Commit Graph

942 Commits

Author SHA1 Message Date
jamesagnew 8aef580aed Bump core library 2021-12-07 10:57:43 -05:00
Mark Iantorno d60d07b697
Validate contains change (#3209)
* wip

* The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version.

* pointing to stable core version

* review feedback

* Add changelog

Co-authored-by: markiantorno <miantorno@pop-os.localdomain>
2021-12-06 11:25:00 -05:00
James Agnew d072357c2a
Move graphql provider (#3214)
* Move graphql provider

* Version bump
2021-12-05 17:22:20 -05:00
James Agnew aa09e59255
Migrate to OpenAPI (#3206)
* Migrate to OpenAPI

* Update spring

* Test fix
2021-12-02 13:01:50 -05:00
jamesagnew 0099749a27 Bump thymeleaf version 2021-11-30 11:05:49 -05:00
James Agnew aae53d6ec7
Improve loading performance (#3197)
* Synthea perf work

* Cleanup

* Work on performance

* Ongoing perf work

* More perf work

* Perf work

* Test fixes

* Updates

* Test fix

* Test fixes

* Clean up tests

* Test cleanup

* Cleanup

* Add test

* One more perf tweak

* Fixes

* Add changelog

* Add changelog

* License header update

* License header updates
2021-11-28 10:47:30 -05:00
jmarchionatto d496ca98ad
Issue 3172 support member match operation (#3187)
* Suppress unresolved maven properties errors to avoid IntelliJ complains

* Support for $member-match operation

* Add more reference cases

* Adjust tests

* Add test and handle missed condition

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-11-26 14:20:14 -05:00
michaelabuckley 1487e03037
Publish test jars during snapshot build (#3162)
* publish test-jar from hapi-fhir-storage

* Extract BaseDateSearchDaoTests up to hapi-fhir-storage.

Share a date search tests between JPA and Mongo.

* Use ITestDataBuilder for setup

* Move Mongo date cases into common set

* cleanup

* More cleanup

* naming

* fix equal case

* Use -DskipTests instead of the more agressive -Dmaven.test.skip
2021-11-12 15:40:24 +00:00
michaelabuckley 7d7865ab17
Mb share jpa date tests (#3154)
* publish test-jar from hapi-fhir-storage

* Extract BaseDateSearchDaoTests up to hapi-fhir-storage.

Share a date search tests between JPA and Mongo.

* Use ITestDataBuilder for setup

* Move Mongo date cases into common set

* cleanup

* More cleanup

* naming
2021-11-10 21:07:36 +00:00
TipzCM 25c025cdee
3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)
* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-11-10 16:06:09 -05:00
TipzCM 59bf8b836f
Issue 3120 support adding retry extension (#3137)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

* issue-3120 updates for new release

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-11-03 18:21:10 -04:00
Tadgh a10c58e839
Bump version, add version to versionenum (#3135) 2021-11-02 09:40:56 -04:00
Tadgh 7c63441663
Revert "Issue 1134 retry mechanic on subscriptions (#3121)" (#3128)
This reverts commit 9b23e9e825.
2021-10-30 19:46:42 +00:00
TipzCM 9b23e9e825
Issue 1134 retry mechanic on subscriptions (#3121)
* issue-1134 initial work on adding retry handler

* issue-1134 subdscription creation fixes

* issue-1134 update the test

* issue-1134 retry policy off canonicalsubscription

* issue 1134 base subscription changes

* add failing test

* issue 1134 retry configs on base parameters

* issue 1134 passing forward params

* issue-1134 added more tests for making sure subscriptions create their channels correctly

* issue-1134 updates to get the retry to channels

* issue-1134 updating channel factory

* issue-1134 remove the dlq since it's not defineable

* issue-3120 changelog added

* issue-3120 cleaning up

* issue-3120 test fix

* issue-3120 review fixes

* issue-3120 fixed bad master merge

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-10-29 11:21:43 -04:00
jamesagnew e600663eb0 Credit for #2754 2021-10-27 05:57:38 -04:00
dependabot[bot] d94284b2e8
Bump wagon-scm from 3.0.0 to 3.4.3 (#3084)
Bumps wagon-scm from 3.0.0 to 3.4.3.

---
updated-dependencies:
- dependency-name: org.apache.maven.wagon:wagon-scm
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-10-21 18:41:38 -04:00
Tadgh 2d55af1ec4
Fix postgresql regression (#3101)
* Bump elastic version

* Fix broken types for sql builder in postgres

* Add changelog

* Fix changelog
2021-10-21 16:23:41 -04:00
dependabot[bot] bbcf202b90
Bump jersey_version from 3.0.0 to 3.0.3 (#3027)
Bumps `jersey_version` from 3.0.0 to 3.0.3.

