poi_version>4.1.2</poi_version>
<poi_ooxml_schemas_version>1.4</poi_ooxml_schemas_version>
<resteasy_version>6.2.9.Final</resteasy_version>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<ph_schematron_version>7.1.2</ph_schematron_version>
<ph_commons_version>9.5.4</ph_commons_version>
<plexus_compiler_api_version>2.13.0</plexus_compiler_api_version>
<reflections_version>0.9.11</reflections_version>
<servicemix_saxon_version>9.8.0-15</servicemix_saxon_version>
<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
<swagger_version>2.2.22</swagger_version>
<slf4j_version>2.0.13</slf4j_version>
<log4j_to_slf4j_version>2.19.0</log4j_to_slf4j_version>
<spring_version>6.1.8</spring_version>
<spring_data_bom_version>2023.1.6</spring_data_bom_version>
<spring_batch_version>4.3.10</spring_batch_version>
<spring_boot_version>3.2.6</spring_boot_version>
<spring_retry_version>2.0.6</spring_retry_version>
<json_path_version>2.9.0</json_path_version>
<stax2_api_version>3.1.4</stax2_api_version>
<testcontainers_version>1.19.3</testcontainers_version>
<thymeleaf-version>3.1.2.RELEASE</thymeleaf-version>
<woodstox_core_asl_version>4.4.1</woodstox_core_asl_version>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
<elastic_apm_version>1.44.0</elastic_apm_version>
<elasticsearch_version>8.14.3</elasticsearch_version>
<ucum_version>1.0.8</ucum_version>
GM1 Mergeback (#5203) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
2023-08-15 15:32:10 -04:00
<!-- Clinical Reasoning & CQL Support -->
Update Clinical Reasoning to 3.13.0 (#6358) * Update Clinical Reasoning to 3.12.0 * Update to 3.13.0 * add stub for new not document parameter * Add new client Timezone header and enhance JsonUtil to handle ZonedDateTime. * Add StringTimePeriodHandler and test. Add new code to DateUtils and new test class. Inject StringTimePeriodHandler into MeasureOperationsProvider and CareGapsOperationProvider. Change CareGapsOperationProvider to take String params instead of IPrimitiveType<Date>. * Remove old LibraryEvaluationOperationProvider * Fix test * Fix tests * Add $data-requirement parameters to docs * Update docs for new measures timezone header. * Add prefetchData parameter to $apply doc * Add changelog * Fix test * Update snapshot version * Add new $extract parameters to docs * Remove old test * fix test and properties for care-gaps * Fix dstu3 config * remove property for fhirserverurl * update upgrade.md doc * fix formatting of upgrade doc * comment on measureidentifier param * nonDocument parameter inclusion * java doc on care-gaps * No longer dead code. * Spotless. * Change CareGapsOperationProvider to R4 BooleanType. * Update to release * change log update * change log edit * cleanup * Use existing bean * spotless * Ensure CollectDataOperationProvider uses StringTimePeriodHandler to convert periods. * Spotless. * Add tests for id * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md Co-authored-by: Tadgh <garygrantgraham@gmail.com> * cleanup and comments * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Code review feedback: Add logging for StringTimePeriodHandler. * Spotless. * cleanup * Code review feedback: measures.md style changes. Change code 2560 to 2561. * Change error code. --------- Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2024-10-17 08:38:42 -04:00
<clinical-reasoning.version>3.13.0</clinical-reasoning.version>
2018-11-30 17:19:16 -05:00
<!-- Site properties -->
<fontawesomeVersion>5.4.1</fontawesomeVersion>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<maven.compiler.release>11</maven.compiler.release>
<maven.compiler.testSource>17</maven.compiler.testSource>
<maven.compiler.testTarget>17</maven.compiler.testTarget>
<maven.compiler.testRelease>17</maven.compiler.testRelease>
<maven_checkstyle_version>3.4.0</maven_checkstyle_version>
<!-- Jacoco -->
<argLine></argLine>
</properties>
2014-02-17 17:58:32 -05:00
2015-08-16 22:09:01 -04:00
<dependencyManagement>
<dependencies>
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>org.hl7.fhir.utilities</artifactId>
<version>${fhir_core_version}</version>
<exclusions>
<exclusion>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
</exclusion>
</exclusions>
</dependency>
Rel 6 1 mergeback (#3927) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * Fix illegalstateexception when an exception is thrown during stream response (#3882) * Finish up changelog, minor refactor * reset buffer only * Hack for some replacements * Failure handling * wip * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * Implemented seventh character extended code and the corresponding dis… (#3709) * Implemented seventh character extended code and the corresponding display * Modifications * Changes on previous test according to modifications made in ICD10-CM XML file * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * updated pointcuts to work as intended (#3903) * updated pointcuts to work as intended * added changelog * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 3899 code in limits (#3901) * Add implementation, changelog, test * Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> * 3884 overlapping searchparameter undetected rel 6 1 (#3909) * Applying all changes from previous dev branch to current one pointing to rel_6_1 * Fixing merge conflict related to Msg.code value. * Fixing Msg.code value. * Making checkstyle happy. * Making sure that all tests are passing. * Passing all tests after fixing Msg.code * Passing all tests. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746) * 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete * created unit test for skip of delete operation while processing duplicating create entries * moved unit test to FhirSystemDaoR4Test * 3379 mdm fixes (#3906) * added MdmLinkCreateSvcimplTest * fixed creating mdm-link not setting the resource type correctly * fixed a bug where ResourcePersistenceId was being duplicated instead of passed on * Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java Change order of tests such that assertEquals takes expected value then actual value Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * Fix to the issue (#3855) * Fix to the issue * Progress * fixed the issue * Addressing suggestions * add response status code to MethodOutcome * Addressing suggestions Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix for caching appearing broken in batch2 for bulkexport jobs (#3912) * Respect caching in bullk export, fix bug with completed date on empty jobs * add changelog * Add impl * Add breaking test * Complete failing test * more broken tests * Fix more tests' * Fix paging bug * Fix another brittle test * 3915 do not collapse rules with filters (#3916) * do not attempt to merge compartment permissions with filters * changelog * Rename to IT for concurrency problems Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <ken@smilecdr.com> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 3922 delete expunge large dataset (#3923) * lower batchsize of delete requests so that we do not get sql exceptions * blah * fix test * updated tests to not fail Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * add index * Fix up colun grab * Bump Version for non-breaking purposes * Fix broken test * bump error code * revert internal logic * Revert offset mode change * wip * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-08-18 20:21:27 -04:00
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-bom</artifactId>
<version>${spring_data_bom_version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
2015-09-08 08:14:55 -04:00
<dependency>
<groupId>aopalliance</groupId>
<artifactId>aopalliance</artifactId>
<version>1.0</version>
</dependency>
2015-08-17 15:54:00 -04:00
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback_version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback_version}</version>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
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</dependency>
<dependency>
<groupId>com.atlassian.commonmark</groupId>
<artifactId>commonmark</artifactId>
<version>0.9.0</version>
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</dependency>
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<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
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<version>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
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<version>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson_databind_version}</version>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
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<version>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
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<version>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.module</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jackson-module-jakarta-xmlbind-annotations</artifactId>
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<version>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<version>${json_path_version}</version>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path-assert</artifactId>
<version>${json_path_version}</version>
</dependency>
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
<version>${caffeine_version}</version>
</dependency>
<dependency>
<groupId>com.googlecode.owasp-java-html-sanitizer</groupId>
<artifactId>owasp-java-html-sanitizer</artifactId>
<version>20211018.2</version>
</dependency>
<dependency>
<groupId>com.graphql-java</groupId>
<artifactId>graphql-java</artifactId>
rel_7_4 Merge-back (#6212) * use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments * Add path value to _id search parameter and other missing search param… (#6128) * Add path value to _id search parameter and other missing search parameters to IAnyResource. * Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource * Revert unneeded change * _security param is not token but uri * Add tests for new defined resource-level standard parameters * Adjust test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#6151) * Handle 400 and 404 codes returned by remote terminology operation. * Some simplification * Adjust changelog * Add a comment to explain alternate solution which can be reused. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * 6051 bulk export security errors (#5915) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * refactor bulk export rule, add concept of appliestoallpatients, fix tests * spotless * Cahgnelog, tests * more tests * refactor style checks --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> * Convert a few nulls to aggressive denies * Change chain sort syntax for MS SQL (#5917) * Change sort type on chains * Change sort type on chains * Test for MS SQL * Comments * Version bump * Updating version to: 7.2.1 post release. * Fix queries with chained sort with Lucene by checking supported SortSpecs (#5958) * First commit with very rough solution. * Solidify solutions for both requirements. Add new tests. Enhance others. * Spotless. * Add new chained sort spec algorithm. Add new Msg.codes. Finalize tests. Update docs. Add changelog. * pom remove the snapshot * Updating version to: 7.2.2 post release. * cherry-picked pr 6051 * changelog fix * cherry-picked 6027 * docs and changelog * merge fix for issue with infinite cache refresh loop * Use lockless mode when adding index on Azure Sql server (#6100) (#6129) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * added fix for 6133 * failing Test * Add fix * spotless * Remove useless file * Fix claeaner * cleanup * Remove dead class * Changelog * test description * Add test. Fix broken logic. * fix quantity search parameter test to pass * reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT * spotless * cleanup mistake during merge * added missing imports * fix more mergeback oopsies * bump to 7.3.13-snapshot --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> * Patient validate operation with remote terminology service enabled returns 400 bad request (#6124) * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security * Add tests and changelog * Increase snapshot version * Irrelevant change to force new build --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Fix $reindex job with custom partition interceptor based on resource type. Update reindex job to always run with urls. (#6185) * Refactor logic to bring together partition related logic in batch2 jobs using IJobPartitionProvider. Update logic such that reindex job without urls will attempt to create urls for all supported resource types. * Small changes and fix of pipeline error. * Small change to enable mdm-submit to use PartitionedUrl in the job parameters * Revert logback change. Fix dependency version generating errors in the pipeline. * Spotless fix. Add test dependency back without version. * Upgrade test dependency to another version * Add javadoc for PartitionedUrl. Other small fixes and refactoring in tests. * Spotless fix. * Change to JobParameters to fix some of the tests. * Small changes for code review in test * Address code review comments. * Revert change from bad merge. * Address remaining code review comments * 6188 subscription not marked as a cross partition subscription matches operation on resources in other partitions (#6191) * initial failing test * WIP * fixing/adding tests * added changelog * spotless * fixing tests * Cleaning up tests * addressing commetns from first code review. * no-op to get pipelines going --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Resolve 6173 - Log unhandled Exceptions in RestfulServer (#6176) (#6205) * 6173 - Log unhandled Exceptions in RestfulServer. * Use placeholder for failed streams. * Starting test for server handling. * Got test working. * Fixed use of synchronized keyword. * Applied mvn spotless. --------- Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Partition aware transactions (#6167) * Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Add license header * rel_7_4 mergeback --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-08-14 17:03:35 -04:00
