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>6.5.5-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-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>
</modules>
2014-02-17 17:58:32 -05:00
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2018-05-03 18:34:29 -04:00
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2015-06-21 00:56:23 -04:00
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2014-02-17 17:58:32 -05:00
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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
<fhir_core_version>5.6.97</fhir_core_version>
<ucum_version>1.0.3</ucum_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
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
<ucum_version>1.0.3</ucum_version>
<!-- 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>3.1.1</caffeine_version>
<checkstyle_version>10.6.0</checkstyle_version>
<maven_checkstyle_version>3.2.0</maven_checkstyle_version>
<maven_changes_version>2.12.1</maven_changes_version>
<commons_codec_version>1.15</commons_codec_version>
<commons_compress_version>1.21</commons_compress_version>
<commons_text_version>1.10.0</commons_text_version>
<commons_io_version>2.11.0</commons_io_version>
<commons_lang3_version>3.12.0</commons_lang3_version>
<com_jamesmurty_utils_version>1.2</com_jamesmurty_utils_version>
<derby_version>10.14.2.0</derby_version>
<error_prone_core_version>2.10.0</error_prone_core_version>
<mockito_version>4.8.1</mockito_version>
<nullaway_version>0.7.9</nullaway_version>
<guava_version>31.0.1-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>
<jaxb_runtime_version>3.0.0</jaxb_runtime_version>
<jena_version>4.2.0</jena_version>
<jersey_version>3.0.3</jersey_version>
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
<jetty_version>10.0.13</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<junit_version>5.9.1</junit_version>
<flexmark_version>0.50.40</flexmark_version>
<flyway_version>9.4.0</flyway_version>
<hibernate_version>5.6.12.Final</hibernate_version>
<hibernate_search_version>6.1.6.Final</hibernate_search_version>
<logback_version>1.4.4</logback_version>
<!-- Update lucene version when you update hibernate-search version -->
<lucene_version>8.11.1</lucene_version>
<hamcrest_version>2.2</hamcrest_version>
<hibernate_validator_version>6.1.5.Final</hibernate_validator_version>
<httpcore_version>4.4.13</httpcore_version>
<httpclient_version>4.5.13</httpclient_version>
<jackson_version>2.14.1</jackson_version>
<jackson_databind_version>2.14.1</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>4.10.0</okhttp_version>
<poi_version>4.1.2</poi_version>
<poi_ooxml_schemas_version>1.4</poi_ooxml_schemas_version>
<resteasy_version>5.0.2.Final</resteasy_version>
<ph_schematron_version>5.6.5</ph_schematron_version>
<ph_commons_version>9.5.4</ph_commons_version>
<plexus_compiler_api_version>2.9.0</plexus_compiler_api_version>
<servicemix_saxon_version>9.8.0-15</servicemix_saxon_version>
<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
<swagger_version>2.1.12</swagger_version>
<slf4j_version>2.0.3</slf4j_version>
<log4j_to_slf4j_version>2.19.0</log4j_to_slf4j_version>
<spring_version>5.3.23</spring_version>
<spring_data_bom_version>2021.2.2</spring_data_bom_version>
<spring_batch_version>4.3.3</spring_batch_version>
<spring_boot_version>2.7.5</spring_boot_version>
<spring_retry_version>1.2.2.RELEASE</spring_retry_version>
<stax2_api_version>3.1.4</stax2_api_version>
<testcontainers_version>1.17.1</testcontainers_version>
<thymeleaf-version>3.0.14.RELEASE</thymeleaf-version>
<woodstox_core_asl_version>4.4.1</woodstox_core_asl_version>
2015-06-21 22:10:13 -04:00
<!-- We are aiming to still work on a very old version of SLF4j even though we depend on the newest, just to be nice to users of the API. This version is tested in the hapi-fhir-cobertura. -->
<slf4j_target_version>1.6.0</slf4j_target_version>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
<elastic_apm_version>1.28.4</elastic_apm_version>
<!-- CQL Support -->
<cqframework.version>2.4.0</cqframework.version>
<cql-engine.version>2.3.0</cql-engine.version>
<cql-evaluator.version>2.3.0</cql-evaluator.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>
<!-- 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>
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<dependency>
<groupId>aopalliance</groupId>
<artifactId>aopalliance</artifactId>
<version>1.0</version>
</dependency>
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<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
2017-08-13 14:39:47 -04:00
</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>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.module</groupId>
<artifactId>jackson-module-jaxb-annotations</artifactId>
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<version>${jackson_version}</version>
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</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<version>2.5.0</version>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path-assert</artifactId>
<version>2.5.0</version>
</dependency>
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
<version>${caffeine_version}</version>
</dependency>
<dependency>
<groupId>com.graphql-java</groupId>
<artifactId>graphql-java</artifactId>
<version>19.2</version>
</dependency>
<!-- mail start -->
<dependency>
<groupId>org.simplejavamail</groupId>
<artifactId>simple-java-mail</artifactId>
<version>6.6.1</version>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail</artifactId>
<version>1.6.4</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail-junit5</artifactId>
<version>1.6.4</version>
<scope>compile</scope>
</dependency>
<!-- mail end -->
2016-09-17 16:55:21 -04:00
<dependency>
<groupId>com.github.dnault</groupId>
<artifactId>xml-patch</artifactId>
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<version>0.3.1</version>
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</dependency>
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<dependency>
<groupId>io.dogote</groupId>
<artifactId>json-patch</artifactId>
<version>1.15</version>
</dependency>
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<dependency>
<groupId>com.google.errorprone</groupId>
<artifactId>error_prone_core</artifactId>
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<version>${error_prone_core_version}</version>
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</dependency>