Updates `jersey-server` from 3.0.0 to 3.0.3

Updates `jersey-container-servlet-core` from 3.0.0 to 3.0.3

Updates `jersey-container-jetty-http` from 3.0.0 to 3.0.3

Updates `jersey-media-moxy` from 3.0.0 to 3.0.3

---
updated-dependencies:
- dependency-name: org.glassfish.jersey.core:jersey-server
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: org.glassfish.jersey.containers:jersey-container-servlet-core
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: org.glassfish.jersey.containers:jersey-container-jetty-http
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: org.glassfish.jersey.media:jersey-media-moxy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-17 18:02:54 -04:00
Tadgh b427135b04
Patient/$everything _id parameter (#3077)
* Add tests. Add implementation in R4. Add changelog

* Wip partial fixup of other STU versions

* Updated usages of new patient type everything api

* Partial commit of incomplete documentation

* Remove docs

* Cut to token instead of string

* Bump hapi version due to breaking api changes
2021-10-17 14:34:33 +00:00
jamesagnew f6c8ecdc43 Credit for #3022 2021-10-17 09:09:22 -04:00
dependabot[bot] 7e87890ae3
Bump fhir_core_version from 5.5.4 to 5.5.7 (#3082)
Bumps `fhir_core_version` from 5.5.4 to 5.5.7.

Updates `org.hl7.fhir.utilities` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.convertors` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.validation` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.dstu2` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.dstu2016may` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.dstu3` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.r4` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.r4` from 5.5.4 to 5.5.7

Updates `org.hl7.fhir.r5` from 5.5.4 to 5.5.7

---
updated-dependencies:
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.utilities
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.convertors
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.validation
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.dstu2
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.dstu3
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.r4
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.r4:javadoc
  dependency-type: direct:production
  update-type: version-update:semver-patch
- dependency-name: ca.uhn.hapi.fhir:org.hl7.fhir.r5
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-17 07:01:33 -04:00
dependabot[bot] 41111cae29
Bump maven-enforcer-plugin from 3.0.0-M2 to 3.0.0 (#3078)
Bumps [maven-enforcer-plugin](https://github.com/apache/maven-enforcer) from 3.0.0-M2 to 3.0.0.
- [Release notes](https://github.com/apache/maven-enforcer/releases)
- [Commits](https://github.com/apache/maven-enforcer/compare/enforcer-3.0.0-M2...enforcer-3.0.0)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-enforcer-plugin
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-10-16 17:27:09 -04:00
dependabot[bot] e1a0a59c14
Bump maven-plugin-plugin from 3.5 to 3.6.0 (#1888)
Bumps [maven-plugin-plugin](https://github.com/apache/maven-plugin-tools) from 3.5 to 3.6.0.
- [Release notes](https://github.com/apache/maven-plugin-tools/releases)
- [Commits](https://github.com/apache/maven-plugin-tools/compare/maven-plugin-tools-3.5...maven-plugin-tools-3.6.0)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-10-16 17:26:46 -04:00
Tadgh 120443e561
Bump core version (#3067)
* Bump core version

* Changes for version bump

* Resolve NPE:

* Test fix

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-10-16 14:13:13 -04:00
dependabot[bot] a0388db672
Bump testcontainers_version from 1.15.3 to 1.16.0 (#3076)
Bumps `testcontainers_version` from 1.15.3 to 1.16.0.

Updates `testcontainers` from 1.15.3 to 1.16.0
- [Release notes](https://github.com/testcontainers/testcontainers-java/releases)
- [Changelog](https://github.com/testcontainers/testcontainers-java/blob/master/CHANGELOG.md)
- [Commits](https://github.com/testcontainers/testcontainers-java/compare/1.15.3...1.16.0)

Updates `elasticsearch` from 1.15.3 to 1.16.0
- [Release notes](https://github.com/testcontainers/testcontainers-java/releases)
- [Changelog](https://github.com/testcontainers/testcontainers-java/blob/master/CHANGELOG.md)
- [Commits](https://github.com/testcontainers/testcontainers-java/compare/1.15.3...1.16.0)

