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🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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longma1 0c42229985
Rel 6 8 2 mb (#5299) 
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)

* Initial failing test.

* Solution with changelog.

* fixing format.

* Addressing comment from code review.

* fixing failing test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* documentation update (#5154)

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Fix hsql jdbc driver deps (#5168)

Avoid non-included classes in jdbc driver dependencies.

* $delete-expunge over 10k resources will now delete all resources (#5144)

* First commit with very rough fix and unit test.

* Refinements to ResourceIdListStep and Batch2DaoSvcImpl.  Make LoadIdsStepTest pass.   Enhance Batch2DaoSvcImplTest.

* Spotless

* Fix checkstyle errors.

* Fix test failures.

* Minor refactoring.  New unit test.  Finalize changelist.

* Spotless fix.

* Delete now useless code from unit test.

* Delete more useless code.

* Test pre-commit hook

* More spotless fixes.

* Address most code review feedback.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Fix the noUrl case by passing an unlimited Pegeable instead.  Effectively stop using page size for most databases.

* Deprecate the old method and have it call the new one by default.

* updating documentation (#5170)

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* _source search parameter modifiers for Subscription matching (#5159)

* _source search parameter modifiers for Subscription matching - test, implementation and changelog

* Removal of meta tags during updates do not trigger subscription (#5181)

* Initial failing test.

* adding solution;
fixing documentation;

* spotless apply

* adding changelog

* modifying current test

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Issue 5173 get gateway everything doesnt return all patients (#5174)

* Failing test

* Also set offset and count in base DAO override

* Changelog

* Fix for specific case where count has been set in parameters

* spotless

* Improve checks

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)

* First commit with failing unit test and small tweaks.

* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead.  Add more detailed unit testing.

* Tweaks to logic and update the changelog.  Reverse all changes to TermReadSvcImpl.

* Revert PackageResourceParsingSvc to release branch baseline.

* Accept code reviewer suggestion to change changelog description.

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Fix link

* Remove target slf4j version

* dont use new API for a bit (#5191)

* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)

DropIdGeneratorTask.

* Dqm performance bug update and provider loader fix (#5180)

* update tests, move properties, update operation loader

* update wip

* remove test

* fixing tests, adding config

* update config and provider loader

* fix bundles

* fix cache settings on tests

* version bump and change log

* version bump

* fix formatting

* CVE-2022-45868

* wip cve change

* cve h2 add back in

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>

* bulkExportReuse with POST and GET (#5161)

* string manipulation

* Code to ensure bulkExportReuse works with POST and GET requests

* Added formatting changes

* Fixed tests that were not working

* Formatting

* Code clean up

* fixing test failures

* fixing test failures

* Removed arrOfParams to now utilize ObjectMapper

* Removing stack trace and adding an exception

* Fixed test issue

* formatting

* formatting

* Resolving code review comments

* Reduce size of subscription max results (#5194)

* Reduce MAX_SUBSCRIPTION_RESULTS to 10000

* Add changelog

* 5037 goldenresource remains when target resource deleted (#5038)

* draft test and fix

* remove unused fields

* remove unused fields

* remove unused fields

* draft test + solution for possible match case

* combine sql statement + more error checking

* add test case for possible duplicate

* add config for autodeleting grs

* refactoring, adding support for mongo, docs

* refactoring + fixing mongo queries

* add changelogs

* fix both way link removal

* clean up test comments

* rename method

* remove unnecessary bean

* merge master/resolve conflicts

* mvn spotless

* address comment

* changes to avoid version bumping

* spotless

* change error code

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* dont use new API for a bit (#5190)

* licenses

* Fixing terminology upload with large file. (#5204)

* create initial test

* adding fix;
adding changelog;

* fixing format.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* up version to 6.8.0 from snapshot

* fix up some duplicate deps for skipping

* Force deployment of other projects

* make dummy java class to pass sonatype checks

* make dummy java class to pass sonatype checks

* Cheeky test removal

* Another test removal

* Updating version to: 6.8.1 post release.

* adding back in tests for release pipelines

* Fix bad version insert

* Bump to core library version 6.0.22.2 (#5261)

* Bump to core library version 6.0.22.2

* Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2

* up version to 6.8.1

* Prevent remote deployment

* Updating version to: 6.8.2 post release.