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<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava_version}</version>
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</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava-testlib</artifactId>
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<version>${guava_version}</version>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>2.1.214</version>
</dependency>
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<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<version>${ph_schematron_version}</version>
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</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-commons</artifactId>
<version>${ph_commons_version}</version>
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</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
2017-08-13 14:39:47 -04:00
<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>
<version>3.2.0</version>
</dependency>
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<dependency>
<groupId>com.sun.activation</groupId>
<artifactId>javax.activation</artifactId>
<version>${activation_api_version}</version>
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</dependency>
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<dependency>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
<version>2.0.0</version>
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</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>${flexmark_version}</version>
</dependency>
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.9.4</version>
</dependency>
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<dependency>
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<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.5.0</version>
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</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${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>${commons_compress_version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.8</version>
</dependency>
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
<version>1.9.5</version>
</dependency>
<dependency>
<groupId>org.hl7.fhir.testcases</groupId>
<artifactId>fhir-test-cases</artifactId>
<version>1.1.14</version>
</dependency>
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<dependency>
<groupId>org.jdom</groupId>
<artifactId>jdom2</artifactId>
<version>2.0.6.1</version>
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</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
<version>23.0.0</version>
</dependency>
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<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${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
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<dependency>
<groupId>es.nitaur.markdown</groupId>
<artifactId>txtmark</artifactId>
<version>0.16</version>
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</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
<version>1.3.5</version>
</dependency>
<dependency>
<groupId>jakarta.transaction</groupId>
<artifactId>jakarta.transaction-api</artifactId>
<version>1.3.3</version>
</dependency>
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<dependency>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
<version>${activation_api_version}</version>
</dependency>
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<dependency>
<groupId>javax.ejb</groupId>
<artifactId>ejb-api</artifactId>
<version>3.0</version>
</dependency>
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<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
<version>3.0.0</version>
</dependency>
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<version>1.2</version>
</dependency>
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<dependency>
<groupId>javax.json</groupId>
<artifactId>javax.json-api</artifactId>
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<version>1.1</version>
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</dependency>
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<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>${jaxb_api_version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson_version}</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>com.healthmarketscience.sqlbuilder</groupId>
<artifactId>sqlbuilder</artifactId>
<version>3.0.2</version>
</dependency>
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<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>9.4.1.jre8</version>
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</dependency>
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<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
</dependency>
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<dependency>
<groupId>javax.transaction</groupId>
<artifactId>javax.transaction-api</artifactId>
<version>1.2</version>
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</dependency>
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
<version>2.0.1.Final</version>
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</dependency>
<dependency>
<!--
We use JUnit 5 in HAPI FHIR, but some libraries still pull in / require JUnit 4
(e.g. Testcontainers) so we enforce a current version to avoid OWASP flags
-->
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.2</version>
</dependency>
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-models</artifactId>
<version>${swagger_version}</version>
</dependency>
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-core</artifactId>
<version>${swagger_version}</version>
</dependency>
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<dependency>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
<version>8.0.32</version>
</dependency>
<dependency>
<groupId>org.springdoc</groupId>
<artifactId>springdoc-openapi-ui</artifactId>
6.4.0 Mergeback (#4563) * 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 * 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 * re-add checkstyle * respect move-up into storage settings from jpastoragesettings * remove duplicate test --------- 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: 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>
2023-02-17 16:16:44 -05:00
<version>1.5.13</version>
</dependency>
<dependency>
<groupId>net.sourceforge.htmlunit</groupId>
<artifactId>htmlunit</artifactId>