<version>21.5</version>
</dependency>
<!-- mail start -->
<dependency>
<groupId>org.simplejavamail</groupId>
<artifactId>simple-java-mail</artifactId>
<version>8.11.2</version>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<exclusions>
<exclusion>
<groupId>com.github.bbottema</groupId>
<artifactId>jetbrains-runtime-annotations</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
</exclusion>
<exclusion>
<groupId>jakarta.mail</groupId>
<artifactId>jakarta.mail-api</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>jakarta.mail</groupId>
<artifactId>jakarta.mail-api</artifactId>
<version>2.1.3</version>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail</artifactId>
<version>2.1.0-rc-1</version>
<exclusions>
<exclusion>
<groupId>jakarta.mail</groupId>
<artifactId>jakarta.mail-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail-junit5</artifactId>
<version>2.1.0-rc-1</version>
<scope>compile</scope>
</dependency>
<!-- mail end -->
2016-09-17 16:55:21 -04:00
<dependency>
<groupId>com.github.dnault</groupId>
<artifactId>xml-patch</artifactId>
2019-09-11 17:33:31 -04:00
<version>0.3.1</version>
2016-09-17 16:55:21 -04:00
</dependency>
2019-04-24 14:10:21 -04:00
<dependency>
<groupId>io.dogote</groupId>
<artifactId>json-patch</artifactId>
<version>1.15</version>
</dependency>
2017-04-01 09:03:42 -04:00
<dependency>
<groupId>com.google.errorprone</groupId>
<artifactId>error_prone_core</artifactId>
2019-01-09 21:20:46 -05:00
<version>${error_prone_core_version}</version>
2017-04-01 09:03:42 -04:00
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava_version}</version>
2015-08-31 08:20:24 -04:00
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava-testlib</artifactId>
2019-07-07 10:14:08 -04:00
<version>${guava_version}</version>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<version>2.2.224</version>
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>com.helger.commons</groupId>
<artifactId>ph-collection</artifactId>
<version>11.1.2</version>
</dependency>
<dependency>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-api</artifactId>
<version>${ph_schematron_version}</version>
2015-08-31 08:20:24 -04:00
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-xslt</artifactId>
<version>${ph_schematron_version}</version>
2015-08-31 08:20:24 -04:00
</dependency>
<dependency>
<groupId>com.jamesmurty.utils</groupId>
<artifactId>java-xmlbuilder</artifactId>
<version>${com_jamesmurty_utils_version}</version>
</dependency>
<dependency>
<groupId>com.puppycrawl.tools</groupId>
<artifactId>checkstyle</artifactId>
<version>${checkstyle_version}</version>
</dependency>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
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<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
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<version>${okhttp_version}</version>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
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</dependency>
Rel 6 2 mergeback (#4257) * jm wrong bundle entry url (#4213) * Bug test * here you go * Generate relative URIs for bundle entry.request.url, as specified * Point jira issue in changelog * Adjust tests to fixes Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * improved logging (#4217) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Rel 6 1 3 mergeback (#4215) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * Fix illegalstateexception when an exception is thrown during stream response (#3882) * Finish up changelog, minor refactor * reset buffer only * Hack for some replacements * Failure handling * wip * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * Implemented seventh character extended code and the corresponding dis… (#3709) * Implemented seventh character extended code and the corresponding display * Modifications * Changes on previous test according to modifications made in ICD10-CM XML file * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * updated pointcuts to work as intended (#3903) * updated pointcuts to work as intended * added changelog * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 3899 code in limits (#3901) * Add implementation, changelog, test * Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> * 3884 overlapping searchparameter undetected rel 6 1 (#3909) * Applying all changes from previous dev branch to current one pointing to rel_6_1 * Fixing merge conflict related to Msg.code value. * Fixing Msg.code value. * Making checkstyle happy. * Making sure that all tests are passing. * Passing all tests after fixing Msg.code * Passing all tests. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746) * 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete * created unit test for skip of delete operation while processing duplicating create entries * moved unit test to FhirSystemDaoR4Test * 3379 mdm fixes (#3906) * added MdmLinkCreateSvcimplTest * fixed creating mdm-link not setting the resource type correctly * fixed a bug where ResourcePersistenceId was being duplicated instead of passed on * Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java Change order of tests such that assertEquals takes expected value then actual value Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * Fix to the issue (#3855) * Fix to the issue * Progress * fixed the issue * Addressing suggestions * add response status code to MethodOutcome * Addressing suggestions Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix for caching appearing broken in batch2 for bulkexport jobs (#3912) * Respect caching in bullk export, fix bug with completed date on empty jobs * add changelog * Add impl * Add breaking test * Complete failing test * more broken tests * Fix more tests' * Fix paging bug * Fix another brittle test * 3915 do not collapse rules with filters (#3916) * do not attempt to merge compartment permissions with filters * changelog * Rename to IT for concurrency problems Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <ken@smilecdr.com> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 3922 delete expunge large dataset (#3923) * lower batchsize of delete requests so that we do not get sql exceptions * blah * fix test * updated tests to not fail Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * add index * Fix up colun grab * Revert offset mode change * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic * Updating version to: 6.1.1 post release. * fix compile error * Deploy to sonatype (#3934) * adding sonatype profile to checkstyle module * adding sonatype profile to tinder module * adding sonatype profile to base pom * adding final deployToSonatype profile * wip * Revert version enum * Updating version to: 6.1.1 post release. * Add test, changelog, and implementation * Add backport info * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient * wip * Add backport info * Add info of new version * Updating version to: 6.1.2 post release. * bump info and backport for 6.1.2 * Bump for hapi * Implement bug fixes, add new tests (#4022) * Implement bug fixes, add new tests * tidy * Tidy * refactor for cleaning * More tidying * Lower logging * Split into nested tests, rename, add todos * Typo * Code review * add backport info * Updating version to: 6.1.3 post release. * Updating version to: 6.1.3 post release. * removed duplicate mention of ver 6.1.3 in versionEnum * backport pr 4101 * mdm message key (#4111) * begin with failing test * fixed 2 tests * fix tests * fix tests * change log Co-authored-by: Ken Stevens <ken@smilecdr.com> * backport 6.1.3 docs changes * fixed typo on doc backport message * fix test breaking * Updating version to: 6.1.4 post release. * wip Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> * pin okio-jvm for kotlin vuln (#4216) * Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220) * First commit: Failing unit test and a TODO with a vague idea of where the bug happens. * Don't escape "+" in a URL GET parameter if it starts with "application". * Remove unnecessary TODO. * Add changelog. * Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens. * Ks 20221031 migration lock (#4224) * started design * complete with tests * changelog * cleanup * tyop Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209) * Added test * Added solution * Changelog * Changes made based on comments * Fix bug with MDM submit * fix * Version bump * 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236) * Add constant for interceptor * add test, changelog * Allow Batch2 transition from ERRORED to COMPLETE (#4242) * Allow Batch2 transition from ERRORED to COMPLETE * Add changelog * Test fix Co-authored-by: James Agnew <james@jamess-mbp.lan> * 3685 When bulk exporting, if no resource type param is provided, defa… (#4233) * 3685 When bulk exporting, if no resource type param is provided, default to all registered types. * Update test case. * Cleaned up changelog. * Added test case for multiple resource types. * Added failing test case for not returning Binary resource. * Refactor solution. Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Add next version * bulk export permanently reusing cached results (#4249) * Add test, fix bug, add changelog * minor refactor * Fix * Bump HAPI version * Remove jetbrains * Fix broken test Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: James Agnew <james@jamess-mbp.lan> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-11-07 18:57:57 -05:00
<!-- Pinned here for CVE: CVE-2022-24329 -->
<dependency>
<groupId>com.squareup.okio</groupId>
<artifactId>okio-jvm</artifactId>
Rel 6 10 mb (#5441) * Allow cached search with consent active when safe (#5387) Allow the search cache when using consent if safe * Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376) * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation * Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * first fix * tests and preliminary fixes * wip, commit before switching to release branch. * adding capability to handle _lastUpdated in reverse search (_has) * adding changelog * applying spotless. * addressing code review comments. --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Br 20231019 add cr settings for cds hooks (#5394) * Add settings used in CR CDS Services. Remove config dependency on Spring Boot. * Add changelog * Use String.format rather than concat strings * spotless apply * Add javadoc * Upgrade notes for the forced-id change (#5400) Add upgrade notes for forced-id * Clean stale search results more aggressively. (#5396) Use bulk DMA statements when cleaning the search cache. The cleaner job now works as long as possible until a deadline based on the scheduling frequency. * bump version of clinical reasoning (#5406) * Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added * removed unused alias from SQL query of mdm-clear (#5416) * Issue 5418 support Boolean class return type in BaseInterceptorService (#5421) * Enable child classes to use Boolean class return type * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420) * If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix * Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423) This reverts commit 4e295a59fb143a2ba54bc44305474096e2acd578. Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> * Use new FHIR_ID column for sorting (#5405) * Sort `_id` using new FHIR_ID column. * Fix old tests that put client-assigned ids first. * Better indexing for sort * Bump core to 6.1.2.2 (#5425) * Bump core to 6.1.2.1 Patch release that uses https for primary org.hl7.fhir.core package server * Bump core to 6.1.2.2 * Make sure to return always a value for Boolean class return type. (#5424) Implement change in a non-disruptive way for overriders Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) Add a non-standard __pid SP. * Review changes for new _pid SP. (#5430) Change name to _pid to match our standard and add warning. * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432) * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition. * Fix spotless issue * CVEs for 6.10.0 (#5433) * Bump jetty * Bump okio-jvm * 8.2.0 mysql connector * Jena and elastic bumps * Fix test * 5412 post bundle on partition incorrect response.link shown (#5413) * Initial fix and unit test provided * spottless check * Made relevant changes to make solution version agnostic * relevant logic changes made * spotless changes made * New logic added to fix failing test cases * formatting * New logic to make the function more robust * spotless checks * Left a trailing slash in the tests * Made relevant test changes and changed logic * spotless changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml changing changelog Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Formatting requirements --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414) * first fix * - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber - refactored code to reduce repeated code - cleaned unnecessary comments and reformatted files * Changed myResourceModifiedMessagePersistenceSvc to be autowired * removed unused import * added error handling when inflating the message to email and message subscriber * reformatted code * Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc * Changes by gary * Reformatted file * fixed failed tests * implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File. * - implemented IT - fixed logical error - added changelog * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * resolve code review comments * reformatted files * fixed tests * Fix for failing IT test in jpaserver-starter (#5435) Co-authored-by: dotasek <dotasek.dev@gmail.com> * wip --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: dotasek <dotasek.dev@gmail.com>
