e600663eb0
Credit for #2754
2021-10-27 05:57:38 -04:00
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
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
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
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
f6c8ecdc43
Credit for #3022
2021-10-17 09:09:22 -04:00
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
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
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
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
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
39c5c757c2
Fix typo in root pom
2021-10-14 16:44:49 -04:00
1c8f364f0e
Credit for #3043
2021-10-14 16:37:13 -04:00
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
87e594d416
Bump JENA to deal with CVE-2021-29349 ( #3063 )
2021-10-13 16:17:43 -04:00
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
2581cd1446
Bump postgres DB version
2021-10-04 10:54:33 -04:00
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
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
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
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
9f778a5b82
Add attribution in the pom
2021-09-10 13:05:03 -04:00
3ec47cb0ba
Bump version as we break the localcontainerentitymanagerfactory bean constructors args
2021-09-07 13:58:22 -04:00
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
37ad73a422
Bump PRE version so we don't conflict downstream
2021-08-23 15:42:18 -04:00
bd0cf2b6ae
Fix master pom reference
2021-08-23 15:38:16 -04:00
8145a2ecb2
Tidy pom
2021-08-12 10:05:13 -04:00
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
4fadc62066
Bump Hapi Version
2021-08-06 13:44:04 -04:00
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
e076b30eef
bump Jetty for CVEs
2021-07-27 15:49:00 -04:00
07cb3ff427
Bump commons-compress version
2021-07-27 09:14:05 -04:00
0a256fef77
Upgrade net.java.dev.jna dependency to support Mac M1 ARM architecture.
2021-07-23 14:58:10 -04:00
a5e6674e84
Version bump to 5.5.0-PRE7-SNAPSHOT
2021-07-22 08:41:16 -04:00
f66f9b992e
Bump pre-version as this will break downstream implementations
2021-06-30 15:37:19 -04:00
59653759ed
Update tests
2021-06-23 15:58:14 -04:00
8b205b23d0
Fix history paging ( #2741 )
...
* Fix history paging
* Add changelog
* Add license header
2021-06-18 17:47:51 -04:00
659efa786c
ValueSet Expansion Should Preserve Order ( #2724 )
...
* Add test
* FIxed
* Add changelog
* Add test
* Intermittent test failure fix
* Build fix
* Build fix
* Test fix
* Test fixes
* Fix checkstyle issue
* Test fix
* Add test logging
2021-06-16 07:20:59 -04:00
134631fdee
Convert delete expunge to use Spring Batch ( #2697 )
...
* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
2021-06-15 10:36:05 -04:00
376a84d213
Version bump
2021-06-14 13:12:34 -04:00
c4b96d6dc7
Bump jetty_version from 9.4.39.v20210325 to 9.4.42.v20210604 ( #2722 )
...
Bumps `jetty_version` from 9.4.39.v20210325 to 9.4.42.v20210604.
Updates `jetty-http` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-servlets` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-io` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-continuation` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `jetty-security` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-servlet` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-server` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-util` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-webapp` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-xml` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `websocket-api` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `websocket-client` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `websocket-server` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `jetty-maven-plugin` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
---
updated-dependencies:
- dependency-name: org.eclipse.jetty:jetty-http
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-servlets
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-io
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-continuation
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-security
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-servlet
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-server
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-util
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-webapp
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-xml
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-api
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-client
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-server
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-maven-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>
2021-06-11 15:54:48 -04:00
dc627dc019
Add bulk export authorization layer ( #2712 )
...
* Add bulk export authorization layer
* Add docs
* Version bump
* Authorize any
* Add bulk export - all
* Address lgtm issue
2021-06-06 20:47:43 -04:00
fe763dd2d6
Upgrade deps ( #2695 )
...
* Upgrade deps
* Fix build error
* Branch tweak
* Build fix
* Build fix
* Undo bump
* Test fixes
2021-06-01 12:03:29 -04:00
f5c75e80de
Credit for #2693
2021-06-01 10:53:53 -04:00
786112284b
Bump spring version ( #2687 )
2021-05-30 19:04:14 -04:00
8d377fbf76
Add bulk import instrumentation ( #2685 )
...
* Add batch job instrumentation
* Add bulk import instrumentation
* Fix build
2021-05-30 11:47:51 -04:00
2c722e64c2
Add support for including qualified star syntax ( #2672 )
...
* Add support for including qualified star syntax
* Add changelog
* Add docs
* Build fix
2021-05-23 16:50:37 -04:00
ff2698d4d1
Merge branch 'rel_5_4'
2021-05-19 09:22:11 -04:00
994f09e125
Version bump
2021-05-18 21:05:50 -04:00
de56f440cb
Version bump
2021-05-18 17:14:14 -04:00
b31bb945ad
Add include clause to MSSQL forcedid table index ( #2659 )
...
* Add include clause to MSSQL forcedid table index
* Add changelog
* Test fix
* Bump MSSQL version
2021-05-16 19:14:51 -04:00
2068372998
Version bump
2021-05-07 17:43:54 -04:00
63c4b22cd3
Undo bump
2021-05-07 17:42:50 -04:00
17e41520a4
Version bump
2021-05-07 17:41:39 -04:00
9e61136c2d
Bump greenmail from 1.5.11 to 1.6.3 ( #2626 )
...
Bumps [greenmail](https://github.com/greenmail-mail-test/greenmail ) from 1.5.11 to 1.6.3.
- [Release notes](https://github.com/greenmail-mail-test/greenmail/releases )
- [Commits](https://github.com/greenmail-mail-test/greenmail/compare/release-1.5.11...release-1.6.3 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-05-03 17:31:03 -04:00
91fa23b11a
Bump fhir_core_version from 5.3.10 to 5.3.11 ( #2625 )
...
Bumps `fhir_core_version` from 5.3.10 to 5.3.11.
Updates `org.hl7.fhir.utilities` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.convertors` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.validation` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu2` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu2016may` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu3` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r4` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r4` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r5` from 5.3.10 to 5.3.11
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-05-03 07:58:55 -04:00
5db01f3139
Build fixes
2021-05-03 05:57:45 -04:00
593230f6bf
Fix openapi redirect ( #2624 )
...
* Fix redirect for openapi
* FIx deps
2021-05-03 05:32:34 -04:00
0cea403800
Fix vulnerability warning on maven plugin ( #2621 )
...