<version>2.67.0</version>
<exclusions>
<exclusion>
<!-- Don't let HTMLUnit bring in Jetty 9 -->
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
</exclusion>
</exclusions>
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</dependency>
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<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>
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<dependency>
<groupId>net.ttddyy</groupId>
<artifactId>datasource-proxy</artifactId>
<version>1.7</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>
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<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
<version>2.9.0</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>
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<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
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<version>${commons_text_version}</version>
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</dependency>
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<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<version>${derby_version}</version>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
<version>${derby_version}</version>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
<version>${derby_version}</version>
</dependency>
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<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyshared</artifactId>
<version>${derby_version}</version>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
<version>${derby_version}</version>
</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>
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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>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
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<artifactId>lucene-analyzers-phonetic</artifactId>
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<version>${lucene_version}</version>
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</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
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<artifactId>lucene-backward-codecs</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>
<version>3.6.3</version>
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</dependency>
<dependency>
<groupId>org.apache.maven.plugin-tools</groupId>
<artifactId>maven-plugin-annotations</artifactId>
<version>3.6.0</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>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-http</artifactId>
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<version>${jetty_version}</version>
</dependency>
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<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
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<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-io</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-continuation</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-security</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
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<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
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<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
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<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
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<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-xml</artifactId>
<version>${jetty_version}</version>
</dependency>
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<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-api</artifactId>
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<version>${jetty_version}</version>
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</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-core-client</artifactId>
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<version>${jetty_version}</version>
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</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-server</artifactId>
2015-12-01 18:35:24 -05:00
<version>${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>2.4.0</version>
2015-09-13 22:06:31 -04:00
</dependency>
2015-09-08 08:14:55 -04:00
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.el</artifactId>
<version>3.0.0</version>
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.json</artifactId>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb_runtime_version}</version>
</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>
<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>
2015-09-08 08:14:55 -04:00
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate_version}</version>
<exclusions>
<exclusion>
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
<exclusion>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
</exclusion>
<exclusion>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
</exclusion>
<exclusion>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.jboss.spec.javax.transaction</groupId>
<artifactId>jboss-transaction-api_1.2_spec</artifactId>
</exclusion>
</exclusions>
2015-09-08 08:14:55 -04:00
</dependency>
2020-02-07 15:18:06 -05:00
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-java8</artifactId>
<version>${hibernate_version}</version>
</dependency>
2015-09-08 08:14:55 -04:00
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>${hibernate_version}</version>
<exclusions>
<exclusion>
<groupId>org.jboss.spec.javax.transaction</groupId>
<artifactId>jboss-transaction-api_1.2_spec</artifactId>
</exclusion>
</exclusions>
2015-09-08 08:14:55 -04:00
</dependency>
<dependency>
2020-04-13 11:50:49 -04:00
<groupId>org.hibernate.validator</groupId>
2015-09-08 08:14:55 -04:00
<artifactId>hibernate-validator</artifactId>
<version>${hibernate_validator_version}</version>
</dependency>
<dependency>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-to-slf4j</artifactId>
<version>${log4j_to_slf4j_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-mapper-orm</artifactId>
2017-01-30 17:59:01 -05:00
<version>${hibernate_search_version}</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
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
2017-10-09 10:59:36 -04:00
<dependency>
<!--
Be careful bumping this, you need to match the maximum version supported by Hibernate Search.