2023-11-10 17:00:08 -05:00
<version>3.4.0</version>
Rel 6 2 mergeback (#4257) * jm wrong bundle entry url (#4213) * Bug test * here you go * Generate relative URIs for bundle entry.request.url, as specified * Point jira issue in changelog * Adjust tests to fixes Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * improved logging (#4217) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Rel 6 1 3 mergeback (#4215) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * Fix illegalstateexception when an exception is thrown during stream response (#3882) * Finish up changelog, minor refactor * reset buffer only * Hack for some replacements * Failure handling * wip * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * Implemented seventh character extended code and the corresponding dis… (#3709) * Implemented seventh character extended code and the corresponding display * Modifications * Changes on previous test according to modifications made in ICD10-CM XML file * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * updated pointcuts to work as intended (#3903) * updated pointcuts to work as intended * added changelog * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 3899 code in limits (#3901) * Add implementation, changelog, test * Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> * 3884 overlapping searchparameter undetected rel 6 1 (#3909) * Applying all changes from previous dev branch to current one pointing to rel_6_1 * Fixing merge conflict related to Msg.code value. * Fixing Msg.code value. * Making checkstyle happy. * Making sure that all tests are passing. * Passing all tests after fixing Msg.code * Passing all tests. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746) * 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete * created unit test for skip of delete operation while processing duplicating create entries * moved unit test to FhirSystemDaoR4Test * 3379 mdm fixes (#3906) * added MdmLinkCreateSvcimplTest * fixed creating mdm-link not setting the resource type correctly * fixed a bug where ResourcePersistenceId was being duplicated instead of passed on * Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java Change order of tests such that assertEquals takes expected value then actual value Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * Fix to the issue (#3855) * Fix to the issue * Progress * fixed the issue * Addressing suggestions * add response status code to MethodOutcome * Addressing suggestions Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix for caching appearing broken in batch2 for bulkexport jobs (#3912) * Respect caching in bullk export, fix bug with completed date on empty jobs * add changelog * Add impl * Add breaking test * Complete failing test * more broken tests * Fix more tests' * Fix paging bug * Fix another brittle test * 3915 do not collapse rules with filters (#3916) * do not attempt to merge compartment permissions with filters * changelog * Rename to IT for concurrency problems Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <ken@smilecdr.com> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 3922 delete expunge large dataset (#3923) * lower batchsize of delete requests so that we do not get sql exceptions * blah * fix test * updated tests to not fail Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * add index * Fix up colun grab * Revert offset mode change * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic * Updating version to: 6.1.1 post release. * fix compile error * Deploy to sonatype (#3934) * adding sonatype profile to checkstyle module * adding sonatype profile to tinder module * adding sonatype profile to base pom * adding final deployToSonatype profile * wip * Revert version enum * Updating version to: 6.1.1 post release. * Add test, changelog, and implementation * Add backport info * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient * wip * Add backport info * Add info of new version * Updating version to: 6.1.2 post release. * bump info and backport for 6.1.2 * Bump for hapi * Implement bug fixes, add new tests (#4022) * Implement bug fixes, add new tests * tidy * Tidy * refactor for cleaning * More tidying * Lower logging * Split into nested tests, rename, add todos * Typo * Code review * add backport info * Updating version to: 6.1.3 post release. * Updating version to: 6.1.3 post release. * removed duplicate mention of ver 6.1.3 in versionEnum * backport pr 4101 * mdm message key (#4111) * begin with failing test * fixed 2 tests * fix tests * fix tests * change log Co-authored-by: Ken Stevens <ken@smilecdr.com> * backport 6.1.3 docs changes * fixed typo on doc backport message * fix test breaking * Updating version to: 6.1.4 post release. * wip Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> * pin okio-jvm for kotlin vuln (#4216) * Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220) * First commit: Failing unit test and a TODO with a vague idea of where the bug happens. * Don't escape "+" in a URL GET parameter if it starts with "application". * Remove unnecessary TODO. * Add changelog. * Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens. * Ks 20221031 migration lock (#4224) * started design * complete with tests * changelog * cleanup * tyop Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209) * Added test * Added solution * Changelog * Changes made based on comments * Fix bug with MDM submit * fix * Version bump * 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236) * Add constant for interceptor * add test, changelog * Allow Batch2 transition from ERRORED to COMPLETE (#4242) * Allow Batch2 transition from ERRORED to COMPLETE * Add changelog * Test fix Co-authored-by: James Agnew <james@jamess-mbp.lan> * 3685 When bulk exporting, if no resource type param is provided, defa… (#4233) * 3685 When bulk exporting, if no resource type param is provided, default to all registered types. * Update test case. * Cleaned up changelog. * Added test case for multiple resource types. * Added failing test case for not returning Binary resource. * Refactor solution. Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Add next version * bulk export permanently reusing cached results (#4249) * Add test, fix bug, add changelog * minor refactor * Fix * Bump HAPI version * Remove jetbrains * Fix broken test Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: James Agnew <james@jamess-mbp.lan> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com>
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</dependency>
GM1 Mergeback (#5203) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
2023-08-15 15:32:10 -04:00
<!-- Architecture Test -->
<dependency>
<groupId>com.tngtech.archunit</groupId>
<artifactId>archunit-junit5</artifactId>
<version>1.0.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.vladsch.flexmark</groupId>
<artifactId>flexmark</artifactId>
<version>${flexmark_version}</version>
</dependency>
<dependency>
<groupId>com.vladsch.flexmark</groupId>
<artifactId>flexmark-ext-tables</artifactId>
<version>${flexmark_version}</version>
</dependency>
<dependency>
<groupId>com.vladsch.flexmark</groupId>
<artifactId>flexmark-profile-pegdown</artifactId>
<version>${flexmark_version}</version>
</dependency>
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.9.4</version>
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
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<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.5.0</version>
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</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons_codec_version}</version>
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</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>4.4</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
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<version>${commons_compress_version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.10.0</version>
</dependency>
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
<version>1.9.5</version>
</dependency>
<dependency>
<groupId>org.hl7.fhir.testcases</groupId>
<artifactId>fhir-test-cases</artifactId>
<version>1.5.15</version>
</dependency>
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<dependency>
<groupId>org.jdom</groupId>
<artifactId>jdom2</artifactId>
<version>2.0.6.1</version>
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</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
<version>23.0.0</version>
</dependency>
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<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons_io_version}</version>
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</dependency>
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<dependency>
<groupId>directory-naming</groupId>
<artifactId>naming-java</artifactId>
<version>0.8</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
2017-08-13 14:39:47 -04:00
<dependency>
<groupId>es.nitaur.markdown</groupId>
<artifactId>txtmark</artifactId>
<version>0.16</version>
2018-03-28 06:15:28 -04:00
</dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<dependency>
<groupId>jakarta.activation</groupId>
<artifactId>jakarta.activation-api</artifactId>
<version>2.1.2</version>
</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<version>2.1.1</version>
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.ejb</groupId>
<artifactId>jakarta.ejb-api</artifactId>
<version>4.0.1</version>
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.interceptor</groupId>
<artifactId>jakarta.interceptor-api</artifactId>
<version>2.1.0</version>
</dependency>
2018-05-30 05:45:08 -04:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
<version>6.0.0</version>
2018-05-30 05:45:08 -04:00
</dependency>
2015-11-29 11:43:09 -05:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.transaction</groupId>
<artifactId>jakarta.transaction-api</artifactId>
<version>2.0.1</version>
2015-11-29 11:43:09 -05:00
</dependency>
2015-09-08 08:14:55 -04:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.websocket</groupId>
<artifactId>jakarta.websocket-client-api</artifactId>
<version>2.1.1</version>
2015-09-08 08:14:55 -04:00
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.ws.rs</groupId>
<artifactId>jakarta.ws.rs-api</artifactId>
<version>3.1.0</version>
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.1</version>
2015-08-31 08:20:24 -04:00
</dependency>
2018-01-31 07:41:24 -05:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.validation</groupId>
<artifactId>jakarta.validation-api</artifactId>
<version>3.0.2</version>
2018-01-31 07:41:24 -05:00
</dependency>
Introduce hibernate envers, use it only for MdmLink, disable it for now, add to MdmLink Dao and unit test revisions. (#4615) * First commit with new maven deps for envers and stubbed changelist. * Add repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class to BaseAppCtxPersistence. Comment it out in JpaConfig. Add constant for hibernate.integration.envers.enabled. Hard-code envers to false. App starts without error. Basic smoke testing for MpmLink update works. * Add mdmLink code to retrieve envers history and unit test it. * Initial code to handle envers from HapiFhirEnversRevision along with a custom extension of the revision/REVINFO entity. * Add changelist and tweak table/sequence/field names and clean up the HapiFhirJpaMigrationTasks method. * Fix some unit test failures and address TODOs. * Ensure hard-coded deactivation of envers is overridden by unit tests. * Remove commented-out code. * Address code review comments. * Remove sysout traces. * Tweaks to poms with comments explaining why I left the versions in the plugin dependencies. Get rid of a duplicate envers dependency. * Bump hapi-fhir version to 6.5.5-SNAPSHOT. * Disable intermittently failing test: PartitionedSubscriptionTriggeringR4Test.testCreateSubscriptionInPartitionAndResourceInDifferentPartition * Try disabling Batch2CoordinatorIT failing test and see if branch pipeline passes. * Add back hapi-fhir-validation-resources-r4b to hapi-fhir-jpaserver-base pom.xml. * Bump hapi-fhir to 6.5.6-SNAPSHOT. * Bump rest of hapi-fhir to 6.5.6-SNAPSHOT. * Fix compile error on Batch2CoordinatorIT. * Change revision ID column from integer to long in both the revision entity and the migration tasks. Fix a bug with the migration tasks having the wrong name for the timestamp column. * Fix interface in MongoDB to return Long for the revision ID instead of Int. Implement TINYINT for all supported database products. Keep TARGET_TYPE column at 40 instead of 100 for now since otherwise the schema migration test will fail. Also, don't try to rename the foreign key or the schema migration test will fail.