* Fix vulnerability warning on maven plugin
* Compile fixes
* Fix bootstrap dep
* Test fix
* Fix tests
* FIx deps
2021-05-02 12:14:32 -04:00
970a9884f0
Avoid tag definition constraint ( #2620 )
...
* Avoid tag definition constraint failure
* Version bumps
* Add changelog
* Avoid guava issue
* Test fix
* Test fix
* Bump pom
2021-05-01 17:16:15 -04:00
292b350f2c
Bump Junit for to avoid OWASP flag ( #2618 )
2021-04-30 14:39:16 -04:00
983d811af6
Merge pull request #2587 from hapifhir/issue-2585-enhance-placeholder-targets-logic
...
Issue 2585 enhance placeholder targets logic
2021-04-30 12:55:27 -04:00
78271a2931
Create tests for all possiblye use cases
2021-04-29 15:25:11 -04:00
646faa10e1
2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.10 ( #2545 )
...
* 2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.9.
* 2540 - Updated the Unit Test messages due to the upgraded dependencies.
* 2540 - Fixed some additional Unit Test message checks.
* 2540 - Updated the POM to refer to fhir_core_version 5.3.10-SNAPSHOT so a FULL Pipeline Build can run to verify that everything is fixed now.
* 2540 - Added some DEBUG Sysout logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Added some more logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Updated a Unit Test to account for a newly returned search param.
* 2540 - Updated a Unit Test to account for a newly returned search param and removed some debug output.
2021-04-29 15:00:37 -04:00
239d2496ea
CQL hardening and Dstu3 unit tests ( #2450 )
...
* WIP for elm caching
* Bug fixes and a working DSTU3 unit test
* More tests, Address review feedback, add initial docs
* Update to cql-evaluator 1.2.0
* Fixes for documentation
2021-04-29 14:52:13 -04:00
95d7ba6fa8
Streamline Search SQLs ( #2576 )
...
* Streamline SQL queries
* SQL query tidying
* Add changelog
* Test fixes
* Tests passing
* Ongoing work
* Test fixes
* Test fixes
* Build fix
* Cleanup
* Fixes
2021-04-28 10:29:09 -04:00
1d054054c7
Test fixes
2021-04-27 07:03:24 -04:00
987264b271
Version bump JENA
2021-04-25 17:38:04 -04:00
2ba1005762
OpenAPI Support ( #2560 )
...
* Start work on OpenAPI
* Fixes
* Work on OpenAPI
* Cleanup
* Cleanup
* More swagger work
* Build fix
* More work
* More work
* Add documentation
* Docs fixes
* Add changelog
* License updates
* Add API
* Cleanup
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Work on scripts
* Add docs
* Compile fix
* Work on fixes
* Fix tests
* Test fix
* Test fix
* Build fix
* Tests
* Build fix
* Work on pipeline
* Version bump
* Test fix
* Version bump
* Test fix attempts
* Test fix
* Test fix
* Remove accidentally committed files
* Fixes
* Tets fixes
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Test fixes
* License header updates
* test fix
* Test fixes
* Test fix
* Test fixes
* Test fix
* Checkstyle bump
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
2021-04-25 15:40:50 -04:00
4e266462ec
Bumped up version due to breaking changes
2021-04-20 16:17:27 -04:00
d94611edf6
Bump junit_version from 5.7.0 to 5.7.1 ( #2554 )
...
Bumps `junit_version` from 5.7.0 to 5.7.1.
Updates `junit-jupiter` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Updates `junit-jupiter-api` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Updates `junit-jupiter-engine` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Updates `junit-jupiter-params` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-04-15 08:23:30 -04:00
05b1323638
Bump jarchivelib from 1.0.0 to 1.1.0 ( #2553 )
...
Bumps [jarchivelib](https://github.com/thrau/jarchivelib ) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/thrau/jarchivelib/releases )
- [Commits](https://github.com/thrau/jarchivelib/compare/v1.0.0...v1.1.0 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-04-15 08:21:33 -04:00
9a67f3ee0c
Bump spring_boot_version from 2.4.1 to 2.4.4 ( #2550 )
...
Bumps `spring_boot_version` from 2.4.1 to 2.4.4.
Updates `spring-boot-starter-test` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-test` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-maven-plugin` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-dependencies` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-autoconfigure` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-configuration-processor` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-04-14 20:09:37 -04:00
ca2088f3ad
Add framework for Bulk Import ( #2538 )
...
* Start work on bul;k import
* Work on bulk import
* Have batch working
* Working
* Working
* More work
* More work on bulk export
* Address fixmes
* License header updates
* Test fixes
* License header updates
* Test fix
* Test fix
* Version bumps
* Work on config
* Test cleanup
* One more version bump
* Version bump
* CLeanup
* A few additions
* Test fixes
* Test fix
* Test fix
* Migration fix
* Test fix
* Test fix
2021-04-14 17:41:32 -04:00
7cf061d76b
Jetty version bump
2021-04-06 21:15:11 -04:00
a6cbf7eebd
Add support for hierarchycal valueset expansion ( #2525 )
...
* Add support for hierarchycal valueset expansion
* Add changelog
* Add tests
* Cleanup
* Test fix
* Test fixes
2021-04-06 17:36:54 -04:00
b617c7690d
Search Parameter Infrastructure Cleanup ( #2522 )
...
* Search param service cleanup
* Work on collapsing search param
* Search param cleanup
* Work on build
* Test fix
* Test fixes
* Ongoing work
* Test fix
* Compile fix
* Test fixes
* Test fix
* Test fix
* License header updates
* Remove fixme
* Cleanup
* Cleanup
2021-04-05 17:40:10 -04:00
8759cdae00
Additional cleanup
2021-03-30 08:20:14 -04:00
b720c32c1d
Version bump
2021-03-29 18:23:16 -04:00
dc41d5ad61
Add terminology mapping and display population interceptors ( #2488 )
...
* Start work on code mapping interceptors
* Work on generation
* Add terminology mapping and display population interceptors
* Add changelog
* License header updates
* Test fixes
* Fix typo
* Interceptor fixes
* License header update
* Test fixes
* Mapping fixes
* Version bump
* License header updates
* Add null tests
* Add null guard
* Intermittent fix
2021-03-21 12:03:57 -04:00
807d9d53f0
Improve performance for large transactions ( #2462 )
...
