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🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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Tadgh d3367cfede
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 23:57:57 +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 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-android Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-android-realm Work on JPA 2017-02-02 06:23:28 -05:00
hapi-fhir-base Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-batch Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-bom Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-checkstyle Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-cli Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-client Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-client-okhttp Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-converter Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-dist Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-docs Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jacoco Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jaxrsserver-base Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpa Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-base Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-cql Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-elastic-test-utilities Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-mdm Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-model Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-searchparam Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-subscription Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-test-dstu2 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-test-dstu3 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-test-r4 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-test-r4b Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-test-r5 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-test-utilities Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-jpaserver-uhnfhirtest Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-server Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-server-mdm Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-server-openapi Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-spring-boot Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-sql-migrate Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-storage Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-storage-batch2 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-storage-batch2-jobs Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-storage-mdm Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-storage-test-utilities Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-dstu2 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-dstu2.1 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-dstu3 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-hl7org-dstu2 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-r4 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-r4b Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-structures-r5 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-test-utilities Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-testpage-overlay Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-validation Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-validation-resources-dstu2 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-validation-resources-dstu2.1 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-validation-resources-dstu3 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-validation-resources-r4 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-fhir-validation-resources-r5 Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-tinder-plugin Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
hapi-tinder-test Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
osgi encode narratives of contained resources (#3402) 2022-02-17 18:54:03 +00:00
src Standardize on one Transactional annotation (#4130) 2022-10-13 16:26:11 -04:00
tests Rel 6 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
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 fixed bug (#4069) 2022-09-26 13:43:11 +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 Add R4B Support (#4150) 2022-10-20 13:57:06 -07:00
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 2 mergeback (#4257) 2022-11-07 23:57:57 +00:00
release-pipeline.yml code coverage needs to run only for JACOCO PROFILE (#4230) 2022-11-02 15:34:27 -04:00
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 code coverage needs to run only for JACOCO PROFILE (#4230) 2022-11-02 15:34:27 -04:00
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.