* Re-add deploy plugin skip

* re-add version

* Bump core library version to 6.0.22.2

* Bump HAPI to 6.8.2-SNAPSHOT

* Fix up version enum

* Version bump

* Updating version to: 6.8.3 post release.

* mvn spotless:apply

---------

Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
 		2023-09-13 14:21:38 -07:00
.github wip (#5091) 2023-07-13 15:56:23 -07:00
.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 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-android rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-android-realm Work on JPA 2017-02-02 06:23:28 -05:00
hapi-fhir-base Rel 6 8 2 mb (#5299) 2023-09-13 14:21:38 -07:00
hapi-fhir-bom rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-checkstyle rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-cli rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-client rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-client-okhttp rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-converter rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-dist rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-docs Rel 6 8 2 mb (#5299) 2023-09-13 14:21:38 -07:00
hapi-fhir-jacoco rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jaxrsserver-base rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpa rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-base Fix timeout in large $everything operation (#5298) 2023-09-13 21:08:00 +00:00
hapi-fhir-jpaserver-elastic-test-utilities rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-hfql rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-ips rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-mdm rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-model rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-searchparam Allow absolute links for refs with an identifier (#5295) 2023-09-13 09:55:02 +00:00
hapi-fhir-jpaserver-subscription rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-test-dstu2 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-test-dstu3 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-test-r4 Fix timeout in large $everything operation (#5298) 2023-09-13 21:08:00 +00:00
hapi-fhir-jpaserver-test-r4b rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-test-r5 Allow absolute links for refs with an identifier (#5295) 2023-09-13 09:55:02 +00:00
hapi-fhir-jpaserver-test-utilities rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-jpaserver-uhnfhirtest rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-server rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-server-cds-hooks rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-server-mdm rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-server-openapi rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-serviceloaders rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-spring-boot rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-sql-migrate rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage-batch2 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage-batch2-jobs rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage-batch2-test-utilities rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage-cr rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage-mdm rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-storage-test-utilities rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-structures-dstu2 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-structures-dstu2.1 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-structures-dstu3 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-structures-hl7org-dstu2 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-structures-r4 Rel 6 8 2 mb (#5299) 2023-09-13 14:21:38 -07:00
hapi-fhir-structures-r4b rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-structures-r5 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-test-utilities rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-testpage-overlay rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation-resources-dstu2 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation-resources-dstu2.1 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation-resources-dstu3 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation-resources-r4 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation-resources-r4b rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-fhir-validation-resources-r5 rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-tinder-plugin rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
hapi-tinder-test rebuild golden resource from survivorship on link edit (#5250) 2023-09-12 23:03:24 -04:00
osgi use ClasspathUtil (#5263) 2023-08-31 13:23:00 -04:00
src/assembly Checkstyle cleanup (#4501) 2023-02-03 09:40:32 -05:00
tests Rel 6 8 2 mb (#5299) 2023-09-13 14:21:38 -07:00
vagrant Bump dependencies for CVES (#3359) 2022-02-07 07:56:25 -05:00
.editorconfig Modify editorconfig to match spotless rules (#5241) 2023-08-24 19:12:53 +00:00
.gitignore nickname svc refatoring (#5006) 2023-06-22 08:26:47 -04:00
.pre-commit-config.yaml New formatting rules and pre-commit hooks (#5027) 2023-07-11 17:36:44 -07:00
.whitesource Add .whitesource configuration file 2021-04-29 13:42:31 +00:00
HELPWANTED.md New formatting rules and pre-commit hooks (#5027) 2023-07-11 17:36:44 -07:00
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 New formatting rules and pre-commit hooks (#5027) 2023-07-11 17:36:44 -07:00
azure-pipelines.yml Initial HFQL SQL Implementation (#5083) 2023-07-21 22:51:23 +00:00
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 Rel 6 8 2 mb (#5299) 2023-09-13 14:21:38 -07:00
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 adding nightly build for SNAPSHOTS 2023-03-23 10:16:24 -04:00
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 merge release branch to master (#4811) 2023-05-03 19:51:43 +00:00
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.