* Performance tweaks
* Work on processing speed
* Disable no longer relevant tests
* Work on performance
* Work on tests
* Work on large transaction performance
* Add changelog
* Perf tweaks
* Test fixes
* Resolve FIXME
* Fixes
* Test cleanup
* Fix broken changelog entry
2021-03-09 18:16:02 -05:00
11ee6dedd3
Address CVE-2020-27223; bumped minor version of Jetty in root POM
2021-03-06 16:33:05 -05:00
b108e43600
Allow partition date for non-partitionable resources ( #2407 )
...
* Allow partition date for searchparam resources
* Cleanup
* Test fix
* Documentation update
* Docs tweak
2021-02-22 20:49:09 -05:00
3eda19c65a
Version bump ( #2400 )
...
* Version bump
* Docs changes
* Docs tweaks
* Docs tweak
* Spelling fixes
* Docs tweaks
2021-02-18 11:07:49 -05:00
919c1dbddc
Version bump to 5.3.0
2021-02-17 07:10:13 -05:00
028ef1b088
Credit for #2365
2021-02-08 09:15:04 -05:00
da847ad08a
Credit for #2282
2021-02-07 12:32:41 -05:00
703f7b2e65
Bump mariadb-java-client from 2.5.1 to 2.7.2 ( #2334 )
...
Bumps [mariadb-java-client](https://github.com/mariadb-corporation/mariadb-connector-j ) from 2.5.1 to 2.7.2.
- [Release notes](https://github.com/mariadb-corporation/mariadb-connector-j/releases )
- [Changelog](https://github.com/mariadb-corporation/mariadb-connector-j/blob/master/CHANGELOG.md )
- [Commits](https://github.com/mariadb-corporation/mariadb-connector-j/compare/2.5.1...2.7.2 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-02-06 17:34:26 -05:00
cfc5b87e3e
Removed an old comment from the root pom. ( #2359 )
2021-02-04 15:21:39 -05:00
222bb7a8c0
Update to release versions of cql components ( #2357 )
2021-02-04 15:00:03 -05:00
e195bdc065
Try to avoid codecov fluctuations ( #2344 )
...
* Try to avoid codecov fluctuations
* Less slowdown
* Another build tweak
* Build tweak
* Container bump
* Another build attempt
* One more test
2021-02-03 09:44:57 -05:00
c0142a67b1
Credit for #2340
2021-02-02 14:27:42 -05:00
d65ed820a5
Javadoc build fix
2021-02-01 12:13:47 -05:00
2308d8f44b
Merge CQL Initial Implementation Into master ( #2330 )
...
* CQL initial implementation
2021-01-29 16:35:38 -05:00
589eb3158e
Credit for #2310
2021-01-29 11:02:51 -05:00
909d9f742c
Enable Auto-reference versions in JPA ( #2323 )
...
* Automatic reference versions
* Auto reference versions
* resolve fixmes
* Add changelog
* Test fixes
* Test fixes
* Resolve fixmes
* Work on versioning
* Add support for _includes
* Update headers
* Change visibility
* One more tweak
* One more API tweak
* Fixes
* Account for review comments
* Fix errorprone reported issue
* Test fix
* Test fixes
* Test fixes
2021-01-27 14:49:10 -05:00
feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 ( #2289 )
...
* Bump jaxb-runtime from 2.3.1 to 3.0.0
Bumps jaxb-runtime from 2.3.1 to 3.0.0.
Signed-off-by: dependabot[bot] <support@github.com>
* Bump jaxb-runtime from 2.3.1 to 3.0.0
Bumps jaxb-runtime from 2.3.1 to 3.0.0.
Signed-off-by: dependabot[bot] <support@github.com>
* Add jakarta bindings
* Dependency cleanup
* More depndency cleanup
* Work on deps
* Replace transaction annotation
* Cleanup
* Another fix
* Build fix
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-22 11:24:23 -05:00
7159d65902
bump databind version for CVE
2021-01-21 10:03:16 -05:00
14b0688f69
Bump core version to 5.2.16 ( #2308 )
...
* Bump core library version
* Test fix
* Build fixes
* Some test fixes
* One more bit of docs
* Build fix
* Test fix
* Test fix
* Docs fix
2021-01-21 05:30:23 -05:00
fa17ea35cd
Minor version bump for CVE-2021-22132
2021-01-20 11:31:00 -05:00
2db35f4dcb
Bump spring_version from 5.3.2 to 5.3.3 ( #2295 )
...
Bumps `spring_version` from 5.3.2 to 5.3.3.
Updates `spring-beans` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-context` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-context-support` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-core` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-jdbc` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-messaging` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-orm` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-test` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-tx` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-web` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-webmvc` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Updates `spring-websocket` from 5.3.2 to 5.3.3
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.3.2...v5.3.3 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-17 17:43:11 -05:00
391a6d1a3f
Bump ph-schematron from 5.2.0 to 5.6.5 ( #2184 )
...
* Bump ph-schematron from 5.2.0 to 5.6.5
Bumps [ph-schematron](https://github.com/phax/ph-schematron ) from 5.2.0 to 5.6.5.
- [Release notes](https://github.com/phax/ph-schematron/releases )
- [Commits](https://github.com/phax/ph-schematron/compare/ph-schematron-parent-pom-5.2.0...ph-schematron-parent-pom-5.6.5 )
Signed-off-by: dependabot[bot] <support@github.com>
* Fix compile error
* Build fix
* Add test logging
* Test fix
* Resolve classpath duplicates
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-17 14:27:26 -05:00
cc2a1c16c8
Bump commons-collections4 from 4.3 to 4.4 ( #2292 )
...
Bumps commons-collections4 from 4.3 to 4.4.
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-17 13:27:48 -05:00
9d8bbaf868
Add credit for #2054
2021-01-17 09:44:18 -05:00
8a0b0885f2
Bump jersey_version from 2.25.1 to 3.0.0 ( #2245 )
...
Bumps `jersey_version` from 2.25.1 to 3.0.0.
Updates `jersey-server` from 2.25.1 to 3.0.0
Updates `jersey-container-servlet-core` from 2.25.1 to 3.0.0
Updates `jersey-container-jetty-http` from 2.25.1 to 3.0.0
Updates `jersey-media-moxy` from 2.25.1 to 3.0.0
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-16 19:13:54 -05:00
472eba040a
Bump jansi from 1.18 to 2.1.1 ( #2253 )
...