Updates `junit-jupiter` from 1.15.3 to 1.16.0
- [Release notes](https://github.com/testcontainers/testcontainers-java/releases)
- [Changelog](https://github.com/testcontainers/testcontainers-java/blob/master/CHANGELOG.md)
- [Commits](https://github.com/testcontainers/testcontainers-java/compare/1.15.3...1.16.0)

---
updated-dependencies:
- dependency-name: org.testcontainers:testcontainers
  dependency-type: direct:production
  update-type: version-update:semver-minor
- dependency-name: org.testcontainers:elasticsearch
  dependency-type: direct:production
  update-type: version-update:semver-minor
- dependency-name: org.testcontainers:junit-jupiter
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-15 06:28:33 -04:00
jamesagnew 39c5c757c2 Fix typo in root pom 2021-10-14 16:44:49 -04:00
jamesagnew 1c8f364f0e Credit for #3043 2021-10-14 16:37:13 -04:00
Jing Tang b25b186044
Remove the unused dependency on net.sf.saxon:Saxon-HE (#3043)
* Remove the unused dependency on net.sf.saxon:Saxon-HE

* Remove Saxon-HE dependency in hapi-fhir-jpaserver-base

* Remove unused comment in hapi-fhir-structures-dstu2.1/pom.xml
2021-10-14 16:34:48 -04:00
Tadgh 87e594d416
Bump JENA to deal with CVE-2021-29349 (#3063) 2021-10-13 16:17:43 -04:00
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016)
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
2021-10-11 16:47:37 -04:00
jamesagnew 2581cd1446 Bump postgres DB version 2021-10-04 10:54:33 -04:00
James Agnew d320b78ae1
Improve synthea ingest performance (#3033)
* Improve synthea ingest performance

* Tweaks

* Fix param splitting

* Update to test

* Add changelog

* Test fix

* Add some runtime checks

* Remove useless test

* Test fix
2021-10-04 05:46:06 -04:00
Ken Stevens 53c7476dae
hapi storage (#3024)
* first pass moving core storage classes to storage-api

* move term service apis

* nearly done

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* create new SearchConstants class to store platform independent search constants

* move a couple of subscription services

* move transaction processor adapter to storage

* version bump

* move searchparam

* fix test

* fix compile includes

* fix text

* fix docs
2021-09-23 22:04:46 -04:00
Ken Stevens 060791aeb4
hapi-fhir-storage-api (#3006)
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence

* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api

* move bulk import apis

* create hapi-fhir-jpa

* create hapi-fhir-jpa

* move CircularQueueCaptureQueriesListener to japi-fhir-jpa

* move mdm logs to storage-api

* move gziputil to storage-api

* move quartz scheduling to hapi-fhir-jpa

* move default subscription channel factory to storage-api

* consolidated batch constants

* correct accidental Logs change

* remove dependency of cdr-api on cdr-persistence

* fix javadoc

* pom descriptions

* review feedback
2021-09-21 15:36:08 +00:00
James Agnew 5554431146
Avoid dead SearchParameter links in CapabilityStatement (#2790)
* Avoid dead SearchParameter links in CapabilityStatement

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
Tadgh 9f778a5b82 Add attribution in the pom 2021-09-10 13:05:03 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929)
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

* rearrange method calls so persistence module can perform clear operation on its own

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* review feedback

* review feedback

* Remove inheritance

* fix beans

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2021-09-03 14:58:19 -04:00
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh bd0cf2b6ae Fix master pom reference 2021-08-23 15:38:16 -04:00
Tadgh 8145a2ecb2 Tidy pom 2021-08-12 10:05:13 -04:00
VK-SMILECDR 1e0f843d6c
2852 - Simplify java mail code (#2874)
* testing

* [2852] adding SimpleJavaEmail

* [2852] refactor email sender code

* [2852] dependency cleanup

* [2852] add missing dependency

* [2852] add missing spring framework test dependency

* [2852] add change log

* [2852] add change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* [2852] minor test code cleanup

* [2852] add more tests

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-08-09 15:59:47 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845)
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml

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

* review feedback

* review feedback

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

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

* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceSearch.java

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

* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java

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

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-07-29 19:18:49 -04:00
Tadgh e076b30eef bump Jetty for CVEs 2021-07-27 15:49:00 -04:00
Tadgh 07cb3ff427 Bump commons-compress version 2021-07-27 09:14:05 -04:00
Michael Buckley 0a256fef77 Upgrade net.java.dev.jna dependency to support Mac M1 ARM architecture. 2021-07-23 14:58:10 -04:00
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
jamesagnew 59653759ed Update tests 2021-06-23 15:58:14 -04:00