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🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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Tadgh 428acff31b
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 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'

* 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 21:16:44 +00:00
.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 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-android JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-android-realm Work on JPA 2017-02-02 06:23:28 -05:00
hapi-fhir-base 6.4.0 Mergeback (#4563) 2023-02-17 21:16:44 +00:00
hapi-fhir-bom JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-checkstyle JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-cli JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-client JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-client-okhttp JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-converter JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-dist JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-docs 4523 subscription sources (#4543) 2023-02-17 13:09:06 -05:00
hapi-fhir-jacoco JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jaxrsserver-base JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpa JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-base 4523 subscription sources (#4543) 2023-02-17 13:09:06 -05:00
hapi-fhir-jpaserver-elastic-test-utilities JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-ips JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-mdm JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-model JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-searchparam JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-subscription 6.4.0 Mergeback (#4563) 2023-02-17 21:16:44 +00:00
hapi-fhir-jpaserver-test-dstu2 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-test-dstu3 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-test-r4 4523 subscription sources (#4543) 2023-02-17 13:09:06 -05:00
hapi-fhir-jpaserver-test-r4b JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-test-r5 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-jpaserver-test-utilities 4523 subscription sources (#4543) 2023-02-17 13:09:06 -05:00
hapi-fhir-jpaserver-uhnfhirtest JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-server JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-server-mdm JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-server-openapi Revert "Clean up dependencies (#4306)" (#4557) 2023-02-16 00:30:29 +00:00
hapi-fhir-serviceloaders 6.4.0 Mergeback (#4563) 2023-02-17 21:16:44 +00:00
hapi-fhir-spring-boot JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-sql-migrate JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-storage 6.4.0 Mergeback (#4563) 2023-02-17 21:16:44 +00:00
hapi-fhir-storage-batch2 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-storage-batch2-jobs JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-storage-cr typedbundleprovider getallresources override (#4552) 2023-02-16 20:59:40 +00:00
hapi-fhir-storage-mdm JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-storage-test-utilities JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-structures-dstu2 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-structures-dstu2.1 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-structures-dstu3 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-structures-hl7org-dstu2 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-structures-r4 Revert "Clean up dependencies (#4306)" (#4557) 2023-02-16 00:30:29 +00:00
hapi-fhir-structures-r4b JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-structures-r5 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-test-utilities JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-testpage-overlay JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-validation JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-validation-resources-dstu2 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-validation-resources-dstu2.1 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-validation-resources-dstu3 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-validation-resources-r4 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-fhir-validation-resources-r5 JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-tinder-plugin JPA config refactoring (#4545) 2023-02-15 08:43:01 -05:00
hapi-tinder-test JPA config refactoring (#4545) 2023-02-15 08:43:01 -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 JPA config refactoring (#4545) 2023-02-15 08:43:01 -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 6.4.0 Mergeback (#4563) 2023-02-17 21:16:44 +00:00
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.