Bumps [jansi](https://github.com/fusesource/jansi ) from 1.18 to 2.1.1.
- [Release notes](https://github.com/fusesource/jansi/releases )
- [Changelog](https://github.com/fusesource/jansi/blob/master/changelog.md )
- [Commits](https://github.com/fusesource/jansi/compare/jansi-project-1.18...jansi-2.1.1 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-16 19:05:31 -05:00
1dc4fb2206
Make quantity indexes use double datatype ( #2290 )
...
* Make quantity indexes use double datatype
* Add changelog
* Test fixes
* Test fixes
* Disable test
2021-01-16 18:44:15 -05:00
24ac055b50
Bump jackson_version from 2.11.2 to 2.12.1 ( #2287 )
...
Bumps `jackson_version` from 2.11.2 to 2.12.1.
Updates `jackson-annotations` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson/releases )
- [Commits](https://github.com/FasterXML/jackson/commits )
Updates `jackson-core` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson-core/releases )
- [Commits](https://github.com/FasterXML/jackson-core/compare/jackson-core-2.11.2...jackson-core-2.12.1 )
Updates `jackson-datatype-jsr310` from 2.11.2 to 2.12.1
Updates `jackson-dataformat-yaml` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson-dataformats-text/releases )
- [Commits](https://github.com/FasterXML/jackson-dataformats-text/compare/jackson-dataformats-text-2.11.2...jackson-dataformats-text-2.12.1 )
Updates `jackson-module-jaxb-annotations` from 2.11.2 to 2.12.1
- [Release notes](https://github.com/FasterXML/jackson-modules-base/releases )
- [Commits](https://github.com/FasterXML/jackson-modules-base/compare/jackson-modules-base-2.11.2...jackson-modules-base-2.12.1 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-16 13:47:30 -05:00
ef407d85bf
Add logging
2021-01-12 08:56:12 -05:00
128d384153
Credit for #2273
2021-01-07 06:03:31 -05:00
b79d154d81
Dependency version bumps
2021-01-06 10:21:25 -05:00
efc6809ea6
Replacing Hibernate Search 5 with Hibernate Search 6 ( #2190 )
...
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)
* Fix spatial API changes, work on BaseTermReadSvcImpl
* Most of the way through the various filter property conversions
* Finished i think with BaseTermReadSvcImpl
* Compiling, but definitely broken
* Start test compilation failures
* All tests compiling (i think)
* remove suggest keywords operation
* Fix bootstrap errors, still have to deal with transient fields
* Rollback CR
* More refactoring, got IDs baked back into docs
* Fix coord util, fix a few more fields which require projection
* merge fixes
* begin refactor of valuesetexpansion tests
* fix another test
* Update tests
* remove todos, add TestContainers
* Fix descendant in
* Add testcontainers, fix another test
* fix more tests, replace embedded es
* Rip out embedded elastic, replace with TestContainer
* merge conflicts for new analyzers
* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs
* Remove dead deps, update testcontainer
* Remove java-hamcrest
* Pull asserts up, refactor tests to pass in RP tests
* Update V2 check
* Remove suggest keyword tests
* Split line for testing
* Fix perhaps one of the dumbest programming mistakes in my career so far
* Refactor tests which no longer rely on a strict known order
* Fix up test config, disable log test temporarily
* Remove log4j from being transitively pulled in. re-enable test
* Update log4j exclusions with new bridge. Update test to check for core class
* Move dependency to root pom in dep management section
* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment
* update testst, remove todos
* Add hibernate props provider method, add elastic regexp query
* Add todo for high level client builder
* Modify ElasticsearchRestClientFactory to support HTTPS hosts
* Remove protocol extraction from rest url
* do we even need to index this...?
* remove purge of non-indexed resources
* Add longer timeout to testcontainers
* Add task to add docker CLI to azure pipeline via task, for testcontainers
* WIP remove this
* Dont update version
* Add test for duplicate termconcepts
* Use real hibernate ORM methods
* merge issues
* Add partitionsettigns bean to match master
* Trying to debug testcontainers on azure...
* Trying to debug testcontainers on azure...
* Run even on previous failure
* Fix testcontainer port binds
* Add full text logs attaching, and test reporting
* I love yaml
* Remove comment
* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue
* Modify TX beheaviour
* wip
* Rework to use config and mocked beans for partition-aware lastN
* rework to not use beans and just inject vars i need for test, keps test envs cleaner
* update azure pipeline to only copy test results
* Remove erroneous publish
* Always get test logs
* Make it so indexing works,
* Add todos
* revert deleteByPid
* Work on test fixes
* Test fixes
* Test fixes
* Another test fix
* Test fix
* Work on tests
* Test fixes
* All tests passing locally
* Fix test failure
* FIx build error
* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider
* Update ngram of token filters
* Tidying
* subvert the purpose of hibernate elastic props builder to inject template
* dead space
* Rename changed class
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
86f254cd66
Bump datasource-proxy from 1.5.1 to 1.7 ( #2267 )
...
* Bump datasource-proxy from 1.5.1 to 1.7
Bumps [datasource-proxy](https://github.com/ttddyy/datasource-proxy ) from 1.5.1 to 1.7.
- [Release notes](https://github.com/ttddyy/datasource-proxy/releases )
- [Changelog](https://github.com/ttddyy/datasource-proxy/blob/1.x/CHANGELOG.md )
- [Commits](https://github.com/ttddyy/datasource-proxy/compare/datasource-proxy-1.5.1...datasource-proxy-1.7 )
Signed-off-by: dependabot[bot] <support@github.com>
* Add changelog
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-04 10:32:52 -05:00
aa584d5b2d
Bump maven-dependency-plugin from 3.0.2 to 3.1.2 ( #2266 )
...
Bumps [maven-dependency-plugin](https://github.com/apache/maven-dependency-plugin ) from 3.0.2 to 3.1.2.
- [Release notes](https://github.com/apache/maven-dependency-plugin/releases )
- [Commits](https://github.com/apache/maven-dependency-plugin/compare/maven-dependency-plugin-3.0.2...maven-dependency-plugin-3.1.2 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-04 06:49:12 -05:00
0ac9ea643a
Bump plexus_compiler_api_version from 2.8.5 to 2.8.8 ( #2243 )
...
