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Batch2 workchunk states hapi (#5851)
* step 1

* updated batch 2 framework with READY state

* spotless

* remove entity manager

* spotless

* fixing up more tests for batch2

* updating documentation

* cleanup

* removing checkstyle violation

* code review points

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* review poitns finished

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* updated

* step 1

* updated

* sketch out test cases

* basic state transition shell work

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* waiting step 1

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* some tweaks

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* review comments 1

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* review points round 1

* revert

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* review fixes round 2

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* - Implemented GATE_WAITING state for the batch2 state machine.
- This will be the initial status for all workchunks of a gated job.
- made compatible with the equivalent "fake QUEUED" state in the Old batch2 implementation.
- Updated corresponding docs.
- added corresponding tests and changelog

* Revert "- Implemented GATE_WAITING state for the batch2 state machine."

This reverts commit 32a00f4b81.

* - Implemented GATE_WAITING state for the batch2 state machine.
- This will be the initial status for all workchunks of a gated job.
- made compatible with the equivalent "fake QUEUED" state in the Old batch2 implementation.
- Updated corresponding docs.
- added corresponding tests and changelog

* fixing a bug

* spotless

* fixing

* - fix merges conflicts
- set first chunk to be always created in READY

* - have only one path through the equeueReady method
- fixed tests

* - hid the over-powered transition function behind a proper state action

* spotless

* resolved review comments

* fixing tests

* resolved review comments

* resolved review comments

* resolved review comments

* resolved review comments

* resolved review comments

* updating migration script number

* fixed bugs

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* fix test high concurrency

* fixing a test

* code fix

* fixing tests in bulkexportit

* fixing tests

* fixing tests

* cleanup

* completed instance will not be sent to the reduction step service

* Revert "completed instance will not be sent to the reduction step service"

This reverts commit aa149b6691.

* Revert "Revert "completed instance will not be sent to the reduction step service""

This reverts commit e18f5796a1.

* removing dead code

* changed db query for step advance to take statuses as parameter instead

* test fixes

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* test fix

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* fixing tests

* migration fix

* fixing test

* testing pipeline with `testGroupBulkExportNotInGroup_DoesNotShowUp` disabled

* fixing some tests

* Add new race test for simultaneous queue/dequeue

* re-enabling `testGroupBulkExportNotInGroup_DoesNotShowUp`

* cascade tag deletes

* test fixes

* some logging

* a test case

* adding job id

* more test code

* marking purge checks

* test fix

* testing

* pausing schedulers on cleanup

* adding a wait

* max thread count guarantee

* fixing the tests again

* removing dead code

* spotless

* checking

* msg codes:

* Fixing a test

* review points

* spotless

* required pom values

* step 1 of reduction ready

* update

* reductoin ready

* annother test

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* cleanup

* cleanup

* simplifying check in reduction step

* review fixes

* updating version

* using 7.3.1

* adding check

* test finessing

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: tyner <tyner.guo@smilecdr.com>
2024-05-07 18:23:03 -04:00
.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 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-android Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-android-realm Work on JPA 2017-02-02 06:23:28 -05:00
hapi-fhir-base Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-bom Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-checkstyle Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-cli Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-client Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-client-okhttp Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-converter Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-dist Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-docs Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jacoco Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jaxrsserver-base Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpa Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-base Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-elastic-test-utilities Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-hfql Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-ips Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-mdm Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-model Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-searchparam Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-subscription Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-test-dstu2 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-test-dstu3 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-test-r4 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-test-r4b Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-test-r5 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-test-utilities Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-jpaserver-uhnfhirtest Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-server Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-server-cds-hooks Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-server-mdm Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-server-openapi Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-serviceloaders Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-spring-boot Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-sql-migrate Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage-batch2 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage-batch2-jobs Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage-batch2-test-utilities Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage-cr Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage-mdm Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-storage-test-utilities Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-dstu2 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-dstu2.1 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-dstu3 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-hl7org-dstu2 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-r4 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-r4b Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-structures-r5 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-test-utilities Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-testpage-overlay Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation-resources-dstu2 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation-resources-dstu2.1 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation-resources-dstu3 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation-resources-r4 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation-resources-r4b Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-fhir-validation-resources-r5 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-tinder-plugin Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
hapi-tinder-test Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
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 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
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 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
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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 Batch2 workchunk states hapi (#5851) 2024-05-07 18:23:03 -04:00
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 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 HAPI FHIR Dependency Bumps (#5576) 2024-01-14 14:15:08 -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.