2023-03-14 15:32:00 -04:00
<dependency>
<groupId>javax.json</groupId>
<artifactId>javax.json-api</artifactId>
<version>1.1</version>
</dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<dependency>
<groupId>co.elastic.clients</groupId>
<artifactId>elasticsearch-java</artifactId>
<version>${elasticsearch_version}</version>
Introduce hibernate envers, use it only for MdmLink, disable it for now, add to MdmLink Dao and unit test revisions. (#4615) * First commit with new maven deps for envers and stubbed changelist. * Add repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class to BaseAppCtxPersistence. Comment it out in JpaConfig. Add constant for hibernate.integration.envers.enabled. Hard-code envers to false. App starts without error. Basic smoke testing for MpmLink update works. * Add mdmLink code to retrieve envers history and unit test it. * Initial code to handle envers from HapiFhirEnversRevision along with a custom extension of the revision/REVINFO entity. * Add changelist and tweak table/sequence/field names and clean up the HapiFhirJpaMigrationTasks method. * Fix some unit test failures and address TODOs. * Ensure hard-coded deactivation of envers is overridden by unit tests. * Remove commented-out code. * Address code review comments. * Remove sysout traces. * Tweaks to poms with comments explaining why I left the versions in the plugin dependencies. Get rid of a duplicate envers dependency. * Bump hapi-fhir version to 6.5.5-SNAPSHOT. * Disable intermittently failing test: PartitionedSubscriptionTriggeringR4Test.testCreateSubscriptionInPartitionAndResourceInDifferentPartition * Try disabling Batch2CoordinatorIT failing test and see if branch pipeline passes. * Add back hapi-fhir-validation-resources-r4b to hapi-fhir-jpaserver-base pom.xml. * Bump hapi-fhir to 6.5.6-SNAPSHOT. * Bump rest of hapi-fhir to 6.5.6-SNAPSHOT. * Fix compile error on Batch2CoordinatorIT. * Change revision ID column from integer to long in both the revision entity and the migration tasks. Fix a bug with the migration tasks having the wrong name for the timestamp column. * Fix interface in MongoDB to return Long for the revision ID instead of Int. Implement TINYINT for all supported database products. Keep TARGET_TYPE column at 40 instead of 100 for now since otherwise the schema migration test will fail. Also, don't try to rename the foreign key or the schema migration test will fail.
2023-03-14 15:32:00 -04:00
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson_version}</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>com.healthmarketscience.sqlbuilder</groupId>
<artifactId>sqlbuilder</artifactId>
<version>3.0.2</version>
</dependency>
2018-09-07 19:14:43 -04:00
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>12.4.2.jre11</version>
2018-09-07 19:14:43 -04:00
</dependency>
<dependency>
<!--
We use JUnit 5 in HAPI FHIR, but some libraries still pull in / require JUnit 4
(e.g. Testcontainers) so we enforce a current version to avoid OWASP flags
-->
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.2</version>
</dependency>
<dependency>
<groupId>io.swagger.core.v3</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>swagger-annotations-jakarta</artifactId>
<version>${swagger_version}</version>
</dependency>
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-models-jakarta</artifactId>
<version>${swagger_version}</version>
</dependency>
<dependency>
<groupId>io.swagger.core.v3</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>swagger-core-jakarta</artifactId>
<version>${swagger_version}</version>
</dependency>
2018-09-07 19:14:43 -04:00
<dependency>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
Rel 6 10 mb (#5441) * Allow cached search with consent active when safe (#5387) Allow the search cache when using consent if safe * Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376) * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation * Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * first fix * tests and preliminary fixes * wip, commit before switching to release branch. * adding capability to handle _lastUpdated in reverse search (_has) * adding changelog * applying spotless. * addressing code review comments. --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Br 20231019 add cr settings for cds hooks (#5394) * Add settings used in CR CDS Services. Remove config dependency on Spring Boot. * Add changelog * Use String.format rather than concat strings * spotless apply * Add javadoc * Upgrade notes for the forced-id change (#5400) Add upgrade notes for forced-id * Clean stale search results more aggressively. (#5396) Use bulk DMA statements when cleaning the search cache. The cleaner job now works as long as possible until a deadline based on the scheduling frequency. * bump version of clinical reasoning (#5406) * Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added * removed unused alias from SQL query of mdm-clear (#5416) * Issue 5418 support Boolean class return type in BaseInterceptorService (#5421) * Enable child classes to use Boolean class return type * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420) * If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix * Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423) This reverts commit 4e295a59fb143a2ba54bc44305474096e2acd578. Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> * Use new FHIR_ID column for sorting (#5405) * Sort `_id` using new FHIR_ID column. * Fix old tests that put client-assigned ids first. * Better indexing for sort * Bump core to 6.1.2.2 (#5425) * Bump core to 6.1.2.1 Patch release that uses https for primary org.hl7.fhir.core package server * Bump core to 6.1.2.2 * Make sure to return always a value for Boolean class return type. (#5424) Implement change in a non-disruptive way for overriders Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) Add a non-standard __pid SP. * Review changes for new _pid SP. (#5430) Change name to _pid to match our standard and add warning. * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432) * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition. * Fix spotless issue * CVEs for 6.10.0 (#5433) * Bump jetty * Bump okio-jvm * 8.2.0 mysql connector * Jena and elastic bumps * Fix test * 5412 post bundle on partition incorrect response.link shown (#5413) * Initial fix and unit test provided * spottless check * Made relevant changes to make solution version agnostic * relevant logic changes made * spotless changes made * New logic added to fix failing test cases * formatting * New logic to make the function more robust * spotless checks * Left a trailing slash in the tests * Made relevant test changes and changed logic * spotless changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml changing changelog Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Formatting requirements --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414) * first fix * - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber - refactored code to reduce repeated code - cleaned unnecessary comments and reformatted files * Changed myResourceModifiedMessagePersistenceSvc to be autowired * removed unused import * added error handling when inflating the message to email and message subscriber * reformatted code * Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc * Changes by gary * Reformatted file * fixed failed tests * implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File. * - implemented IT - fixed logical error - added changelog * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * resolve code review comments * reformatted files * fixed tests * Fix for failing IT test in jpaserver-starter (#5435) Co-authored-by: dotasek <dotasek.dev@gmail.com> * wip --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: dotasek <dotasek.dev@gmail.com>
2023-11-10 17:00:08 -05:00
<version>8.2.0</version>
</dependency>
<dependency>
<groupId>org.springdoc</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
<version>2.2.0</version>
</dependency>
2016-06-05 09:40:06 -04:00
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>
<version>2.4</version>
<classifier>jdk15</classifier>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>
<version>2.4</version>
<classifier>jdk15-sources</classifier>
</dependency>
2017-06-14 08:35:41 -04:00
<dependency>
<groupId>net.ttddyy</groupId>
<artifactId>datasource-proxy</artifactId>
<version>1.10</version>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
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</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>ST4</artifactId>
<version>4.0.8</version>
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</dependency>
<dependency>
<!--
Note if you bump the version here - The commons-dbcp2 2.11.0 version
explicitly depends on commons-pool2 2.12.0, so we explicitly specify that
version below as well. If you bump this, make sure you're bumping the
pool2 version appropriately too.
-->
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<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
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<version>${commons_dbcp2_version}</version>
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</dependency>
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<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${commons_lang3_version}</version>
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</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-pool2</artifactId>
<!-- See the note above about commons-dbcp2 before bumping versions here -->
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<version>${commons_pool2_version}</version>
</dependency>
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<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
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<version>${commons_text_version}</version>
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</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
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<version>${httpclient_version}</version>
</dependency>
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<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-cache</artifactId>
<version>${httpclient_version}</version>
</dependency>
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<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>fluent-hc</artifactId>
<version>${httpclient_version}</version>
</dependency>
<dependency>
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<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-android</artifactId>
<version>4.3.5.1</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
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<version>${httpcore_version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-osgi</artifactId>
<version>${httpcore_version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-nio</artifactId>
<version>${httpcore_version}</version>
</dependency>
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<dependency>
<groupId>co.elastic.apm</groupId>
<artifactId>apm-agent-api</artifactId>
<version>${elastic_apm_version}</version>
</dependency>
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<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>${jena_version}</version>
<type>pom</type>
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</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>${jena_version}</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>${jena_version}</version>
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</dependency>
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<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analysis-phonetic</artifactId>
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<version>${lucene_version}</version>
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</dependency>
<dependency>
<groupId>org.apache.maven.doxia</groupId>
<artifactId>doxia-module-markdown</artifactId>
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<version>1.8</version>
</dependency>
<dependency>
<groupId>org.apache.maven.scm</groupId>
<artifactId>maven-scm-api</artifactId>
<version>1.12.0</version>
</dependency>
<dependency>
<groupId>org.apache.maven.scm</groupId>
<artifactId>maven-scm-manager-plexus</artifactId>
<version>1.12.0</version>
</dependency>
<dependency>
<groupId>org.apache.maven.scm</groupId>
<artifactId>maven-scm-provider-gitexe</artifactId>
<version>1.12.0</version>
</dependency>
<dependency>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-scm</artifactId>
<version>3.4.3</version>
</dependency>
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<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-project</artifactId>
<version>2.2.1</version>
</dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-plugin-api</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<version>3.8.6</version>
<scope>provided</scope>
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</dependency>
<dependency>
<groupId>org.apache.maven.plugin-tools</groupId>
<artifactId>maven-plugin-annotations</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<version>3.9.0</version>
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</dependency>
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<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>${poi_ooxml_schemas_version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
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<version>${poi_version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
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<version>${poi_version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
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<version>${poi_version}</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
<version>2.3</version>
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</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<version>4.2.0</version>