Bumps `plexus_compiler_api_version` from 2.8.5 to 2.8.8.
Updates `plexus-compiler-api` from 2.8.5 to 2.8.8
- [Release notes](https://github.com/codehaus-plexus/plexus-compiler/releases )
- [Commits](https://github.com/codehaus-plexus/plexus-compiler/compare/plexus-compiler-2.8.5...plexus-compiler-2.8.8 )
Updates `plexus-compiler-javac` from 2.8.5 to 2.8.8
Updates `plexus-compiler-javac-errorprone` from 2.8.5 to 2.8.8
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-04 06:18:36 -05:00
8df8ed7838
Bump hibernate version
2021-01-03 16:56:02 -05:00
57347ddb63
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2021-01-01 15:52:06 -05:00
ec712e086c
Version bump mockito
2021-01-01 15:50:00 -05:00
ed4d7d7eb6
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2021-01-01 15:07:37 -05:00
f30999b053
License header updates
2021-01-01 15:07:23 -05:00
4373b47207
Library version bumps
2021-01-01 15:06:55 -05:00
e79114e2ec
Un-revert the MDM changes, now that issues have been addressed ( #2226 )
...
* Backward compatibility changes
* Revert "Revert "Remove all references to Person from EMPI.""
* Updated docs
* Removed mdm channel references
* Initial implementation
* fix coarseness bug. Fix tests. reinitialize silly bean
* Add forgotten json file
* Generic provider PoC
* Refactored provider to use BundleBuilder
* Removed version-specific MDM providers
* Addressed code review comments
* Fixed after merge
* Fixed docs
* MDM SVG for Update Use Cases
* Removed obsolete docs
Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
a689beffc5
Bump spring_version from 5.2.3.RELEASE to 5.2.9.RELEASE ( #2085 )
...
Bumps `spring_version` from 5.2.3.RELEASE to 5.2.9.RELEASE.
Updates `spring-beans` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-context` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-context-support` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-core` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-jdbc` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-messaging` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-orm` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-test` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-tx` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-web` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-webmvc` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Updates `spring-websocket` from 5.2.3.RELEASE to 5.2.9.RELEASE
- [Release notes](https://github.com/spring-projects/spring-framework/releases )
- [Commits](https://github.com/spring-projects/spring-framework/compare/v5.2.3.RELEASE...v5.2.9.RELEASE )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-12-14 14:29:34 -05:00
092da2e93f
Bump slf4j_version from 1.7.28 to 1.7.30 ( #2242 )
...
Bumps `slf4j_version` from 1.7.28 to 1.7.30.
Updates `slf4j-android` from 1.7.28 to 1.7.30
Updates `slf4j-api` from 1.7.28 to 1.7.30
- [Release notes](https://github.com/qos-ch/slf4j/releases )
- [Commits](https://github.com/qos-ch/slf4j/compare/v_1.7.28...v_1.7.30 )
Updates `jcl-over-slf4j` from 1.7.28 to 1.7.30
- [Release notes](https://github.com/qos-ch/slf4j/releases )
- [Commits](https://github.com/qos-ch/slf4j/compare/v_1.7.28...v_1.7.30 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-12-14 10:49:19 -05:00
9036df25fa
2229 - Remove support for the upload-igpack CLI command. ( #2233 )
...
* 2229 - Remove support for the upload-igpack CLI command.
* 2229 - Revert changes made to the ValidateCommand class since it only takes an igpack as a parameter and therefore, should NOT have been removed.
* 2229 - Remove the igpack option from the Validate command.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_0/2229-remove-upload-igpack-command.yaml
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Kevin Dougan <kevindougan@kevins-mbp.lan>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-12-14 09:50:16 -05:00
0dc0e91766
Credit for #2241
2020-12-14 06:06:07 -05:00
0938d72b51
Revert "Remove all references to Person from EMPI."
2020-12-09 14:57:00 -05:00
4352e0a61f
Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references
2020-12-03 11:28:21 -05:00
1b263f1c32
Bump jetty_version from 9.4.34.v20201102 to 9.4.35.v20201120 ( #2210 )
...
Bumps `jetty_version` from 9.4.34.v20201102 to 9.4.35.v20201120.
Updates `jetty-http` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-servlets` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-io` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-continuation` from 9.4.34.v20201102 to 9.4.35.v20201120
Updates `jetty-security` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-servlet` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-server` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-util` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-webapp` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `jetty-xml` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Updates `websocket-api` from 9.4.34.v20201102 to 9.4.35.v20201120
Updates `websocket-client` from 9.4.34.v20201102 to 9.4.35.v20201120
Updates `websocket-server` from 9.4.34.v20201102 to 9.4.35.v20201120
Updates `jetty-maven-plugin` from 9.4.34.v20201102 to 9.4.35.v20201120
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.34.v20201102...jetty-9.4.35.v20201120 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-12-02 14:47:10 -05:00
d63c580e82
Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references
2020-12-01 13:18:42 -05:00
1e5def260c
Bump woodstox version ( #2199 )
2020-11-27 19:49:06 -05:00
2a3b72db17
Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references
2020-11-27 16:54:04 -05:00
da75ff8da2
Credit for #2197
2020-11-26 10:08:56 -05:00
27cff8153b
Bump jetty_version from 9.4.30.v20200611 to 9.4.34.v20201102 ( #2176 )
...
Bumps `jetty_version` from 9.4.30.v20200611 to 9.4.34.v20201102.
Updates `jetty-http` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-servlets` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-io` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-continuation` from 9.4.30.v20200611 to 9.4.34.v20201102
Updates `jetty-security` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-servlet` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-server` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-util` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-webapp` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `jetty-xml` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Updates `websocket-api` from 9.4.30.v20200611 to 9.4.34.v20201102
Updates `websocket-client` from 9.4.30.v20200611 to 9.4.34.v20201102
Updates `websocket-server` from 9.4.30.v20200611 to 9.4.34.v20201102
Updates `jetty-maven-plugin` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-11-19 20:20:01 -05:00
4bbe4a3ef7
Merge branch 'gg_20201105-remove-person-references' of https://github.com/jamesagnew/hapi-fhir into gg_20201105-remove-person-references
2020-11-19 14:56:31 -05:00
4378df7dcb
Removed more EMPI refs from the docs
2020-11-19 14:56:18 -05:00
953b662827
Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references
2020-11-19 14:24:51 -05:00
75c0c25d7b
remove references to EMPI
2020-11-18 19:50:00 -05:00
0c31741eec
Version bump to 5.3.0-SNAPSHOT
2020-11-18 14:52:43 -05:00
4d441ad7f2
Version bump to 5.2.0
2020-11-18 06:30:20 -05:00
228e75b501
Bump core to latest versions ( #2154 )
...
