f3a8b8fd74
[3097] add doc ( #3098 )
2021-10-20 20:29:09 +00:00
b93f33d4ff
When uploading loinc CodeSystem take copyright from loinc.xml input file. ( #3092 )
...
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-10-20 15:05:04 +00:00
3d681134e9
Add SearchBundleEntryParts ( #3095 )
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* Add the ability to parse a search bundle into its component parts
* remove deadspace
* wip
2021-10-19 23:41:33 +00:00
d07764e8e5
Jr 20211013 chained references ( #3079 )
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* Create index entries for outbound references of contained resources
* build query for chained reference
* fix case where the contained reference is an explicit id rather than a continued chain
* fix contained index to use path names not search param names
* make qualified search work
* cleanup and changelog
* code review
* fix broken tests
2021-10-19 18:07:29 +00:00
34010fa78d
Batch job refactor ( #3087 )
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* added AbstractResourceToFileWriter
* Added AbstractBaseBulkItemReader
* added bulkExportStatusEnum fromBatchStatus test
* Code review name change
Co-authored-by: Long Ma <longma@Longs-MBP.hitronhub.home>
Co-authored-by: Steven Li <steven@smilecdr.com>
2021-10-19 09:07:05 -04:00
92e9859272
Issue 3072 using an external terminology server in the fhir server for codes in fhir resources ( #3081 )
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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
* Consider ValueSets with multiple component includes
* Fix typo
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-10-18 15:40:17 -04:00
c89d12232f
added support for R4 profile validation alongside a passing test ( #3074 )
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Co-authored-by: tom <tom.daudelin@smilecdr>
2021-10-18 16:37:51 +00:00
b5e31abf9b
add authorization check to inline matches ( #3048 )
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* add authorization check to inline matches
* code review feedback: cached results case
* Add query count test
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3047-inline-match-security.yaml
Accept code review suggestion
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-18 12:21:26 +00:00
5ba07e2e7c
Bump kotlin.version from 1.5.0 to 1.5.31 ( #3083 )
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Bumps `kotlin.version` from 1.5.0 to 1.5.31.
Updates `kotlin-maven-allopen` from 1.5.0 to 1.5.31
Updates `kotlin-maven-noarg` from 1.5.0 to 1.5.31
Updates `kotlin-maven-plugin` from 1.5.0 to 1.5.31
---
updated-dependencies:
- dependency-name: org.jetbrains.kotlin:kotlin-maven-allopen
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.jetbrains.kotlin:kotlin-maven-noarg
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.jetbrains.kotlin:kotlin-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>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-17 18:03:09 -04:00
bbcf202b90
Bump jersey_version from 3.0.0 to 3.0.3 ( #3027 )
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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 )
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* 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
2e5aed4016
Adds a NDJSON parser, in preparation for adding NDJSON $import to HAPI ( #3022 )
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* NDJsonParser with one example test.
* Add test for empty NDJson, and fix bug for empty NDJson.
* Adds multi-Patient test, and fixes bug whereby all multi-line NDJSON would be put into the same line.
* Adds test for NDJson with newlines in it.
* Adds test for converting non-Bundle types to NDJSON failing.
* Confirm that we can only extract to Bundle types in test.
* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Documents behavior of the NDJsonParser in FhirContext.
* Attempt to fix failing build by using TestUtil to clear context in the manner of r4 parser tests instead of dstu
Also clean up indentation.
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-10-17 09:06:31 -04:00
721b1817a7
Add Systematic (Columna Cura) to HAPI FHIR Global Atlas ( #3052 )
2021-10-17 09:03:38 -04:00
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 )
...
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 )
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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 )
...
* 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:
...
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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* Avoid redundant PID lookups in transaction processing
* Add changelog
* Test fix
2021-10-11 13:45:57 -04:00
6ad0dffd00
build fix ( #3058 )
...
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 )
...
* [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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* Improve parallel model scanning
* Add changelog
* Resolve fixme
* Test fix
2021-10-03 19:40:24 -04:00
katiesmilecdr
jmarchionatto
Tadgh
JasonRoberts-smile
StevenXLi
tom-daudelin-smilecdr
dependabot[bot]
jamesagnew
Ben Li-Sauerwine
Thomas Vitale
Tadgh
Jing Tang
TipzCM