</dependency>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
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<dependency>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-compiler-api</artifactId>
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<version>${plexus_compiler_api_version}</version>
Merge in HAPI 3.0.0 working branch! Squashed commit of the following: commit 12f89a423a1691fdbc360706fd94a03bd9144d17 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:38:51 2017 -0400 Minimize validation resources commit f6868cce5c73b34d5ecd53bf1a220fdccd6b4e09 Merge: 3b80779fd3 1e158311d8 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 14:05:34 2017 -0400 Forward port fix for #710 Merge branch 'master' into hapi3_refactor commit 3b80779fd3905cbf5322e6973334eb0ecb3d8426 Merge: 1f534985e8 356d9acaf7 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 12:31:09 2017 -0400 Forward port #705, #708, and #710 Merge branch 'master' into hapi3_refactor commit 1f534985e8106347d9cc9da2dd8145fdd869547f Merge: 7c39a47852 dedd3d635b Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 10:52:59 2017 -0400 Forward port #695 Merge branch 'master' into hapi3_refactor commit 7c39a47852142bee398101120678217ab0917c7e Merge: e0ffb84d21 6efafe62f1 Author: James <jamesagnew@gmail.com> Date: Sun Aug 13 09:53:17 2017 -0400 Forward port #688 Merge branch 'master' into hapi3_refactor commit e0ffb84d2129c209ccffc2611038592f37dddfd2 Merge: 52388c11c1 d19b00ff09 Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 14:59:46 2017 -0400 Merge branch 'master' into hapi3_refactor commit 52388c11c17cf038591244548f2a592f6b655cee Author: James <jamesagnew@gmail.com> Date: Sat Aug 12 06:21:46 2017 -0400 Cleanup commit 209752cd638266b39574ae11c5989b624d5e85d3 Author: James <jamesagnew@gmail.com> Date: Thu Aug 10 11:18:19 2017 -0400 Fix tests commit 4543408dc8d63b5b9682a275e261d3168cdc2196 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:55:50 2017 -0400 Fix a potential deadlock commit ee360f537692672df473f94dae75c176b2287415 Author: James <jamesagnew@gmail.com> Date: Sat Aug 5 06:22:06 2017 -0400 Add R4 code to CLI commit 1a95ba3b6529afdaf81232b82cc303718c0187d6 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Aug 3 06:14:01 2017 -0400 More cleanup commit f0d88026817296edaa65132accd67d0c8ad8088c Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 11:27:43 2017 -0400 Tests are working! commit a4cbda357e8e7d024f24e3ee9a660b5366983ca1 Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:42:04 2017 -0400 Connection handling cleanup for new tests commit 0e2cecfbd0d7a546444a66e8411600040fd9a17b Author: James Agnew <jamesagnew@gmail.com> Date: Wed Aug 2 10:16:28 2017 -0400 Clean up R4 JPA tests commit 40317a650d72c86e2529d5179cffe63399301de5 Author: James <jamesagnew@gmail.com> Date: Wed Aug 2 09:12:38 2017 -0400 Work on R4 for JPA server commit e7f8f8c30d72ed30d739979964db38d41c5baec1 Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 20:43:47 2017 -0400 More work on porting tests commit 43c9003258696ab33e7bb335e882ab1c66fb61aa Author: James <jamesagnew@gmail.com> Date: Tue Aug 1 07:09:29 2017 -0400 Work on porting DSTU1 tests commit 602857f1e26a69a2284e176b5e44a860d9b828ff Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 22:34:08 2017 -0400 More work on bring unit tests up to date commit e326a7b0cdb8368009119bba41886838a973e03e Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:36:38 2017 -0400 Credit for #686 and forward port the fix to R4 validator commit 96543c3992adcb406df3c8899dab79cf4bd5b4b4 Merge: 3fb75aa61a 9901b802c4 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 31 17:12:33 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3fb75aa61ad29d9f3876a1c30c912627486147af Author: James <jamesagnew@gmail.com> Date: Mon Jul 31 15:21:30 2017 -0400 More work on cleanup commit b02fbb6804127e77c61c4792eefd9fc0d23d63d0 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 22:11:07 2017 -0400 Work on porting STU1 tests commit 1ae37b0db3929ea4f37955adf8f026e33ccf43b2 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:56:10 2017 -0400 Try to get coverage report working commit 72b88849b30a94a9ff08d3a1ab50a05b2acbdfdd Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 20:27:02 2017 -0400 Fix android tests commit e5f6c35aeab8bbc056870a038e1862181049a020 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 19:31:18 2017 -0400 More work on getting legacy code cleaned up commit 0b513b0845a082b5c20b0033dfab4e29f5e4a934 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 18:41:13 2017 -0400 Continue work on removing deprecated API commit defea69aa38a2e0f4137ed9c8527956872ff70bf Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 17:10:01 2017 -0400 More cleanup of legacy code commit 9ae7295705cb58f5edcf7ee1259f023cbbe2fe51 Author: James <jamesagnew@gmail.com> Date: Sun Jul 30 07:11:45 2017 -0400 More cleanup of legacy code commit ebd3eeb5ee793cf5805cc726db353f3def35ab00 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jul 30 06:43:25 2017 -0400 More work on removing legacy code commit 92224c2532faf70171473d64429c3ceaf3e3406c Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 18:44:06 2017 -0400 Remove DSTU1 Bundle commit c52cacf71bae3f5c02ffae03881c21de1f3aba22 Author: James <jamesagnew@gmail.com> Date: Sat Jul 29 14:27:42 2017 -0400 Now compiling commit b405e51773baf4ab3a3c387458cdc59541394cd1 Merge: c3ddf04e25 cb2cea54d7 Author: James Agnew <jamesagnew@gmail.com> Date: Fri Jul 28 06:21:02 2017 -0400 Merge branch 'master' into hapi3_refactor commit c3ddf04e2598b8d6214975ab0ae795f850396811 Author: James <jamesagnew@gmail.com> Date: Thu Jul 27 11:06:06 2017 -0400 Sync R4 releases in commit b13333c3c03ddb9a5061c3b22bf011f4592104f8 Author: James <jamesagnew@gmail.com> Date: Fri Jul 14 05:52:33 2017 -0400 JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions. commit 2e60ff7521b42890a32b97c2dda88ab233f5c91e Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 20:02:46 2017 -0400 Fix imports commit a92ace2e0dac6e24f6dada53bf97d03861fd21a1 Merge: 3196db96d1 1a6b3ea867 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 12:02:27 2017 -0400 Merge branch 'master' into hapi3_refactor commit 3196db96d1c485310e746833df59c0e010b5b161 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 13 11:48:10 2017 -0400 Don't add false paging link to request commit bd4e1d338855a664045caa271d41616aed973a4d Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 21:32:16 2017 -0400 Finally building correctly! commit 6464ce9304703cb3c5ecc58491282ddacc900853 Author: James <jamesagnew@gmail.com> Date: Sun Jul 9 16:38:28 2017 -0400 Work on refactor commit 0059f2e48e9d7c812c1d42a57c5b6059814f5155 Author: James <jamesagnew@gmail.com> Date: Sat Jul 8 07:16:20 2017 -0400 Keep working on refactor commit 6c2e87e8cc19863a811c11623d1c878c8b48f031 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 22:35:13 2017 -0400 Lots of work on refactor commit 11cab975047a0c28190e6533074fd3f11ddde240 Merge: 34ec6b8807 6c47bd4c51 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:57 2017 -0400 Merge branch 'master' into hapi3_refactor commit 34ec6b8807946aa6c97f0b5581dca9bd5f7b7a3e Merge: f8e647511b c520e60ac1 Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 21:43:49 2017 -0400 Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor commit f8e647511b4a82e7fde71a8850b8800e3d698b1f Author: James Agnew <jamesagnew@gmail.com> Date: Thu Jul 6 18:46:55 2017 -0400 Work on hapi3 changes commit c520e60ac1198f340cfb9090a7a33f91aa2d1e61 Author: James <jamesagnew@gmail.com> Date: Wed Jul 5 08:08:40 2017 -0400 Keep working on refactor commit f1d2ee90926f7db900a5b3b4ab9a8948d18e49f2 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 22:10:59 2017 -0400 Continue refactor for HAPI 3 commit 9281ccafc32354222932c5a9f5ee8b0f206ebc05 Merge: ea1264cd8e 294d080bd3 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jul 3 20:34:16 2017 -0400 Merge branch 'master' into hapi3_refactor commit ea1264cd8e9b8c5297d218e91cf14bd48d0a92c7 Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 10:26:01 2017 -0400 Continue work on refactor commit fbe2f98a0238f3d4e065db4550dd2ef1b460c0d8 Merge: b2bef47100 0a4dcc32ec Author: James <jamesagnew@gmail.com> Date: Wed Jun 28 06:21:22 2017 -0400 Merge branch 'master' into hapi3_refactor commit b2bef47100370e1248834523d73a630950032d7a Author: James <jamesagnew@gmail.com> Date: Tue Jun 27 21:13:23 2017 -0400 Work on refactor commit 8f76e4e46385daa9ce3442e2d9342453ce373ba3 Author: James Agnew <jamesagnew@gmail.com> Date: Sun Jun 25 21:55:35 2017 -0400 Lots of work on refactoring
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</dependency>
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<dependency>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-compiler-javac</artifactId>
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<version>${plexus_compiler_api_version}</version>
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</dependency>
<dependency>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-compiler-javac-errorprone</artifactId>
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<version>${plexus_compiler_api_version}</version>
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</dependency>
<dependency>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-utils</artifactId>
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<version>3.1.0</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.woodstox</groupId>
<artifactId>woodstox-core</artifactId>
<version>6.4.0</version>
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</dependency>
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<version>${ebay_cors_filter_version}</version>
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<groupId>org.eclipse.jetty.ee10</groupId>
<artifactId>jetty-ee10-servlet</artifactId>
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<version>${jetty_version}</version>
</dependency>
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<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>org.eclipse.jetty.ee10</groupId>
<artifactId>jetty-ee10-servlets</artifactId>
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<version>${jetty_version}</version>
</dependency>
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>org.eclipse.jetty.ee10.websocket</groupId>
<artifactId>jetty-ee10-websocket-jakarta-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.ee10.websocket</groupId>
<artifactId>jetty-ee10-websocket-jakarta-server</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-http</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-io</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-continuation</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-security</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-server</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-util</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-xml</artifactId>
<version>${jetty_version}</version>
</dependency>
2015-09-28 09:06:57 -04:00
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-api</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
2015-09-28 09:06:57 -04:00
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-core-client</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
2015-09-28 09:06:57 -04:00
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<artifactId>jetty-websocket-jetty-server</artifactId>
2015-12-01 18:35:24 -05:00
<version>${jetty_version}</version>
2015-09-28 09:06:57 -04:00
</dependency>
2018-08-23 05:24:13 -04:00
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>${ucum_version}</version>
2018-08-23 05:24:13 -04:00
</dependency>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
<dependency>
<groupId>org.rauschig</groupId>
<artifactId>jarchivelib</artifactId>
<version>1.1.0</version>
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
<scope>test</scope>
</dependency>
2015-09-13 22:06:31 -04:00
<dependency>
<groupId>org.fusesource.jansi</groupId>
<artifactId>jansi</artifactId>
<version>2.4.1</version>
2015-09-13 22:06:31 -04:00
</dependency>
2015-09-08 08:14:55 -04:00
<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>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<version>4.0.2</version>
2015-09-08 08:14:55 -04:00
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.json</artifactId>
<version>1.0.4</version>
</dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-core</artifactId>
<version>${jaxb_runtime_version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb_runtime_version}</version>
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
<exclusions>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
</dependency>
2015-11-29 11:43:09 -05:00
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-server</artifactId>
<version>${jersey_version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet-core</artifactId>
<version>${jersey_version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-jetty-http</artifactId>
<version>${jersey_version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-moxy</artifactId>
<version>${jersey_version}</version>
</dependency>
2018-05-03 18:34:29 -04:00
<dependency>
<groupId>org.jboss.spec.javax.ws.rs</groupId>
<artifactId>jboss-jaxrs-api_2.1_spec</artifactId>
<version>2.0.1.Final</version>
2018-05-03 18:34:29 -04:00
</dependency>
<dependency>
<groupId>org.jboss.resteasy</groupId>
<artifactId>resteasy-client</artifactId>
<version>${resteasy_version}</version>
2015-11-29 11:43:09 -05:00
</dependency>
2015-09-08 08:14:55 -04:00
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
<version>4.3.1</version>
</dependency>
