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8816 Commits

Author SHA1 Message Date
Tadgh 3d681134e9
Add SearchBundleEntryParts (#3095) 
* Add the ability to parse a search bundle into its component parts

* remove deadspace

* wip
 2021-10-19 23:41:33 +00:00
JasonRoberts-smile d07764e8e5
Jr 20211013 chained references (#3079) 
* 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
StevenXLi 34010fa78d
Batch job refactor (#3087) 
* 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
jmarchionatto 92e9859272
Issue 3072 using an external terminology server in the fhir server for codes in fhir resources (#3081) 
* 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
tom-daudelin-smilecdr c89d12232f
added support for R4 profile validation alongside a passing test (#3074) 
Co-authored-by: tom <tom.daudelin@smilecdr>
 2021-10-18 16:37:51 +00:00
JasonRoberts-smile b5e31abf9b
add authorization check to inline matches (#3048) 
* 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
dependabot[bot] 5ba07e2e7c
Bump kotlin.version from 1.5.0 to 1.5.31 (#3083) 
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
dependabot[bot] bbcf202b90
Bump jersey_version from 3.0.0 to 3.0.3 (#3027) 
Bumps `jersey_version` from 3.0.0 to 3.0.3.

Updates `jersey-server` from 3.0.0 to 3.0.3

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

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

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

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

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

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

* Wip partial fixup of other STU versions

* Updated usages of new patient type everything api

* Partial commit of incomplete documentation

* Remove docs

* Cut to token instead of string

* Bump hapi version due to breaking api changes
 2021-10-17 14:34:33 +00:00
jamesagnew f6c8ecdc43 Credit for #3022 2021-10-17 09:09:22 -04:00
Ben Li-Sauerwine 2e5aed4016
Adds a NDJSON parser, in preparation for adding NDJSON $import to HAPI (#3022) 
* 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
Thomas Vitale 721b1817a7
Add Systematic (Columna Cura) to HAPI FHIR Global Atlas (#3052) 2021-10-17 09:03:38 -04:00
jamesagnew ec86ac4088 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2021-10-17 08:10:19 -04:00
dependabot[bot] 7e87890ae3
Bump fhir_core_version from 5.5.4 to 5.5.7 (#3082) 
Bumps `fhir_core_version` from 5.5.4 to 5.5.7.

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

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

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

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

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

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

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

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

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

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

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-10-17 07:01:33 -04:00
Tadgh b9266df1fd Add dependency to unbreak master build 2021-10-16 19:05:11 -04:00
jamesagnew d416bc7101 Build fixes 2021-10-16 18:34:08 -04:00
dependabot[bot] 41111cae29
Bump maven-enforcer-plugin from 3.0.0-M2 to 3.0.0 (#3078) 
Bumps [maven-enforcer-plugin](https://github.com/apache/maven-enforcer) from 3.0.0-M2 to 3.0.0.
- [Release notes](https://github.com/apache/maven-enforcer/releases)
- [Commits](https://github.com/apache/maven-enforcer/compare/enforcer-3.0.0-M2...enforcer-3.0.0)

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

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

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

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

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

* Changes for version bump

* Resolve NPE:

* Test fix

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

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

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

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

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

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

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

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

* Remove unused comment in hapi-fhir-structures-dstu2.1/pom.xml
 2021-10-14 16:34:48 -04:00
jmarchionatto 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
Tadgh 87e594d416
Bump JENA to deal with CVE-2021-29349 (#3063) 2021-10-13 16:17:43 -04:00
jamesagnew 818c54f0b9 Squashed commit of the following: 
commit 408f2d82b762900de53ebe66dde8eec082e7bae7
Merge: 8da38d1a9e be19acb7c3
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Oct 12 12:00:56 2021 -0400

    Merge branch 'master' into ja_20211011_fix_intermittent

commit 8da38d1a9e
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Oct 11 21:31:42 2021 -0400

    Test fixes

commit c73fd288f0
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Oct 11 20:53:04 2021 -0400

    Fix intermittent failure
 2021-10-12 12:01:34 -04:00
jamesagnew be19acb7c3 Fix Postgres migration 2021-10-12 12:00:39 -04:00
Tadgh 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
jamesagnew b2a4ff2f29 Try to avoid intermittent 2021-10-11 19:14:01 -04:00
jamesagnew 56ef55a353 Update postgres schema file name 2021-10-11 17:44:11 -04:00
jamesagnew bc0f5d4ef6 Avoid intermittent failure 2021-10-11 17:28:07 -04:00
jamesagnew a54ebd1d30 License header updates 2021-10-11 17:22:54 -04:00
James Agnew 310a4cdb58
Migrate CLOB columns to LOB (SMILE-3072) (#3016) 
* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
 2021-10-11 16:47:37 -04:00
James Agnew 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
James Agnew 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
TipzCM 6ad0dffd00
build fix (#3058) 
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
 2021-10-07 16:38:42 -04:00
Tadgh 383f76982a Fix broken link in yaml 2021-10-07 15:12:18 -04:00
katiesmilecdr 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
TipzCM 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
jmarchionatto 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
Tadgh bc2cd7cafc
premature optimization is the root of all evil (#3053) 2021-10-06 14:44:39 +00:00
Tadgh 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
jamesagnew 2581cd1446 Bump postgres DB version 2021-10-04 10:54:33 -04:00
jamesagnew 15748f4d54 Add setters 2021-10-04 07:41:24 -04:00
James Agnew d320b78ae1
Improve synthea ingest performance (#3033) 
* Improve synthea ingest performance

* Tweaks

* Fix param splitting

* Update to test

* Add changelog

* Test fix

* Add some runtime checks

* Remove useless test

* Test fix
 2021-10-04 05:46:06 -04:00
jamesagnew d4f01ac4e7 License header updates 2021-10-03 20:20:04 -04:00
James Agnew 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
James Agnew 95e853bdf7
Improve parallel model scanning (#3046) 
* Improve parallel model scanning

* Add changelog

* Resolve fixme

* Test fix
 2021-10-03 19:40:24 -04:00
Tadgh 53a2d3c1ac
Merge pull request #3038 from hapifhir/remove-parallel-non-gets 
Remove parallel non gets
 2021-09-28 17:56:12 -04:00
Tadgh 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