* Bump core to latest versions
* Compile fix
* Bump to non snapshot core library
2020-11-03 15:43:37 -05:00
6ccb7c8312
Bump HTTPClient version
2020-10-28 10:28:04 -04:00
783cbb3cf8
Bump postgres driver version
2020-10-26 19:34:50 -04:00
8000d2d0cf
SQL Join Rework ( #2086 )
...
* switched to adding annotations. Just did a test with Token, but the sql looks clean.
* switched to adding annotations. Just did a test with Token, but the sql looks clean.
* added the other six index links
* trying different annotations
* Start testing
* Update resources on package install
* Add changelog
* Join rework
* CLean up SQL builder
* Add docs
* SP rework
* Join work
* Work on params
* Work on refactor
* Work on chains
* Work on joins
* Rework queries
* Work on queries
* Many more tests passing
* Refs test
* Work on sorting
* Work on tests
* More joins work
* Work on tests
* Work on queries
* Tests passing
* More test fixes
* Test fixes
* Work on SQL
* Tests passing
* Add some tests
* Add some tests
* License headers
* Use entity manager to get datasourcd
* One more fix
* Model cleanup
* Ongoing work
* Fixes
* Fixes
* Work on joins
* Ongoing fixes
* Merge conflict
* Cleanup
* clean up unused fields
* Work on join
* COmpile fix
* Rework querying
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Resolve fixmes
* Test fix
* Test fixes
* Test fix
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-10-26 05:24:26 -04:00
0fdff3e052
Credit for #2142
2020-10-23 10:33:49 -04:00
aa3da9b05f
Bump bootstrap version ( #2128 )
...
* Bump bootstrap version
* Add changelog
* Resolve fixme
* Rmove test code
2020-10-12 20:47:14 -04:00
7d150858dc
Credit for #2118
2020-10-12 20:45:02 -04:00
bd6feec2f4
Initial credit for #2118
2020-10-12 17:19:15 -04:00
844624b6dd
RDF Support in HAPI FHIR ( #2118 )
...
* RDF Support in HAPI FHIR
* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser
* Add null checks to appease LGTM
* Correct null check logic
2020-10-12 17:16:00 -04:00
576f6efc39
Credit for #1607
2020-10-09 11:58:00 -04:00
e8d844f4f3
Merge branch 'master' into gg_20201008_baddeps
2020-10-09 07:53:19 -04:00
2134d40f1c
Account for timezones in lastUpdated search ( #2113 )
...
* Add test
* Fix
* Add changelog
* Test fixes
* Test fix
* Test fixes
* Resolve fixme
* Test fixes
* Remove debug logs
* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
375552ac49
Update hibernate core and validator
2020-10-08 14:15:57 -04:00
5a29fd9945
rollback the elastic changes
2020-10-06 17:20:11 -04:00
6ab7a0bcfe
Bump animal-sniffer-maven-plugin from 1.18 to 1.19 ( #2084 )
...
Bumps [animal-sniffer-maven-plugin](https://github.com/mojohaus/animal-sniffer ) from 1.18 to 1.19.
- [Release notes](https://github.com/mojohaus/animal-sniffer/releases )
- [Commits](https://github.com/mojohaus/animal-sniffer/compare/animal-sniffer-parent-1.18...animal-sniffer-parent-1.19 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-09-16 08:02:01 -04:00
ea5fba6dfb
Remove maven site plugin
2020-09-15 05:40:19 -04:00
5b6ee4e475
Dependency version bump ( #2074 )
...
* Dependency version bump
* More dependency work
* One more fix
2020-09-14 08:42:28 -04:00
f3d5b69da0
Bump flyway-core from 6.4.1 to 6.5.4 ( #2039 )
...
Bumps [flyway-core](https://github.com/flyway/flyway ) from 6.4.1 to 6.5.4.
- [Release notes](https://github.com/flyway/flyway/releases )
- [Commits](https://github.com/flyway/flyway/compare/flyway-6.4.1...flyway-6.5.4 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-08-13 05:47:43 -04:00
92718c7ef2
Version bump to 5.2.0-SNAPSHOT
2020-08-12 10:23:46 -04:00
5fb7bd5156
Version bump to 5.1.0
2020-08-11 17:43:24 -04:00
f0ed640e24
Upgrade core library dependency version
2020-08-10 09:05:04 -04:00
c13e17b4e6
Add changelog and bump Jetty
2020-07-17 11:50:45 -04:00
dbe171d658
Bump jetty_version from 9.4.24.v20191120 to 9.4.29.v20200521 ( #1890 )
...
Bumps `jetty_version` from 9.4.24.v20191120 to 9.4.29.v20200521.
Updates `jetty-http` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-servlets` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-io` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-continuation` from 9.4.24.v20191120 to 9.4.29.v20200521
Updates `jetty-security` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-servlet` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-server` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-util` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-webapp` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `jetty-xml` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Updates `websocket-api` from 9.4.24.v20191120 to 9.4.29.v20200521
Updates `websocket-client` from 9.4.24.v20191120 to 9.4.29.v20200521
Updates `websocket-server` from 9.4.24.v20191120 to 9.4.29.v20200521
Updates `jetty-maven-plugin` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-07-17 11:47:06 -04:00
baba4cc240
Avoid version conflicts on current writes ( #1971 )
...
* Add auto retry of transactions
* Experiment in Maven build
* Transaction autoretry
* Work on transaction retries
* Work on transaction retry
* Work on transaction retry
* Fix tests
* Avoid version conflicts
* Add changelog
* Resolve LGTM issue
* FIx transaction scope error
* Test fixes
* Test fix
* Test fixes
* Test fix
* Test fixes
2020-07-13 08:51:13 -04:00
11ad41d472
Credit for #1893
2020-07-06 05:52:40 -04:00
6fb6675b1e
Resolve validation errors to ValueSet with UCUM ( #1948 )
...