Replace hamcrest with assertj (#5911) * optimize imports * optimize imports * Hamcrest replacement * Hamcrest replacement * Test failures * migrate hapi-fhir-base * docs * Few more cutovers * Full rewrite of all assert cases * Full rewrite of all assert cases * Partial cutover * assert library conversion * wip * fix imports * remove equalto * once-over again * minor cutover * wip * wip * wip * wip * wip * Remove hamcrest asserts replace with assertj * wip * Partial hamcrest rip-out * More hamcrest stripping * wip * Partial completion * spotless * it compiles now * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fix compile issues * fix compile issues * hapi-fhir now compiles * fix test * fix test * fix test * fix tests * fix tests * fix tests * fix test * fix test * fix tests * fix tests * fix tests * yay all tests pass now! * revert assertEquals change * revert assertEquals change * organize imports * organize imports * organize imports * post merge cleanup * organize imports * more cleanup * more cleanup * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * organize imports * organize imports * remove final hamcrest stuff * remove final hamcrest usages * remove final hamcrest usages * Revert "remove final hamcrest usages" This reverts commit eaf5107396af7c0fedbb8f1dce8b75133cc790eb. * fix compile issues from a hacky search/replace * compiles with fixmes * fix tests * fix test * fix test * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge test issues * fix test * fix test * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * all but mdm tests * final hamcrest removed from hapi-fhir yay! * revert mdm changes. it's too hard for now * revert cdr breaking change * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert changes that break cdr * merge master with compile errors * review feedback * review feedback * review feedback: revert bad regexp change * fix test * fix test * convert new hamcrest entries * convert new hamcrest entries --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-06-05 16:02:46 -04:00
<!-- TODO KHS remove hamcrest -->
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest</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
<version>${hamcrest_version}</version>
</dependency>
<dependency>
<groupId>org.htmlunit</groupId>
<artifactId>htmlunit</artifactId>
<version>3.11.0</version>
<exclusions>
<exclusion>
<!-- Don't let HTMLUnit bring in Jetty 9 -->
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-ant</artifactId>
<version>${hibernate_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate_version}</version>
<exclusions>
<exclusion>
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
<exclusion>
<groupId>jakarta.activation</groupId>
<artifactId>activation</artifactId>
</exclusion>
<exclusion>
<groupId>jakarta.activation</groupId>
<artifactId>jakarta.activation-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.jboss.spec.javax.transaction</groupId>
<artifactId>jboss-transaction-api_1.2_spec</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-envers</artifactId>
<version>${hibernate_version}</version>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-envers</artifactId>
<version>${spring_boot_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
<version>${hibernate_validator_version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-to-slf4j</artifactId>
<version>${log4j_to_slf4j_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-mapper-orm</artifactId>
<version>${hibernate_search_version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.elasticsearch</groupId>
<artifactId>elasticsearch</artifactId>
<version>8.9.2</version>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
<version>${hibernate_search_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-lucene</artifactId>
<version>${hibernate_search_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch-aws</artifactId>
<version>${hibernate_search_version}</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.22.0-GA</version>
</dependency>
<dependency>
<groupId>org.junit</groupId>
<artifactId>junit-bom</artifactId>
<version>${junit_version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>${junit_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>${junit_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<version>${junit_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit-pioneer</groupId>
<artifactId>junit-pioneer</artifactId>
<version>1.3.8</version>
</dependency>
<dependency>
<groupId>org.mariadb.jdbc</groupId>
<artifactId>mariadb-java-client</artifactId>
<version>3.0.4</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito_version}</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>${mockito_version}</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.7.3</version>
</dependency>
<dependency>
<groupId>com.oracle.database.jdbc</groupId>
<artifactId>ojdbc11</artifactId>
<version>23.3.0.23.09</version>
</dependency>
<dependency>
<groupId>org.quartz-scheduler</groupId>
<artifactId>quartz</artifactId>
<version>2.3.2</version>
<exclusions>
<exclusion>
<groupId>com.zaxxer</groupId>
<artifactId>HikariCP-java7</artifactId>
</exclusion>
<exclusion>
<groupId>com.mchange</groupId>
<artifactId>c3p0</artifactId>
</exclusion>
<exclusion>
<groupId>com.mchange</groupId>
<artifactId>mchange-commons-java</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-android</artifactId>
<version>1.7.36</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j_version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>${slf4j_version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
<version>${slf4j_version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-expression</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-messaging</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<version>${spring_boot_version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-test</artifactId>
<version>${spring_boot_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-websocket</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<groupId>org.springframework.retry</groupId>
<artifactId>spring-retry</artifactId>
<version>${spring_retry_version}</version>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
<version>${thymeleaf-version}</version>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring6</artifactId>
<version>${thymeleaf-version}</version>
</dependency>
<dependency>
<groupId>org.webjars.npm</groupId>
<artifactId>ace-builds</artifactId>
<version>1.22.0</version>
</dependency>
<dependency>
<groupId>org.webjars.npm</groupId>
<artifactId>bootstrap</artifactId>
<version>4.5.2</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>Eonasdan-bootstrap-datetimepicker</artifactId>
<version>4.17.47</version>
<exclusions>
<exclusion>
<groupId>*</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>font-awesome</artifactId>
<version>5.8.2</version>
</dependency>
<dependency>
<groupId>org.webjars.bower</groupId>
<artifactId>awesome-bootstrap-checkbox</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jstimezonedetect</artifactId>
<version>1.0.6</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>select2</artifactId>
<version>4.0.13</version>
<exclusions>
<exclusion>
<groupId>org.webjars</groupId>
<artifactId>jquery</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.webjars.bower</groupId>
<artifactId>jquery</artifactId>
<version>3.5.1</version>
</dependency>
<dependency>
<groupId>org.webjars.bower</groupId>
<artifactId>moment</artifactId>
<version>2.29.4</version>
</dependency>
<dependency>
<groupId>org.webjars.npm</groupId>
<artifactId>popper.js</artifactId>
<version>1.16.1</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>swagger-ui</artifactId>
<version>4.1.3</version>
</dependency>
<dependency>
<groupId>org.xmlunit</groupId>
<artifactId>xmlunit-core</artifactId>
<version>2.4.0</version>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
<version>${testcontainers_version}</version>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>postgresql</artifactId>
<version>${testcontainers_version}</version>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>mssqlserver</artifactId>
<version>${testcontainers_version}</version>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>oracle-xe</artifactId>
<version>${testcontainers_version}</version>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>elasticsearch</artifactId>
<version>${testcontainers_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<version>${testcontainers_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ogce</groupId>
<artifactId>xpp3</artifactId>
<version>1.1.6</version>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junt</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>${flyway_version}</version>
</dependency>
<dependency>
<groupId>uk.org.webcompere</groupId>
<artifactId>system-stubs-jupiter</artifactId>
<version>2.0.1</version>
</dependency>
<!-- dependencies required for Android -->
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.12.2</version>
<scope>provided</scope>
<optional>true</optional>
</dependency>
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<!-- OpenTelemetry -->
<dependency>
<groupId>io.opentelemetry.instrumentation</groupId>
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<artifactId>opentelemetry-instrumentation-bom</artifactId>
<version>${otel_instrumentation.version}</version>
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<type>pom</type>
<scope>import</scope>
</dependency>
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Replace hamcrest with assertj (#5911) * optimize imports * optimize imports * Hamcrest replacement * Hamcrest replacement * Test failures * migrate hapi-fhir-base * docs * Few more cutovers * Full rewrite of all assert cases * Full rewrite of all assert cases * Partial cutover * assert library conversion * wip * fix imports * remove equalto * once-over again * minor cutover * wip * wip * wip * wip * wip * Remove hamcrest asserts replace with assertj * wip * Partial hamcrest rip-out * More hamcrest stripping * wip * Partial completion * spotless * it compiles now * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fix compile issues * fix compile issues * hapi-fhir now compiles * fix test * fix test * fix test * fix tests * fix tests * fix tests * fix test * fix test * fix tests * fix tests * fix tests * yay all tests pass now! * revert assertEquals change * revert assertEquals change * organize imports * organize imports * organize imports * post merge cleanup * organize imports * more cleanup * more cleanup * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * organize imports * organize imports * remove final hamcrest stuff * remove final hamcrest usages * remove final hamcrest usages * Revert "remove final hamcrest usages" This reverts commit eaf5107396af7c0fedbb8f1dce8b75133cc790eb. * fix compile issues from a hacky search/replace * compiles with fixmes * fix tests * fix test * fix test * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge test issues * fix test * fix test * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * all but mdm tests * final hamcrest removed from hapi-fhir yay! * revert mdm changes. it's too hard for now * revert cdr breaking change * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert changes that break cdr * merge master with compile errors * review feedback * review feedback * review feedback: revert bad regexp change * fix test * fix test * convert new hamcrest entries * convert new hamcrest entries --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-06-05 16:02:46 -04:00
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
<version>3.22.0</version>
</dependency>
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-json</artifactId>
<version>3.22.0</version>
</dependency>
<dependency>
<groupId>net.javacrumbs.json-unit</groupId>
<artifactId>json-unit-assertj</artifactId>
<version>3.2.7</version>
<exclusions>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
</exclusion>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest</artifactId>
</exclusion>
</exclusions>
</dependency>
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</dependencies>
</dependencyManagement>
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<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>com.diffplug.spotless</groupId>
<artifactId>spotless-maven-plugin</artifactId>
<version>${spotless_version}</version>
<executions>
<execution>
<goals>
<goal>apply</goal>
<goal>check</goal>
</goals>
<phase>compile</phase>
</execution>
</executions>
<configuration>
<java>
<excludes>
<exclude>**/test/**/*.java</exclude>
</excludes>
<!--This does the actual code reformatting-->
<palantirJavaFormat/>
<!--After formatting, replace the default 4-space indentation with tabs as per our editorconfig-->
<indent>
<tabs>true</tabs>
<spacesPerTab>4</spacesPerTab>
</indent>
<!--Just removes unused imports-->
<removeUnusedImports/>
<!--Follow the editorconfig-defined order of imports-->
<importOrder>
<wildcardsLast>true</wildcardsLast>
<order>,java|javax,\#</order>
</importOrder>
</java>
<!--This does basic formatting of trailing whitespace and newlines-->
<formats>
<format>
<includes>
<include>*.md</include>
<include>.gitignore</include>
<include>*.java</include>
</includes>
<trimTrailingWhitespace/>
<endWithNewline/>
</format>
</formats>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.3.0</version>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<version>${spring_boot_version}</version>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<version>2.0.1</version>
</plugin>
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<plugin>
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<groupId>de.jpdigital</groupId>
<artifactId>hibernate56-ddl-maven-plugin</artifactId>
<version>2.5.0</version>
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</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>${maven_assembly_plugin_version}</version>
</plugin>
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<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>3.5.0</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-antrun-plugin</artifactId>
<version>3.0.0</version>
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</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<version>3.11.0</version>
