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🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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James Agnew ae1d249d99
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 efae3b5d5f.

* 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 53252b8d15.

* 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 b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* 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 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

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
.github bump compiler settings. JDK 11 for prod, JDK 17 for tests (#3435) 2022-02-28 21:51:32 +00:00
.mvn/wrapper Update and fix maven wrapper (#2847) 2021-11-03 11:21:49 -04:00
.mvn_/wrapper Bump core to latest versions (#2154) 2020-11-03 15:43:37 -05:00
hapi-deployable-pom Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-android Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-android-realm Work on JPA 2017-02-02 06:23:28 -05:00
hapi-fhir-base Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-bom Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-checkstyle Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-cli Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-client Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-client-okhttp Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-converter Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-dist Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-docs Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jacoco Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jaxrsserver-base Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpa Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-base Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-elastic-test-utilities Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-ips Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-mdm Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-model Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-searchparam Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-subscription Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-test-dstu2 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-test-dstu3 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-test-r4 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-test-r4b Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-test-r5 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-test-utilities Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-jpaserver-uhnfhirtest Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-server Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-server-mdm Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-server-openapi Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-serviceloaders Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-spring-boot Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-sql-migrate Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-storage Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-storage-batch2 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-storage-batch2-jobs Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-storage-cr Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-storage-mdm Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-storage-test-utilities Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-dstu2 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-dstu2.1 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-dstu3 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-hl7org-dstu2 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-r4 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-r4b Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-structures-r5 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-test-utilities Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-testpage-overlay Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation-resources-dstu2 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation-resources-dstu2.1 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation-resources-dstu3 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation-resources-r4 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation-resources-r4b Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-fhir-validation-resources-r5 Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-tinder-plugin Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
hapi-tinder-test Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
osgi Demote PHI logging to debug or lower (#4430) 2023-01-13 15:34:29 +00:00
src/assembly Checkstyle cleanup (#4501) 2023-02-03 09:40:32 -05:00
tests Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
vagrant Bump dependencies for CVES (#3359) 2022-02-07 07:56:25 -05:00
.editorconfig Add framework for Bulk Import (#2538) 2021-04-14 17:41:32 -04:00
.gitignore breaking up package installer and package config (#4319) 2023-01-17 01:58:14 +00:00
.whitesource Add .whitesource configuration file 2021-04-29 13:42:31 +00:00
HELPWANTED.md Work on custom params 2017-02-02 20:37:58 -05:00
LICENSE.txt Add license and notice files 2015-03-25 22:32:32 -04:00
LOINC_NOTES.txt More work on loinc 2018-03-19 08:51:02 -04:00
NOTICE.txt Add license and notice files 2015-03-25 22:32:32 -04:00
README.md Improve batch2 error handling (#3482) 2022-03-26 17:40:12 -04:00
azure-pipelines.yml Checkstyle cleanup (#4501) 2023-02-03 09:40:32 -05:00
check_for_maven_updates.sh Fix up examples 2014-09-03 18:03:44 -04:00
lgtm.yml code coverage needs to run only for JACOCO PROFILE (#4230) 2022-11-02 15:34:27 -04:00
list_releases.sh Implement handleException on the server interceptor framework, as well 2014-11-07 14:26:59 -05:00
mvnw Update and fix maven wrapper (#2847) 2021-11-03 11:21:49 -04:00
mvnw.cmd Update and fix maven wrapper (#2847) 2021-11-03 11:21:49 -04:00
pom.xml Bulk export reducer step fix mergeback (#4606) 2023-03-01 14:52:36 -05:00
release-pipeline.yml update to docker installer tool for azure broke docker in the latest version, pinning the version to previous one (#4335) 2022-12-06 18:32:42 -05:00
snapshot-pipeline.yml Fix release pipeline Originally Issue 4106 process map to properties when uploading loinc terminology (#4246) 2022-11-04 13:57:19 -07:00
sync.sh Update resource defs 2015-12-01 18:35:24 -05:00
sync_dstu3.sh Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2016-07-01 14:31:25 -04:00
sync_ri.sh Bump to 1.0.2 FHIR definitions 2015-11-15 12:22:56 -05:00
sync_ri3.fish Bring DSTU3 structs up to FHIR R3 2017-04-18 07:48:38 -04:00
sync_ri3.sh Syn RI - Build still failing :( 2016-05-28 12:53:59 -04:00
sync_ri4.sh Squashed commit of the following: 2018-12-27 17:58:47 -05:00
sync_ri5.sh Bump core to latest versions (#2154) 2020-11-03 15:43:37 -05:00
sync_ri21.sh Update model and definitions to latest definitions 2016-01-30 11:08:16 -05:00
test-job-template.yml update to docker installer tool for azure broke docker in the latest version, pinning the version to previous one (#4335) 2022-12-06 18:32:42 -05:00
update_version.sh Force another travis build 2015-08-05 10:38:38 -04:00

README.md

HAPI FHIR

HAPI FHIR - Java API for HL7 FHIR Clients and Servers

License

CI/CD

CI Status (master) SNAPSHOT Pipeline Current Release
Build Status Build Status Release Artifacts

Coverage and Quality

codecov Language grade: Java

Documentation and wiki

Complete project documentation is available here: http://hapifhir.io

A demonstration of this project is available here: http://hapi.fhir.org/

This project is Open Source, licensed under the Apache Software License 2.0.

Please see this wiki page for information on where to get help with HAPI FHIR.

Please see Smile CDR for information on commercial support.