ec86ac4088
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2021-10-17 08:10:19 -04:00
7e87890ae3
Bump fhir_core_version from 5.5.4 to 5.5.7 ( #3082 )
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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
b9266df1fd
Add dependency to unbreak master build
2021-10-16 19:05:11 -04:00
d416bc7101
Build fixes
2021-10-16 18:34:08 -04:00
41111cae29
Bump maven-enforcer-plugin from 3.0.0-M2 to 3.0.0 ( #3078 )
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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 )
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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 )
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* 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 )
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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 )
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* 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
05aa4447f8
Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet … ( #3073 )
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* Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet work when code system is present, even when theOptions.isInferSystem() is true
* Add test for specific use case added
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-10-14 15:40:27 -04:00
87e594d416
Bump JENA to deal with CVE-2021-29349 ( #3063 )
2021-10-13 16:17:43 -04:00
818c54f0b9
Squashed commit of the following:
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commit 408f2d82b762900de53ebe66dde8eec082e7bae7
Merge: 8da38d1a9ebe19acb7c38da38d1a9ec73fd288f0
2021-10-12 12:01:34 -04:00
be19acb7c3
Fix Postgres migration
2021-10-12 12:00:39 -04:00
d2ea4655a7
Rel 5 5 2 ( #3060 )
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* Add versionenum, bump maven version
* failing tests
* more logs
* Add more test cases, not passing
* fixed the double chain with contained resource second case
* clean up a bit
* add tests for qualifiers
* force the resource table to be the root of the query if we might be traversing a contained reference
* tidy up
* tests for longer chains
* changelog
* code review feedback
* backport changelog
* Add version.yaml
* [2935] Escape "%" in like expression
* Add backport to changelog
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
2021-10-12 14:25:03 +00:00
b2a4ff2f29
Try to avoid intermittent
2021-10-11 19:14:01 -04:00
56ef55a353
Update postgres schema file name
2021-10-11 17:44:11 -04:00
bc0f5d4ef6
Avoid intermittent failure
2021-10-11 17:28:07 -04:00
a54ebd1d30
License header updates
2021-10-11 17:22:54 -04:00
310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) ( #3016 )
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* 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
756b0fdc7b
Fix transaction scoping ( #2799 )
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* Work on transaction boundaries
* Test fixes
* Test fixes
* Test fix
* Resolve FIXME
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fix
* Adjust changelog
* Remove unneeded changelog
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fixes
* Test fix
2021-10-11 16:45:22 -04:00
aed718bd6f
Avoid redundant PID lookups in transaction processing ( #3061 )
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* Avoid redundant PID lookups in transaction processing
* Add changelog
* Test fix
2021-10-11 13:45:57 -04:00
6ad0dffd00
build fix ( #3058 )
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Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-10-07 16:38:42 -04:00
383f76982a
Fix broken link in yaml
2021-10-07 15:12:18 -04:00
3c80dba90e
[3040] finish implementation ( #3049 )
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* [3040] finish implementation
* 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>
* 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>
* 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>
* [3040] throw exception if link exists
* [3040] add matchResult parameter/update documentation
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-10-07 17:42:21 +00:00
a474e88ed4
issue-2397 implementing the mdm expansion on everything and searches ( #3044 )
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* issue-2397 implementing the mdm expansion on everything and searches
* issue-2397 code cleanup and removal of test code
* issue-2397 some tests
* issue-2397 changelog added
* issue-2397 review fixes
* issue-2397 updated change log with example and fixed failing tests
* issue-2397 test fixing
* issue-2397 fixing test
* issue-2397 review fix
* issue 2397 fixing changelog file
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-10-07 10:46:23 -04:00
71e2b82128
Issue 2851 upload terminology valueset parallel versioning ( #3051 )
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* Fix operations for 'loinc-all' ValueSet
* Fix tests
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-10-06 20:56:30 +00:00
bc2cd7cafc
premature optimization is the root of all evil ( #3053 )
2021-10-06 14:44:39 +00:00
59afbe086c
Allow canonical references to support treating given base URLs as local. ( #3050 )
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* Add failling test, works on #2843
* Partial hack to get this working
* Move implementation into pre-processing
* Add changelog
* Move implementation
* Minify Test
* Remove fixmes
* Tidying
* Ensure this only operates on STU versions which support canonical
2021-10-05 11:09:49 -04:00
2581cd1446
Bump postgres DB version
2021-10-04 10:54:33 -04:00
15748f4d54
Add setters
2021-10-04 07:41:24 -04:00
d320b78ae1
Improve synthea ingest performance ( #3033 )
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* 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
d4f01ac4e7
License header updates
2021-10-03 20:20:04 -04:00
eca725afa4
Improve versioned URL support for ValueSet expansion ( #2994 )
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* Add test
* Test fixes
* Work on expansion errors
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Work on fix
* Test fixes
* Test fixes
* Test fix
* Cleanup
* Test fixes
* Remove accidental commit
* Test fixes
* Version bump
* Add changelog
* Fixes
* Test fix
* Fix conflicts
2021-10-03 19:47:23 -04:00
95e853bdf7
Improve parallel model scanning ( #3046 )
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* Improve parallel model scanning
* Add changelog
* Resolve fixme
* Test fix
2021-10-03 19:40:24 -04:00
53a2d3c1ac
Merge pull request #3038 from hapifhir/remove-parallel-non-gets
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Remove parallel non gets
2021-09-28 17:56:12 -04:00
63ef58c0b9
Merge branch 'remove-parallel-non-gets' of github.com:hapifhir/hapi-fhir into remove-parallel-non-gets
2021-09-28 16:43:36 -04:00
040d09cfa6
Remvoe error in moving code over
2021-09-28 16:43:29 -04:00
6f36a0aab3
Merge branch 'master' into remove-parallel-non-gets
2021-09-28 10:17:38 -04:00
cd1a4154c1
Merge branch 'remove-parallel-non-gets' of github.com:hapifhir/hapi-fhir into remove-parallel-non-gets
2021-09-28 09:55:13 -04:00
072c030c2d
Remove modifications, defaults work
2021-09-28 09:55:06 -04:00
e99c470b74
Merge pull request #3023 from hapifhir/jr-20210922-narrowing-interceptor
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Jr 20210922 narrowing interceptor
2021-09-28 09:54:50 -04:00
ad05a5ec09
Merge branch 'master' into remove-parallel-non-gets
2021-09-28 09:43:01 -04:00
39ae66de16
Add tests for invalid inputs
2021-09-28 08:35:04 -04:00
58a2f23c0d
Merge branch 'master' into jr-20210922-narrowing-interceptor
2021-09-28 07:41:39 -04:00
2a86b727fa
Merge pull request #3021 from hapifhir/3020_Add_documentation_for_$partition-management-create-partition
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[3020] add documentation for $partition-management-read-partition
2021-09-27 16:41:50 -04:00
591286a9cc
Add changelog
2021-09-27 15:37:59 -04:00
dde0529b07
Remove extra semicolon
2021-09-27 15:36:17 -04:00
0c123384c7
add test for failing batch bug, remove bounding on queue
2021-09-27 15:34:19 -04:00
jamesagnew
dependabot[bot]
Tadgh
Tadgh
Jing Tang
jmarchionatto
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