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<configuration>
<forceJavacCompilerUse>true</forceJavacCompilerUse>
<encoding>UTF-8</encoding>
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<fork>true</fork>
<meminitial>500m</meminitial>
<maxmem>2000m</maxmem>
<compilerArgs>
<arg>-XDcompilePolicy=simple</arg>
<arg>-Xplugin:ErrorProne -Xep:MissingSummary:OFF -Xep:JavaUtilDate:OFF -XepExcludedPaths:.*/src/test/java/.*</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.main=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.model=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.processing=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED</arg>
<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED</arg>
<arg>-J--add-opens=jdk.compiler/com.sun.tools.javac.code=ALL-UNNAMED</arg>
<arg>-J--add-opens=jdk.compiler/com.sun.tools.javac.comp=ALL-UNNAMED</arg>
</compilerArgs>
<annotationProcessorPaths>
<path>
<groupId>com.google.errorprone</groupId>
<artifactId>error_prone_core</artifactId>
<version>${error_prone_core_version}</version>
</path>
</annotationProcessorPaths>
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</configuration>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.2</version>
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</plugin>
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<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.7.0</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.6.3</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
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<version>3.0.0</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<reuseForks>false</reuseForks>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
<forkCount>1</forkCount>
<threadCount>1</threadCount>
<perCoreThreadCount>true</perCoreThreadCount>
<runOrder>alphabetical</runOrder>
<useModulePath>false</useModulePath>
<includes>
<include>**/*IT.java</include>
</includes>
</configuration>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-plugin-plugin</artifactId>
<version>3.6.1</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
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</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<version>3.1.2</version>
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<configuration>
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<redirectTestOutputToFile>true</redirectTestOutputToFile>
<argLine>@{argLine} ${surefire_jvm_args}</argLine>
<trimStackTrace>false</trimStackTrace>
<runOrder>alphabetical</runOrder>
<argLine>@{argLine} ${surefire_jvm_args} -XX:+HeapDumpOnOutOfMemoryError</argLine>
<forkCount>0.6C</forkCount>
<threadCount>1</threadCount>
<perCoreThreadCount>false</perCoreThreadCount>
<reuseForks>true</reuseForks>
<parallel>classes</parallel>
<includes>
<include>**/*Test.java</include>
</includes>
<excludes>*StressTest*</excludes>
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</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.2</version>
</plugin>
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<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.2.0</version>
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</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<version>2.7</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
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<version>2.0.0</version>
<configuration>
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<verbose>true</verbose>
<addSvnKeyWords>false</addSvnKeyWords>
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<encoding>UTF-8</encoding>
</configuration>
</plugin>
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<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.8.1</version>
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<configuration>
<processDependencyManagementTransitive>false</processDependencyManagementTransitive>
</configuration>
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</plugin>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
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<version>${jetty_version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-changes-plugin</artifactId>
<version>${maven_changes_version}</version>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
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<version>4.3.0</version>
<configuration>
<coberturaReports>
</coberturaReports>
</configuration>
</plugin>
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<plugin>
<groupId>org.jacoco</groupId>
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<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.9</version>
<configuration>
<excludes>
<exclude>ca/uhn/fhir/model/dstu2/**/*.class</exclude>
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<exclude>ca/uhn/fhir/jpa/rp/r5/*.class</exclude>
<exclude>ca/uhn/fhir/jpa/rp/r4/*.class</exclude>
<exclude>ca/uhn/fhir/jpa/rp/r4b/*.class</exclude>
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<exclude>ca/uhn/fhir/jpa/rp/dstu3/*.class</exclude>
<exclude>ca/uhn/fhir/jpa/rp/dstu2/*.class</exclude>
</excludes>
</configuration>
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</plugin>
<!-- Generate the DDL schema files -->
<plugin>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-plugin</artifactId>
<version>7.7.5-SNAPSHOT</version>
<executions>
<execution>
<goals>
<goal>generate-ddl</goal>
</goals>
</execution>
</executions>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself. -->
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<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>
ca.uhn.hapi.fhir
</groupId>
<artifactId>
hapi-tinder-plugin
</artifactId>
<versionRange>
[0.8-SNAPSHOT,)
</versionRange>
<goals>
<goal>
generate-jparest-server
</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore></ignore>
</action>
</pluginExecution>
<pluginExecution>
<pluginExecutionFilter>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-antrun-plugin
</artifactId>
<versionRange>
[1.7,)
</versionRange>
<goals>
<goal>run</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore></ignore>
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<version>1.23</version>
<configuration>
<signature>
<groupId>net.sf.androidscents.signature</groupId>
<artifactId>android-api-level-26</artifactId>
<version>8.0.0_r2</version>
</signature>
</configuration>
<executions>
<execution>
<id>check-android-26-compliance</id>
<phase>test</phase>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
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</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<inherited>true</inherited>
<version>${maven_checkstyle_version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.3.0</version>
<executions>
<execution>
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<id>enforce-maven</id>
<goals>
<goal>enforce</goal>
</goals>
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<configuration>
<rules>
<requireMavenVersion>
<version>3.5.4</version>
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</requireMavenVersion>
<requireJavaVersion>
<version>17</version>
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<message>
HAPI FHIR is targeting JDK 11 for published binaries,
but we require JDK 17 to build and test this library.
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</message>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<inherited>false</inherited>
<executions>
<execution>
<id>copySubProjects</id>
<phase>site</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<copy todir="target/site/apidocs">
<fileset dir="hapi-fhir-base/target/site/apidocs"/>
</copy>
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<copy todir="target/site/apidocs-dstu2">
<fileset dir="hapi-fhir-structures-dstu2/target/site/apidocs"/>
</copy>
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<copy todir="target/site/apidocs-dstu3">
<fileset dir="hapi-fhir-structures-dstu3/target/site/apidocs"/>
</copy>
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<copy todir="target/site/apidocs-r4">
<fileset dir="hapi-fhir-structures-r4/target/site/apidocs"/>
</copy>
<copy todir="target/site/apidocs-r5">
<fileset dir="hapi-fhir-structures-r5/target/site/apidocs"/>
</copy>
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<copy todir="target/site/apidocs-jpaserver">
<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs"/>
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</copy>
<copy todir="target/site/apidocs-jpaserver-ips">
<fileset dir="hapi-fhir-jpaserver-ips/target/site/apidocs"/>
</copy>
<copy todir="target/site/apidocs-jpaserver-mdm">
<fileset dir="hapi-fhir-jpaserver-mdm/target/site/apidocs"/>
</copy>
<copy todir="target/site/apidocs-storage-batch2">
<fileset dir="hapi-fhir-storage-batch2/target/site/apidocs"/>
</copy>
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<copy todir="target/site/apidocs-client">
<fileset dir="hapi-fhir-client/target/site/apidocs"/>
</copy>
<copy todir="target/site/apidocs-server">
<fileset dir="hapi-fhir-server/target/site/apidocs"/>
</copy>
<copy todir="target/site/apidocs-server-mdm">
<fileset dir="hapi-fhir-server-mdm/target/site/apidocs"/>
</copy>
<copy todir="target/site/apidocs-server-openapi">
<fileset dir="hapi-fhir-server-mdm/target/site/openapi"/>
</copy>
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<copy todir="target/site/xref-jpaserver">
<fileset dir="hapi-fhir-jpaserver-base/target/site/xref"/>
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</copy>
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<copy todir="target/site/xref-base">
<fileset dir="hapi-fhir-base/target/site/xref"/>
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</copy>
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<!-- <copy todir="target/site/cobertura"> <fileset dir="hapi-fhir-cobertura/target/site/cobertura" /> </copy> -->
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<copy todir="target/site">
<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*"/>
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</copy>
<echo>Fixing Checkstyle Report</echo>
<replace dir="target/site" summary="true">
<include name="checkstyle.html"/>
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<replacetoken>"../../</replacetoken>
<replacevalue>"./</replacevalue>
</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken>
http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css
</replacetoken>
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<replacevalue>./css/bootstrap-responsive.min.css</replacevalue>
</replace>
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<replace dir="target/site" summary="true">
<include name="*.html"/>
<replacetoken>http://netdna.bootstrapcd</replacetoken>
<replacevalue>https://netdna.bootstrapcd</replacevalue>
</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken>http://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css
</replacetoken>
<replacevalue>https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css
</replacevalue>
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</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
<replacetoken>http://ajax.googleapis</replacetoken>
<replacevalue>https://ajax.googleapis</replacevalue>
</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
<replacetoken>\t</replacetoken>
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<replacevalue>
</replacevalue>
</replace>
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<replace dir="target/site" summary="true">
<include name="index.html"/>
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<replacetoken><![CDATA[<h2 id="Welcome">Welcome</h2>]]></replacetoken>
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<replacevalue><![CDATA[
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<div class="span12">
<div class="pull-left">
<a href="./" id="bannerLeft"><img src="images/hapi_fhir_banner.png" alt='"'HAPI'"' /></a>
</div>
<div class="pull-right">
<a href="./" id="bannerRight"><img src="images/hapi_fhir_banner_right.png" alt='"'FHIR'"' /></a>
</div>
</div>
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<br clear="both"/>
]]></replacevalue>
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</replace>
<!--<replaceregexp file="target/site/checkstyle.html" byline="false" match="&lt;ul class=&quot;breadcrumb.*?&lt;/ul&gt;" replace="" flags="s"/> -->
</target>
</configuration>
</execution>
<execution>
<id>addSyntaxHighlighter</id>
<phase>site</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
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<echo>Adding Fontawesome</echo>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken>
<![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
<replacevalue>
<![CDATA[<a href="download.html" title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
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</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken>
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<![CDATA[<a href="https://github.com/hapifhir/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
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<replacevalue>
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<![CDATA[<a href="https://github.com/hapifhir/hapi-fhir/" title="GitHub Project" class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
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</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken><![CDATA[data-toggle="dropdown">Test Servers <]]></replacetoken>
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<replacevalue>
<![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
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</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken><![CDATA[data-toggle="dropdown">Documentation <]]></replacetoken>
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<replacevalue>
<![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