* Add tests for validation errors
* Work on validation errors
* Bump core version
* Fix validation errors
* Test fixes
* Add changelog
* Test fix
* Test fix
* Test fix
2020-07-05 19:59:21 -04:00
f356c7c385
Migrate to JUnit5 ( #1952 )
...
* Work on junit
* Work on junit 5
* Work on junit 5
* Bump errorprone vcersion
* Work on tests
* Junit 5 tweaks
* Fixes
* Work on tests
* Work on junit5
* Work on tests
* Test fixes
* Work on junit5
* Test work
* Get junit5 working
* Test fix
* Work on tests
* WOrk on tests
* Work on tests
* fixes
* Compile fix
* One more tweak
* Compile fix
* Add changelog
* Fix compile error
* Compile fix
2020-07-04 18:28:16 -04:00
59659b2802
Move order of modules
2020-06-24 10:11:30 -07:00
bb7a773f41
Merge branch 'master' into spring-batch-integration
2020-06-23 16:02:41 -07:00
67d363f9e1
Add setting to allow validation of reference targets ( #1932 )
...
* Add setting to allow validation of reference targets
* Add changelog
* Add changelog
* License headers
* Plugin version bump
* Experiment with Maven build
2020-06-23 11:35:10 -04:00
a9c704c06e
Merge branch 'master' into spring-batch-integration
2020-06-10 12:24:19 -07:00
b8da4f0140
Add package support ( #1911 )
...
* Begin rework of package management
* Work on NPM
* Work on package management
* Work on NPM
* NPM rework
* Work on NPM
* NPM package rework
* Updates
* Updates
* Add license
* Work on package server
* Work on package importing
* Work on package management
* Package rework
* Work on packages
* Work on package manager
* Work on pkgs
* NPM work
* NPM rework
* Work on package cache
* Work on NPM
* Work on NPM
* Package fixes
* Add tests
* Tweaks
* Test fixes
* Add changelog
* Avoid snapshot dep
2020-06-10 05:30:20 -04:00
0d3ad622b5
Correct Validation Performance Regression ( #1895 )
...
* Validation performance regression
* Optimize validation
* More cleanup
* Add changelog
* Test fixes
* Build fixes
2020-06-10 05:26:21 -04:00
278a1070ae
:Merge branch 'master' into spring-batch-integration
2020-06-08 17:16:11 -07:00
f48214deda
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
2020-05-29 23:54:11 -04:00
93a1229789
Removing redundant maven-enforcer-plugin execution.
2020-05-27 12:57:11 -04:00
ed1e103751
Duplicate maven-enforcer-plugin removed, executions consolidated.
2020-05-27 12:39:17 -04:00
35b1533db1
Add new project for spring batch
2020-05-25 22:32:00 -07:00
ee87a2e2d0
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-25 11:37:34 -04:00
6a4f5b9b3a
Credit for #1826
2020-05-24 09:32:44 -04:00
c97ef7adfc
A bit more contributors cleanup
2020-05-23 19:45:00 -04:00
3bf0628436
Updatyes to devs list
2020-05-23 19:17:33 -04:00
d24f075cdb
Update some orgs
2020-05-23 17:22:59 -04:00
b60404dbb8
Credit for #1849
2020-05-23 17:18:37 -04:00
9192d41448
Credit for #1637
2020-05-23 17:16:19 -04:00
4d378ee0ed
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
# hapi-fhir-jpaserver-base/pom.xml
# hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
# hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
2020-05-22 17:04:01 -04:00
d1b963321a
MVP EMPI implementation ( #1857 )
...
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00
e22549e0c4
Bump MySQL JDBC driver version
2020-05-21 21:21:13 -04:00
8ff7d5407a
Bump core version
2020-05-21 19:22:28 -04:00
2360ed4abe
fix build ( #1861 )
2020-05-21 19:22:08 -04:00
5b2181a563
Implement FHIR Patch ( #1850 )
...
* Start working on FHIRPatch
* More work on fhirpatch
* Work on FHIR Patch
* Add patch
* Test fixes
* Test fixes
* Get tests fixed
* Chnage to trigger a build
* Compile fix
* Dependency version fixes
* Test fix
* COmpile fix
* Try to fix build
* Test fix attempt
* Another build attempt
* Another build tweak
* Cleanup
2020-05-20 19:43:55 -04:00
cc92bd7b07
Revert "Start working on FHIRPatch"
...
This reverts commit b3f6e7d521
2020-05-17 11:56:50 -04:00
b3f6e7d521
Start working on FHIRPatch
2020-05-17 11:44:06 -04:00
52c8e3551c
Version bump to 5.1.0-SNAPSHOT
2020-05-15 14:43:32 -04:00
fe0e07a313
Bump to 5.0.1
2020-05-15 05:47:01 -04:00
529e1e1f5e
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-14 12:09:24 -04:00
1d13e29ac0
Version bump to 5.1.0-SNAPSHOT
2020-05-12 20:04:20 -04:00
d631ecff4a
Prepare for 5.0.0
2020-05-12 11:49:18 -04:00
c7da4b0914
Build Cleanup
2020-05-11 13:25:58 -04:00
0c13a65871
Bump to latest Core version ( #1841 )
...
* Start working on bumping core
* Work on tests
* Work on tests
* Bump core definitions
* Bump R5 defs
* Tweak changelog
* Test fix
2020-05-11 12:37:16 -04:00
386f395e4b
Version bump 2 dependencies
2020-05-10 19:10:18 -04:00
4cced40b54
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
2020-05-05 17:19:32 -04:00
ceae417d35
Credit for #1710
2020-05-04 05:42:32 -04:00
586089fc69
Credit for #1749
2020-05-01 07:38:31 -04:00
a786756169
Credit for #1812
2020-05-01 07:27:12 -04:00
439a901e30
Credit for #1734
2020-05-01 05:56:47 -04:00
3d5a8bb3f8
Add UCUM support ( #1824 )
...
