🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
Go to file
longma1 28a1a4d4df
Rel 7 0 mb 2 (#5714)
* pom bump to 7.0.0 (#5615)

* pom bump to 7.0.0

* add version enum

* fixed feb release name

---------

Co-authored-by: Long Ma <long@smilecdr.com>

* Check index existence on raw SQL creation (#5624)

* Add conditional check on index existence before we try again

* Add conditional check on index existence before we try again

* Changelog

* remit

* remit

* debug statements

* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)

* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.

* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.

* adding changelog and spotless.

* Fixing typo.

* Addressing comments from code review.

---------

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

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

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

* simple fix (#5630)

Co-authored-by: Long Ma <long@smilecdr.com>

* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)

* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation

* Oracle:  Ensure migrated database still takes large resource text updates (#5629)

* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.

* First stab at agreed upon solution.

* Fix error with 4001 by removing unnecessary annotation.

* Spotless and TODO.

* Remove annotation for good and set length to LONG32.

* Fix copyright year.

* Finalize changelog.

* Remove migration changes.  Fix unit test.

* Fix compile error.

* Log output.

* Refactor resource history code into new ResourceHistoryCalculator.

* Spotless.

* Convert record to POJO.

* Restore pre-17 switch statement.

* Finalize new resource history calculator code and tests.

* Spotless.

* Remove logging.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml

Apply code reviewer suggestion

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

* Code review feedback.

---------

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

* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)

* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.

* Minor change to fix test

* Rename changelog file

* Remove TODOs as they're replaced by reported issue

* Revert accidental change added with TODO removal

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* Fix Measure group id null pointer exception (#5620)

* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id

* add changelog

---------

Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>

* Rule evaluation:  Allow Bundles with PATCH Parameters (#5641)

* Remove parameters clause.

* Finalize changelog.  Add tests.  Finalize implementation.

* Undo changes to this test.

* Revert all changes to FhirQueryRuleImplTest.  Add new RuleImplOpTest.  Ensure that proper nested Bundle is created for test and other fixes.

* Tweak test.

* Use real rule applier in test and remove all mocks.

* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)

* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.

* Fix test

* Unimportant change to force fresh build

* Implement review suggestions

---------

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

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* Fix conditional creates without leading '?' (#5646)

* First commit with failing test.

* More tests and logs.

* More logs

* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().

* Simplify solution.  Add more tests.

* Changelog.

* javadoc

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Serializing changes for sensitive data (#5655)

* Add new senstiive data serializer

* Add new senstiive data serializer

* Add new senstiive data serializer

* Remove dead comments

* Change up the test

* review comments

* wip

* Tighten tests and push annotation down

* Tighten tests and push annotation down

* Changelog

* Add test

* 7.0.1-SNAPSHOT bump

* Error code

* Add method used by CDR

* add version enum

* Fix test

* Revert change to other safe version to stop problem with deprecated field

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Descendent fix (#5669)

* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>

* pom bump, doc add, version enum add (#5616)

Co-authored-by: Long Ma <long@smilecdr.com>

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

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

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* $poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681)

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor.

* Fix NPE on -export-status operation with PatientIdPartitionInterceptor

* 5654 measurescorer bug for denominator exception (#5677)

* update measure bundles and tests for enforced populationId specification on Measure group resources

* bump CR version to PRE17

* fix bug in versionEnumTest

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698)

* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type.

* Spotless fix

* Address code review comments

* version bump to 7.0.0

* pipeline fix

* Update java home

* Updating version to: 7.0.1 post release.

* post mergeback cleanup

* bump clinical-reasoning.version to pre17

* test fix

* version bump to 7.1.5-snapshot

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
2024-02-23 11:03:26 -07:00
.github Fix publish pipeline (#5613) 2024-01-19 23:23:26 +00:00
.mvn/wrapper Jakarta/Javax Servlet Migration (#5429) 2023-12-03 11:15:37 -05:00
.mvn_/wrapper Bump core to latest versions (#2154) 2020-11-03 15:43:37 -05:00
hapi-deployable-pom Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-android Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-android-realm
hapi-fhir-base Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-bom Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-checkstyle Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-cli Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-client Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-client-okhttp Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-converter Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-dist Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-docs Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jacoco Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jaxrsserver-base Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpa Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-base Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-elastic-test-utilities Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-hfql Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-ips Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-mdm Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-model Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-searchparam Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-subscription Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-test-dstu2 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-test-dstu3 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-test-r4 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-test-r4b Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-test-r5 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-test-utilities Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-jpaserver-uhnfhirtest Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-server Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-server-cds-hooks Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-server-mdm Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-server-openapi Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-serviceloaders Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-spring-boot Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-sql-migrate Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage-batch2 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage-batch2-jobs Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage-batch2-test-utilities Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage-cr Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage-mdm Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-storage-test-utilities Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-dstu2 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-dstu2.1 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-dstu3 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-hl7org-dstu2 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-r4 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-r4b Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-structures-r5 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-test-utilities Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-testpage-overlay Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation-resources-dstu2 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation-resources-dstu2.1 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation-resources-dstu3 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation-resources-r4 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation-resources-r4b Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-fhir-validation-resources-r5 Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-tinder-plugin Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
hapi-tinder-test Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
osgi Jakarta/Javax Servlet Migration (#5429) 2023-12-03 11:15:37 -05:00
src/assembly Checkstyle cleanup (#4501) 2023-02-03 09:40:32 -05:00
tests Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
vagrant Bump dependencies for CVES (#3359) 2022-02-07 07:56:25 -05:00
.editorconfig IPS API Refactor (#5682) 2024-02-11 10:43:56 -05:00
.gitignore nickname svc refatoring (#5006) 2023-06-22 08:26:47 -04:00
.pre-commit-config.yaml Update pre-commit from 0.3.3 to 0..3.4. (#5537) 2023-12-06 00:52:53 +00:00
.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
LOINC_NOTES.txt
NOTICE.txt
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
lgtm.yml code coverage needs to run only for JACOCO PROFILE (#4230) 2022-11-02 15:34:27 -04:00
list_releases.sh
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 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
release-pipeline.yml Rel 7 0 mb 2 (#5714) 2024-02-23 11:03:26 -07:00
snapshot-pipeline.yml Fix publish pipeline (#5613) 2024-01-19 23:23:26 +00:00
sync.sh
sync_dstu3.sh
sync_ri.sh
sync_ri3.fish
sync_ri3.sh
sync_ri4.sh
sync_ri5.sh Bump core to latest versions (#2154) 2020-11-03 15:43:37 -05:00
sync_ri21.sh
test-job-template.yml HAPI FHIR Dependency Bumps (#5576) 2024-01-14 14:15:08 -05:00
update_version.sh

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.