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</replace>
<replace dir="target/site" summary="true">
<include name="*.html"/>
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<replacetoken><![CDATA[data-toggle="dropdown">Get Help <]]></replacetoken>
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<replacevalue>
<![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
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</replace>
<echo>Changing Breadcrumbs</echo>
<replace dir="target/site" summary="true">
<include name="doc_*.html"/>
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<replacetoken><![CDATA[<li class="divider">/</li>]]></replacetoken>
<replacevalue><![CDATA[<li class="divider">/</li>
<li><a href="docindex.html" title="Documentation">Documentation</a></li>
<li class="divider">/</li>]]></replacevalue>
</replace>
<echo>Adding Syntax Highlighter</echo>
<replace dir="target/site" summary="true">
<include name="*.html"></include>
<replacetoken><![CDATA[</body>]]></replacetoken>
<replacevalue><![CDATA[
<script type="text/javascript">
var elements = document.getElementsByClassName("source");
for (var i=0; i < elements.length; i++) {
var pres = elements[i].getElementsByTagName("pre");
for (var j = 0; j < pres.length; j++) {
var pre = pres[j];
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if (pre.innerHTML.match(/^\s*\&lt\;/)) {
pre.className = 'brush: xml';
} else if (pre.innerHTML.match(/\/\*/)) {
pre.className = 'brush: java';
} else if (pre.innerHTML.match(/^\/\//)) {
pre.className = 'brush: java';
} else if (pre.innerHTML.match(/^\{/)) {
pre.className = 'brush: jscript';
} else if (pre.innerHTML.match(/^\#/)) {
pre.className = 'brush: bash';
} else if (pre.innerHTML.match(/\&lt\;\//)) {
pre.className = 'brush: xml';
} else {
pre.className = 'brush: java';
}
}
}
SyntaxHighlighter.all();
</script>
</body>
]]></replacevalue>
</replace>
</target>
</configuration>
</execution>
<execution>
<id>addAnalytics</id>
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<phase>site</phase>
<configuration>
<target>
<echo>Adding Google analytics in target/site for &lt;body&gt;</echo>
<replace dir="target/site" summary="true">
<include name="**/*.html"></include>
<!--suppress UnresolvedMavenProperty -->
<replacefilter token="#build#" value="${label}"/>
<replacefilter token="#version#" value="${project.version}"/>
<replacetoken><![CDATA[</body>]]></replacetoken>
<replacevalue><![CDATA[
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-1395874-5', 'auto');
ga('require', 'displayfeatures');
ga('require', 'linkid', 'linkid.js');
ga('send', 'pageview');
</script>
</body >
]]></replacevalue>
</replace>
<echo>Adding Google analytics in target/site for &lt;BODY&gt;</echo>
<replace dir="target/site" summary="true">
<include name="**/*.html"></include>
<replacetoken><![CDATA[</BODY>]]></replacetoken>
<replacevalue><![CDATA[
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-1395874-5', 'auto');
ga('require', 'displayfeatures');
ga('require', 'linkid', 'linkid.js');
ga('send', 'pageview');
</script>
</BODY >
]]></replacevalue>
</replace>
</target>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-scm-publish-plugin</artifactId>
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<version>3.0.0</version>
<inherited>false</inherited>
<configuration>
<checkoutDirectory>${scmPubCheckoutDirectory}</checkoutDirectory>
<content>\${siteMainDirectory}</content>
<tryUpdate>true</tryUpdate>
<scmBranch>gh-pages</scmBranch>
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<pubScmUrl>scm:git:git@github.com:hapifhir/hapi-fhir.git</pubScmUrl>
</configuration>
<executions>
<execution>
<id>scm-publish</id>
<phase>site-deploy</phase>
<goals>
<goal>publish-scm</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
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</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-changes-plugin</artifactId>
<version>${maven_changes_version}</version>
<inherited>false</inherited>
<reportSets>
<reportSet>
<reports>
<report>changes-report</report>
</reports>
</reportSet>
</reportSets>
<configuration>
<feedType>atom_1.0</feedType>
<issueLinkTemplatePerSystem>
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<default>https://github.com/hapifhir/hapi-fhir/issues/%ISSUE%</default>
</issueLinkTemplatePerSystem>
<escapeHTML>false</escapeHTML>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
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<version>2.19.1</version>
<reportSets>
<reportSet>
<reports>
<report>failsafe-report-only</report>
</reports>
</reportSet>
</reportSets>
<configuration>
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<reportsDirectories>
<reportDirectory>${project.basedir}/hapi-fhir-base/target/surefire-reports/</reportDirectory>
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<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu/target/surefire-reports/
</reportDirectory>
<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu2/target/surefire-reports/
</reportDirectory>
<reportDirectory>${project.basedir}/hapi-fhir-jpaserver-base/target/surefire-reports/
</reportDirectory>
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</reportsDirectories>
</configuration>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
<inherited>false</inherited>
</plugin>
</plugins>
</reporting>
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<profiles>
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<profile>
<id>DIST</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<inherited>false</inherited>
<executions>
<execution>
<id>update-project-license</id>
<phase>package</phase>
<goals>
<goal>update-project-license</goal>
</goals>
<configuration>
<licenseName>apache_v2</licenseName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
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</profile>
<profile>
<id>ROOT</id>
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<reporting>
<plugins>
</plugins>
</reporting>
<modules>
</modules>
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<build>
<plugins>
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Fix #674 - Avoid duplicates in $everything query Squashed commit of the following: commit f3097f423f5f1e1d27f4084aa4ab0daa01618149 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 13:24:29 2017 -0400 more travis fun commit a4b8161597057562d03c2abb3eed3c56dae874ba Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 10:43:33 2017 -0400 More fighting with travis commit fe47d1e8643ae0b7860567ad02db50aac42c509b Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 10:10:55 2017 -0400 More travis attempts commit 4fdfe7a4e81ff28407209f7b03a37cfddf946586 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 09:25:04 2017 -0400 Try and run unit tests in 2 threads to cut time.. Will travis like this? commit 571045b63da04149397acfad6798193b384e541f Author: James <jamesagnew@gmail.com> Date: Mon Jun 19 07:35:46 2017 -0400 Paging now working commit 526a1fa7d03f9ca0d1c4a3921fb7ea0faa783c4c Merge: cebe881a15 55a67ae055 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 06:19:37 2017 -0400 Merge branch '674_everything_improvements' of github.com:jamesagnew/hapi-fhir into 674_everything_improvements commit cebe881a158cfbbf0adb42607029862a39e1e169 Merge: b3b9273ca7 5789cd2a46 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 06:19:12 2017 -0400 Merge branch 'master' into 674_everything_improvements for #674 commit b3b9273ca74a7993bfef362710727c6aa2c05756 Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 06:16:27 2017 -0400 Work on everything fixes for #674 commit 55a67ae05509b197bff4f4d0c331da334a58b85d Author: James Agnew <jamesagnew@gmail.com> Date: Mon Jun 19 06:16:27 2017 -0400 Work on everything fixes
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This profile is basically here to work around an IJ bug where the
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Rel 6 0 mb 3 (#3933) * adding version.yaml, updating version in pom.xml * It is possible to write to a resource in a partition the user is not authorized to. (#3397) * fixed * remove sout * add msg.code * fix failed tests * fix equal sign * update msg code * extract method * Fix up code numbers * Clean changelog Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Revert final artifact version * add graphql test (#3585) * added graphql birthdate test * fix variable name * typo * 3506 mdm log enhancement (#3543) * Providing Fixme's to be reworked at a later time. * Adding // FIXME Anna to assist our Austrian friend. * Adding logging test as a first step in addressing issue #2822. * hapifhir#3506 part 2: enhance logging for (un)successful MDM matching hapifhir#3506 part 2: enhance logging for (un)successful MDM matching * Update MdmMatchLinkSvc.java #3506 move "narrowed down" log to different place * #3506 added scores and tests #3506 added scores and tests * #3506 formatting #3506 formatting * #3506 create changelog file #3506 create changelog file * #3506 fix typo #3506 fix typo * #3506 fix part 3, minor formatting #3506 fix part 3, minor formatting * #3506 fix tests #3506 fix tests Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com> Co-authored-by: Anna <anna@MacBook-Pro.local> * mdm matching (#3579) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328 * Update HapiFhirJpaMigrationTasks.java Corrected ordering * Update HapiFhirJpaMigrationTasks.java Moving index status to be last operation * Revert "Update HapiFhirJpaMigrationTasks.java" This reverts commit 37bfd3e66e4f4dc76de135c1fe108ccbf9e3690c. * Moved to bottom Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> * begin with failing test * fixed * changelog * add jira tag * Update to 6 1 (#3582) * added changelog folder, upped version * version enum * add a few more unit tests to assert proper NO_MATCH exclusion * revert merge master doh! bad reflexes * revert merge origin master * unrevert revert. ugh what a pain * merge recovery. fix poms. * merge recovery. more reverting * merge recovery. more reverting * merge recovery. more reverting * Revert "merge recovery. fix poms." This reverts commit ae6e0ddb06bdcb424f9c4637eb0a987bc112b115. * more revert revert reversions * more revert revert reversions * pre-review cleanup Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> * Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586) * When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller. * License * Ks 20220508 log colour (#3592) * don't use colours when output is redirected to a file * change log * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328 * Update HapiFhirJpaMigrationTasks.java Corrected ordering * Update HapiFhirJpaMigrationTasks.java Moving index status to be last operation * Revert "Update HapiFhirJpaMigrationTasks.java" This reverts commit 37bfd3e66e4f4dc76de135c1fe108ccbf9e3690c. * Moved to bottom Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> * 3584 case sensitive string elasticsearch (#3596) * Fix for case-sensitive search with newer elasticsearch * Test and fix ascii normalization too * more test cases * comments * Docs update empi usecase (#3598) * Update diagram for use case 5 * Add new page for database support * Licnese * Mb norm fix (#3604) * Normalize query since wildcard searches aren't normalized in elastic * Handle batch2 job cancellation (#3603) * Handle batch2 job cancellation * Add CANCELLED status * Remove unuseful test Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add batch2 interfaces to obtain recent instances (#3601) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * changelog folder * Documentation change, added warning log and change log for ticket (#3609) Co-authored-by: Steven Li <steven@smilecdr.com> * fix ne for lastUpdated search param (#3589) * init/wip * add implementation, add tests * add checks and some refactoring * refactor and simplify tests * refactor * get rid of some of the warnings * add changelog * remove my todos * redo ne logic to account for less precise dates * add tests * refactoring * rename to follow convention Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> * Version bump * Add skip of checkstyle to upload * Typo * upping version enum, upping version number, 6.0.1 * Group Bulk Export rules exiting too early. (#3643) * Implementation, test, changelog * Add jira link * adding backport in yaml for 3642 * adding folder for 6.0.1 release * pom changes to publish checkstyle to sonatype * bad version in pom file * Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider * AUtomcplete error code * updating comment indicating final erorr code * Bump error code * fixing version enum so release docs generate correctly, adding additional changelog for 3650 * 3684 subscription for delivering delete events formatted wrong (#3685) * Fixed issue with delivering delete events Subscriptions * Extracted deliverer class name to a constant, now shared across tests and interceptor class * Added change log and doc changes * moved the constant to a more appropriate place Co-authored-by: Steven Li <steven@smilecdr.com> * Version bump * Add version enum * Version enum and folder * adding release pipeline yml file fo azure * Adding autoclose for sonatype publishing (#3797) * Add impl test and changelog (#3713) * fix up changelog, new version * Version bump * Updating version to: 6.0.4 post release. * reverting 6.0.4 commit * Updating version to: 6.0.4 post release. * removing double entry from preious release * Add support for DSTU3 delete subscrion events, add test * Add changelogP * Add version enum * Remove notnull * Add test for DSTU2 * Updating version to: 6.0.5 post release. * Fix up * wip * Adding solution and changeLog file. * Adding failing test. * fix up * Version bump Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com> Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com> Co-authored-by: Anna <anna@MacBook-Pro.local> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-08-29 22:29:02 -04:00
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