* Add UCUM support
* Add changelog
* Some cleanup
* Test fix
* Add flywayDB callback
* Add hooks to schema migrator
2020-04-30 15:22:41 -04:00
885a18e0d8
Credit for #1788
2020-04-29 09:12:36 -04:00
dd749791db
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
2020-04-24 16:55:45 -04:00
6226381595
Merge branch 'master' into ja_20200206_multitenancy
2020-04-21 20:54:56 -04:00
11fade2c2e
Bump boot version
2020-04-21 15:55:35 -04:00
4b93a0d724
Credit for #1806
2020-04-21 15:49:43 -04:00
1f848dde82
Credit for #1791
2020-04-21 15:30:42 -04:00
faddeeb779
Add changelog
2020-04-20 11:15:35 -04:00
95b77af570
Merge branch 'master' into ja_20200206_multitenancy
2020-04-20 11:07:10 -04:00
bcac2b061c
Credit for #1799
2020-04-18 11:14:15 -04:00
48057b9d8e
Merge branch 'master' into ja_20200206_multitenancy
2020-04-17 17:59:48 -04:00
540375a7eb
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-04-17 17:39:27 -04:00
e0b419354f
Bump up hamcrest version and force the use of the latest version
2020-04-17 13:59:22 -04:00
a1b3a97acf
Work on docs
2020-04-17 09:28:44 -04:00
925bbbbcdc
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
# hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
# pom.xml
2020-04-13 18:35:15 -04:00
982b54df57
Work on multitenancy
2020-04-13 11:50:49 -04:00
c26a5553e9
Multitenancy work
2020-04-12 20:47:32 -04:00
e55ccf88fc
Work on multitenancy
2020-04-10 20:01:59 -04:00
e0fcbe1df2
Merge branch 'master' into ja_20200206_multitenancy
2020-04-09 11:52:27 -04:00
6baf1995c9
Work on subscription cleanup
2020-04-02 20:30:19 -04:00
f891634341
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-03-31 13:30:28 -04:00
62d867902f
Work on multitenancy
2020-03-29 18:16:04 -04:00
ec6fe70acb
Merge branch 'master' into ja_20200206_multitenancy
2020-03-27 05:50:08 -04:00
4e4c8dbd9a
Initial commit of changes to support $lastn operation.
2020-03-25 18:02:13 -04:00
c6d23a8bc6
Add chain on _type parameter ( #1772 )
...
* Add chain on _type parameter
* Add changelog
* Test fix
* Address review comments
* Fix azure yaml
* Correct HTTPs in pom
* One more pom tweak
* Test fix
* Try azure again
2020-03-24 09:44:57 -04:00
bb4cbb6af5
One more pom tweak
2020-03-24 06:10:29 -04:00
22e0c7a596
Correct HTTPs in pom
2020-03-24 06:09:03 -04:00
fa29f3e8ab
Credit for #1770
2020-03-23 19:12:05 -04:00
14316147c5
Resolve some docs issues
2020-03-23 10:34:12 -04:00
22413911bf
Validation api changes ( #1719 )
...
* Validation enhancements
* Work on validation api reworking
* Keep working on validation API
* Keep working on new term API
* Work on validation api
* Ongoing work on validation
* Work on integrating validation
* Work on validation API
* Add to validation API
* Work on validation
* Work on API
* Work on validation
* Work on validation API
* Work on validation API
* Work on validation api
* Work on validation API
* Work on validation api
* Validation API changes
* Work on API
* More work on validationo API
* Work on validation API
* FIxes
* WOrk on validation api
* Work on validation API
* Tests passing!
* More cleanup
* More validation API changes
* Fix intermittent test failure
* Package reorg
* Validation API work
* Work on doocumentation
* Work on API
* More work on new validation API
* Fix errorprone-reported error
* Test fixes
* Documentation updates
* Documentation tweaks
* Work on API
* Bean name adjustments
* Build fixes
* Some test fixes
2020-03-17 13:28:59 -04:00
80139f4800
Update pom.xml ( #1709 )
...
A run on master using https://jeremylong.github.io/DependencyCheck/dependency-check-maven/index.html shows quartz as having a critical security issue in version 2.3.1
2020-03-17 12:47:12 -04:00
4a160a2df3
Merge branch 'master' into ja_20200206_multitenancy
2020-03-03 09:25:19 -05:00
ed7b9fc6b6
Initial attempt at integrating elastic APM for search performance
2020-02-28 16:09:16 -05:00
60f16dd91d
Update to 4.3.x core JAR ( #1715 )
...
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Start working on converter
* Account for compile errors
* Test fix
* Work no validator
* Work on getting core working
* Add some test coverage
* Many test fixes
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
2020-02-17 14:28:29 -05:00
ddc7b601ee
Version bump to 4.3.0-SNAPSHOT
2020-02-16 19:23:22 -05:00
4fd80cfca7
Bump to 4.2.0
2020-02-16 19:00:15 -05:00
ebf395bee9
Merge branch 'master' into ja_20200206_multitenancy
2020-02-09 08:40:29 -05:00
f7ec41ffc5
Work on multitenancy
2020-02-09 08:40:15 -05:00
c5c1e3196b
Resolve FIXMEs ( #1705 )
...
* Resolve FIXMEs
* Test fixes
* Test fixes
* Clean up unused code
* Add some test coverage
* Test fix
* Test fix
* Avoid intermittent
2020-02-09 08:39:46 -05:00
b2d2346228
Work on multitenancy
2020-02-07 15:18:06 -05:00
97289b3a1f
Credit for #1692
2020-02-04 17:38:42 -05:00
3c965183e7
Checkstyle plugin version bump
2020-02-03 19:45:32 -05:00
b5adef43ac
Bump checkstyle from 8.18 to 8.29
...
Bumps [checkstyle](https://github.com/checkstyle/checkstyle ) from 8.18 to 8.29.
- [Release notes](https://github.com/checkstyle/checkstyle/releases )
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-8.18...checkstyle-8.29 )
Signed-off-by: dependabot[bot] <support@github.com>
2020-02-02 20:36:15 -05:00
beab5b3a9c
Credit for #1689
2020-01-29 05:56:36 -05:00
jamesagnew
dependabot[bot]
Tadgh
Jing Tang
Ken Stevens
Tadgh
VK-SMILECDR
Michael Buckley
Kevin Dougan SmileCDR
JP
Nick Goupinets
Diederik Muylwyk
JP
NG
Josh Collins
ianmarshall
Jens Kristian Villadsen
Gary Graham