See: https://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/#getting-started-compatibility
-->
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
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<version>7.17.3</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.yaml</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
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>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
2017-10-09 10:59:36 -04:00
<version>${hibernate_search_version}</version>
</dependency>
2020-04-10 20:01:59 -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
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-lucene</artifactId>
2020-04-12 20:47:32 -04:00
<version>${hibernate_search_version}</version>
2020-04-10 20:01:59 -04:00
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch-aws</artifactId>
<version>${hibernate_search_version}</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
2018-04-06 09:12:22 -04:00
<version>3.22.0-GA</version>
</dependency>
<dependency>
<groupId>org.junit</groupId>
<artifactId>junit-bom</artifactId>
<version>${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>
2020-12-14 06:06:07 -05:00
<dependency>
<groupId>org.junit-pioneer</groupId>
<artifactId>junit-pioneer</artifactId>
<version>1.3.8</version>
2020-12-14 06:06:07 -05:00
</dependency>
2018-09-07 19:14:43 -04:00
<dependency>
<groupId>org.mariadb.jdbc</groupId>
<artifactId>mariadb-java-client</artifactId>
<version>3.0.4</version>
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</dependency>
2016-12-25 12:48:36 -05:00
<dependency>
<groupId>org.mockito</groupId>
2018-05-03 18:34:29 -04:00
<artifactId>mockito-core</artifactId>
<version>${mockito_version}</version>
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</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>${mockito_version}</version>
</dependency>
2018-09-07 19:14:43 -04:00
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
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
<version>42.5.1</version>
2018-09-07 19:14:43 -04:00
</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>
2015-08-31 08:20:24 -04:00
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-android</artifactId>
<version>1.7.36</version>
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</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j_version}</version>
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</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>${slf4j_version}</version>
</dependency>
2015-08-31 08:20:24 -04:00
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
<version>${slf4j_version}</version>
2015-08-31 08:20:24 -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.slf4j</groupId>
<artifactId>jcl-over-slf4j</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>${slf4j_version}</version>
</dependency>
2015-08-16 22:09:01 -04:00
<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>${spring_version}</version>
</dependency>
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<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>${spring_version}</version>
</dependency>
2015-09-28 09:06:57 -04:00
<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>${spring_boot_version}</version>
</dependency>
DeleteConflict hook, SearchableHashMapResourceProvider, and in-memory searching (#1341) * Make IBundle list interface more flexible * Make matchResourceLinks visible * Make matchResourceLinks visible * Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module * Added more accessors to version independent resource classes * improved forcedid matching (needs to be verified by James) filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this) * add AnyComposition * cleanup of Any classes * create searchparam config so people can use that module without using subscriptions * create searchparam config so people can use that module without using subscriptions * fix broken test * added derivedFrom * renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull also added method to add a new dao to the registry and retrieve registered types * TokenParam.equals * add error check to searchable hashmap resource provider * added support for R4 * add successor to measure * delete conflict hook start with failing test * test passes. hook is called. * added delete conflict hook all delete conflict tests pass * added javadoc * Performance test * test bad interceptor case * typo * rename criteria matcher * added support for multiple topics * fix method name * add effective period * Temporarily excluding StressTest from build to try to get Travis under time limit * change log * review feedback * review feedback * review feedback
2019-06-13 13:59:51 -04:00
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-test</artifactId>
<version>${spring_boot_version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>${spring_version}</version>
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</dependency>
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<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring_version}</version>
</dependency>
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<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>
2015-08-31 08:20:24 -04:00
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
<version>${thymeleaf-version}</version>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
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<artifactId>thymeleaf-spring5</artifactId>
<version>${thymeleaf-version}</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>2.27.0</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>
2015-08-31 08:39:49 -04:00
<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
<groupId>org.xmlunit</groupId>
<artifactId>xmlunit-core</artifactId>
<version>2.4.0</version>
</dependency>
<dependency>
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190) * Beginning work on converting to hibernate search 6 * replace all out of date properties * replace all POM references to old versions * remove the shaded ES jars as HS6 supports 7.9 * Convert "Bridges" to RoutingBinder and RoutingBridge * Modernize all indexing annotations * Begin refactoring of search queries (wip) * Fix spatial API changes, work on BaseTermReadSvcImpl * Most of the way through the various filter property conversions * Finished i think with BaseTermReadSvcImpl * Compiling, but definitely broken * Start test compilation failures * All tests compiling (i think) * remove suggest keywords operation * Fix bootstrap errors, still have to deal with transient fields * Rollback CR * More refactoring, got IDs baked back into docs * Fix coord util, fix a few more fields which require projection * merge fixes * begin refactor of valuesetexpansion tests * fix another test * Update tests * remove todos, add TestContainers * Fix descendant in * Add testcontainers, fix another test * fix more tests, replace