🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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Etienne Poirier fb3e141c4d
Messages submitted to the subscription pipeline are lost when submission fails. (#4733)
* One more fix for #4467

* Enabling massIngestionMode causes incomplete resource deletion (#4476)

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

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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.

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

* Change visibility of migration method (#4471)

* change migration visibility

* add empty migration method for 640

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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.

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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

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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

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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.

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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

* initial test implementation/changes and solution wiring.

* adding support for jpa/mongo abstraction.

* refact completed.  need to start implementing scheduling of subscription re-submission with the scheduler service.

* post release, merging in master.

* wip: commit before merging in branch master.

* wip: resuming work on the issue.

* wip: before merging in master.

* wip: partial implementation of mongo support.

* wip: more work to support partial implementation on mongo.

* Test implementation

* providing method getMessageKeyOrDefault();

* providing changelog

* preping codereview.

* wip: passing tests

* wip: finally solving the Meta issue.

* wip: adjusting interfaces

* Adding IT and

* IT test;
fixing rollback issue.

* removing non required logging

* fixing merge conflict

* Preparing for code review.

* Preparing for code review.

* Compiling code after merging in master.

* Fixing checkstyle failure.

* Modifications towards getting all tests to pass.

* addressing comments from code review.

* compiling code after switching target merge branch to rel_pub_2023_05

* compiling code after switching target merge branch to rel_6_6

* Addressing comments made in design meeting.  wip.

* Addressing comments made in design meeting. finally completed.
and last 2 comments addressed.

* removing non required override

* reverting changes as they are not required.

* Modified test and implementation.

* implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only.

* fix tests by modifying the matchingInterceptor to call pointcut when processing

* fixing more tests.

* WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue

* fixing circular dependency

* Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor.

* bumping version 6.7.7-SNAPSHOT

* bumping HAPI version to 6.7.7-SNAPSHOT

* fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline.

* passing all tests.

* unbumping to 6.7.7

* compiling after merging in master.

* creating a custom hapi version

* providing an synchronous subscription matcher interceptor for testing.

* updating pom version to generate artifacts.

* fixing tests, WIP/0

* fixing tests, WIP/1

* fixing tests, WIP/2

* Matching entity annotation with migration task declarations.

* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.

* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.

* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc].

* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again.

* Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction.

* bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline.

* bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline.

* Formatter changes.

* add generic

* add generic

* Addressing code review comments.

* Adding file asynch_subscription_610.md to docs/upgrades

* changing poms to 6.9.2-SNAPSHOT before merging in master.

* compiling after merging in master.

* Lowering logging level to debug.

* Bumping to 6.9.3-SNAPSHOT

* Bumping hapi version to 6.9.4-SNAPSHOT

* Adding update documentation.

* Modifying update file following review.

---------

Co-authored-by: James Agnew <jamesagnew@gmail.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: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-08-28 12:47:53 -04:00
.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 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-android Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-android-realm Work on JPA 2017-02-02 06:23:28 -05:00
hapi-fhir-base Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-bom Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-checkstyle Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-cli Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-client Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-client-okhttp Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-converter Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-dist Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-docs Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jacoco Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jaxrsserver-base Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpa Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-base Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-elastic-test-utilities Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-hfql Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-ips Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-mdm Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-model Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-searchparam Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-subscription Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-test-dstu2 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-test-dstu3 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-test-r4 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-test-r4b Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-test-r5 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-test-utilities Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-jpaserver-uhnfhirtest Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-server Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-server-cds-hooks Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-server-mdm Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-server-openapi Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-serviceloaders Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-spring-boot Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-sql-migrate Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage-batch2 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage-batch2-jobs Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage-batch2-test-utilities Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage-cr Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage-mdm Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-storage-test-utilities Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-dstu2 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-dstu2.1 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-dstu3 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-hl7org-dstu2 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-r4 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-r4b Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-structures-r5 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-test-utilities Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-testpage-overlay Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation-resources-dstu2 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation-resources-dstu2.1 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation-resources-dstu3 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation-resources-r4 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation-resources-r4b Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-fhir-validation-resources-r5 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-tinder-plugin Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
hapi-tinder-test Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
osgi try removing fork count from surefire (#4752) 2023-04-20 13:58:35 -04:00
src/assembly Checkstyle cleanup (#4501) 2023-02-03 09:40:32 -05:00
tests Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
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 Messages submitted to the subscription pipeline are lost when submission fails. (#4733) 2023-08-28 12:47:53 -04:00
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.