embedded es * Rip out embedded elastic, replace with TestContainer * merge conflicts for new analyzers * Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs * Remove dead deps, update testcontainer * Remove java-hamcrest * Pull asserts up, refactor tests to pass in RP tests * Update V2 check * Remove suggest keyword tests * Split line for testing * Fix perhaps one of the dumbest programming mistakes in my career so far * Refactor tests which no longer rely on a strict known order * Fix up test config, disable log test temporarily * Remove log4j from being transitively pulled in. re-enable test * Update log4j exclusions with new bridge. Update test to check for core class * Move dependency to root pom in dep management section * Update changelog, add changelog for HS6 with ES requirements. Remove dead comment * update testst, remove todos * Add hibernate props provider method, add elastic regexp query * Add todo for high level client builder * Modify ElasticsearchRestClientFactory to support HTTPS hosts * Remove protocol extraction from rest url * do we even need to index this...? * remove purge of non-indexed resources * Add longer timeout to testcontainers * Add task to add docker CLI to azure pipeline via task, for testcontainers * WIP remove this * Dont update version * Add test for duplicate termconcepts * Use real hibernate ORM methods * merge issues * Add partitionsettigns bean to match master * Trying to debug testcontainers on azure... * Trying to debug testcontainers on azure... * Run even on previous failure * Fix testcontainer port binds * Add full text logs attaching, and test reporting * I love yaml * Remove comment * Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue * Modify TX beheaviour * wip * Rework to use config and mocked beans for partition-aware lastN * rework to not use beans and just inject vars i need for test, keps test envs cleaner * update azure pipeline to only copy test results * Remove erroneous publish * Always get test logs * Make it so indexing works, * Add todos * revert deleteByPid * Work on test fixes * Test fixes * Test fixes * Another test fix * Test fix * Work on tests * Test fixes * All tests passing locally * Fix test failure * FIx build error * Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider * Update ngram of token filters * Tidying * subvert the purpose of hibernate elastic props builder to inject template * dead space * Rename changed class Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
<version>${testcontainers_version}</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>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>elasticsearch</artifactId>
<version>${testcontainers_version}</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>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<version>${testcontainers_version}</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>
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>xpp3</groupId>
<artifactId>xpp3</artifactId>
<version>1.1.4c</version>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
<version>1.1.4c</version>
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</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
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<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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</dependencies>
</dependencyManagement>
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<build>
<pluginManagement>
<plugins>
<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>${spring_boot_version}</version>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<version>1.5.0</version>
</plugin>
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<plugin>
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<groupId>de.jpdigital</groupId>
<artifactId>hibernate56-ddl-maven-plugin</artifactId>
<version>2.5.0</version>
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</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>${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>
<version>3.10.1</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>
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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.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</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>3.2.0</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>
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<version>3.0.0-M5</version>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</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>
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<version>3.0.0-M5</version>
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<configuration>
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<redirectTestOutputToFile>true</redirectTestOutputToFile>
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<runOrder>random</runOrder>
<argLine>@{argLine} ${surefire_jvm_args}</argLine>
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<forkCount>1.0C</forkCount>
<trimStackTrace>true</trimStackTrace>
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</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.2</version>
</plugin>
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<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.2.0</version>
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</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<version>2.7</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
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<version>2.0.0</version>
<configuration>
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<verbose>true</verbose>
<addSvnKeyWords>false</addSvnKeyWords>
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<encoding>UTF-8</encoding>
</configuration>
</plugin>
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<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.8.1</version>
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<configuration>
<processDependencyManagementTransitive>false</processDependencyManagementTransitive>
</configuration>
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</plugin>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
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<version>${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>0.8.8</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>
<!--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>
<version>1.22</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-enforcer-plugin</artifactId>
<version>3.0.0</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>
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</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");
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for (var j = 0; j < pres.length; j++) {
var pre = pres[j];
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if (pre.innerHTML.match(/^\s*\&lt\;/)) {
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pre.className = 'brush: java';
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} else if (pre.innerHTML.match(/^\{/)) {
pre.className = 'brush: jscript';
} else if (pre.innerHTML.match(/^\#/)) {
pre.className = 'brush: bash';
} else if (pre.innerHTML.match(/\&lt\;\//)) {
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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="${project.version}"/>
<replacetoken><![CDATA[</body>]]></replacetoken>
<replacevalue><![CDATA[
<script>
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})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-1395874-5', 'auto');
ga('require', 'displayfeatures');
ga('require', 'linkid', 'linkid.js');
ga('send', 'pageview');
</script>
</body >
]]></replacevalue>
</replace>
<echo>Adding Google analytics in target/site for &lt;BODY&gt;</echo>
<replace dir="target/site" summary="true">
<include name="**/*.html"></include>
<replacetoken><![CDATA[</BODY>]]></replacetoken>
<replacevalue><![CDATA[
<script>
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ga('create', 'UA-1395874-5', 'auto');
ga('require', 'displayfeatures');
ga('require', 'linkid', 'linkid.js');
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</BODY >
]]></replacevalue>
</replace>
</target>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-scm-publish-plugin</artifactId>
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<version>3.0.0</version>
<inherited>false</inherited>
<configuration>
<checkoutDirectory>${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>
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<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>${maven_changes_version}</version>
<inherited>false</inherited>
<reportSets>
<reportSet>
<reports>
<report>changes-report</report>
</reports>
</reportSet>
</reportSets>
<configuration>
<feedType>atom_1.0</feedType>
<issueLinkTemplatePerSystem>
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<default>https://github.com/hapifhir/hapi-fhir/issues/%ISSUE%</default>
</issueLinkTemplatePerSystem>
<escapeHTML>false</escapeHTML>
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</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
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<version>2.19.1</version>
<reportSets>
<reportSet>
<reports>
<report>failsafe-report-only</report>
</reports>
</reportSet>
</reportSets>
<configuration>
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<reportsDirectories>
<reportDirectory>${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>${project.basedir}/hapi-fhir-jpaserver-base/target/surefire-reports/
</reportDirectory>
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</reportsDirectories>
</configuration>
</plugin>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
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<inherited>false</inherited>
</plugin>
</plugins>
</reporting>
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<profiles>
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<profile>
<id>DIST</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<inherited>false</inherited>
<executions>
<execution>
<id>update-project-license</id>
<phase>package</phase>
<goals>
<goal>update-project-license</goal>
</goals>
<configuration>
<licenseName>apache_v2</licenseName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
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</profile>
<profile>
<id>ROOT</id>
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<reporting>
<plugins>
</plugins>
</reporting>
<modules>
</modules>
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<build>
<plugins>
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<!-- <plugin> <artifactId>maven-assembly-plugin</artifactId> <version>${maven_assembly_plugin_version}</version> <executions> <execution> <phase>package</phase> <goals> <goal>single</goal> </goals>
<configuration> <attach>false</attach> <descriptors> <descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor> </descriptors> </configuration> </execution> </executions> </plugin> -->
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</plugins>
</build>
</profile>
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<profile>
<id>JACOCO</id>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
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</execution>
</executions>
</plugin>
</plugins>
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</profile>
<profile>
<id>CI</id>
<properties>
<surefire_jvm_args>-Dspring.test.context.cache.maxSize=2 -Dfile.encoding=UTF-8 -Xmx2648m -XX:-TieredCompilation -Dfile.encoding=UTF-8 -Xss128M -XX:MetaspaceSize=512M -XX:MaxMetaspaceSize=2048M -XX:ReservedCodeCacheSize=220M</surefire_jvm_args>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>delete-module-cache-file</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>${maven_checkstyle_version}</version>
<executions>
<execution>
<id>hapi-single-module-checkstyle</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
</plugins>
</build>
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</profile>
<profile>
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<id>NOPARALLEL</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<forkCount>1</forkCount>
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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
2017-06-19 13:56:38 -04:00
<profile>
<id>MINPARALLEL</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<forkCount>2</forkCount>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
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<id>ERRORPRONE</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<fork>true</fork>
<compilerArgs>
<arg>-XDcompilePolicy=simple</arg>
<arg>-Xplugin:ErrorProne</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>
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<version>${error_prone_core_version}</version>
</path>
</annotationProcessorPaths>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>FASTINSTALL</id>
<properties>
<skipTests>true</skipTests>
</properties>
<!-- Profile for a quick local mvn install after a git pull.
We assume upstream ran these checks as part of the build. -->
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<executions>
<execution><id>integration-test</id><phase>none</phase></execution>
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<plugin>
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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
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2022-03-06 15:46:49 -05:00
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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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2014-04-24 07:24:27 -04:00
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