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405 Commits

Author SHA1 Message Date
TipzCM 0c3fb775df
3170 language portion of language code is case insensitive (#3171) 
* 3170 language portion of language code is case insensitive

* 3170 adding changelog

* 3170 house keeping

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
 2021-11-16 15:58:58 +00:00
TipzCM 1478abac3a
3164 updating code review points (#3165) 
* 3164 updating code review points

* 3164 updating code review points

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
 2021-11-12 20:13:42 +00:00
TipzCM 25c025cdee
3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155) 
* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
 2021-11-10 16:06:09 -05:00
James Agnew 106eb75dc6
Allow GraphQL to work with RequestValidatingInterceptor (#3145) 
* Allow GraphQL to work with RequestValidatingInterceptor

* Add test

* Add changelog
 2021-11-08 17:47:56 -05:00
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
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
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
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
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
Ken Stevens b1dd40fdba
Try commenting out clearAllStaticFieldsForUnitTest to see what happens (#3034) 
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens

* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
 2021-09-24 16:01:28 -04:00
juan.marchionatto 751c5d0d05 Implement revision suggestions. Add changelog. 2021-09-23 11:55:50 -04:00
Ken Stevens eee7d7e455
code cleanup (#2986) 
* failed attempt to get it to work

* Use simplified FhirContext.forCached methods

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-09-13 03:09:18 +00:00
Frank Tao 44b0d3e9e7
Fixed $lookup with displayLanguage caching issue (#2932) 
* Fixed $lookup with displayLanguage caching issue

* Added changelog and optimized the test cases
 2021-08-31 22:18:40 +00:00
Tadgh 0304ea2d62 Add requested test 2021-08-26 12:03:00 -04:00
Tadgh fd6dcf6363 Fix bug in code. Add test. Add changelog 2021-08-25 18:16:47 -04:00
Frank Tao 090a8b0821
Impl displayLanguage for $lookup (#2908) 
* Impl displayLanguage for $lookup - first cut

* Added original lookupCode method

* Added original lookupCode method to IFhirResourceDaoCodeSystem

* Added more test cases and changelog
 2021-08-25 14:47:10 -04:00
markiantorno 3cfc41f840 updating all convertor calls to not failfast 2021-08-20 14:11:20 -04:00
Tadgh b352bc5c96 Fix all tests in validation package 2021-08-19 15:25:19 -04:00
Tadgh 101e0d7288 Fix tests in class 2021-08-19 15:19:31 -04:00
Tadgh 77c99e47c1 TIL that anyString() wont match nulls in Mockito, but any() will 2021-08-19 15:15:51 -04:00
markiantorno 3fdb7c8408 conversion issues fixed, validation issues next 2021-08-19 13:48:59 -04:00
markiantorno 367b338d85 Updating HAPI to use latest core lib changes. 2021-08-18 11:06:14 -04:00
James Agnew 95306c3d64
Add NPM validation support module (#2782) 
* Add NPM validation support module

* Add changelog
 2021-07-07 16:28:41 -04:00
ianmarshall a878ef2496 Add null check on code lookup result. 2021-05-25 09:09:41 -04:00
ianmarshall 8e552916ee Add null check on code lookup result. 2021-05-25 09:07:28 -04:00
ianmarshall f2627959c2 Add null check on code lookup result. 2021-05-24 22:09:44 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew 8d0d75356e Test fixes 2021-05-19 05:34:24 -04:00
jamesagnew b463b072c8 Test fixes 2021-05-18 21:32:13 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
James Agnew 26d030f93e
Add language validation (#2644) 
* Add language validation

* Add tests

* Test fix
 2021-05-10 20:09:45 -04:00
Kevin Dougan SmileCDR 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
Kevin Hartmann 4a5b62616c Improved assertions for testBulkDataExport() 2021-04-27 15:01:03 -04:00
Kevin Hartmann 3a901a6671 Cleaned up extra logging. 2021-04-26 16:57:13 -04:00
Kevin Hartmann 2f126a8d9f Merge branch 'master' into kh_2526_Add_Operation_Section_to_Conformance_Statements_resource_section 2021-04-26 16:53:19 -04:00
Kevin Hartmann bb9c7a43e7 Added test to to verify operation section was added to Conformance Statement; Jame's changes to the Conformance Statement code have already made it pass, so no more code changes are necessary. :-) 2021-04-26 14:32:58 -04:00
James Agnew 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
James Agnew edfe1ae8e6
Add lastupdated to capabilitystatement (#2530) 
* Add lastupdated to capabilitystatement

* Test fix

* Test fix
 2021-04-08 13:23:21 -04:00
James Agnew fcffb04c7b
Allow unknown code systems during validation (#2523) 
* Allow unknown code systems during validation

* Add changelog

* Test fix
 2021-04-05 20:59:59 -04:00
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521) 
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
 2021-04-05 08:29:04 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511) 
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
 2021-03-30 05:48:03 -04:00
James Agnew 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
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
Kevin Dougan SmileCDR 2308d8f44b
Merge CQL Initial Implementation Into master (#2330) 
* CQL initial implementation
 2021-01-29 16:35:38 -05:00
jamesagnew 5961fde2dd Docs tweak 2021-01-29 16:12:06 -05:00
Marcel P d11515599a
Added FHIRPathResource Generator for R4 including Test. (#2310) 
Signed-off-by: Marcel Parciak <marcel.parciak@gmail.com>
 2021-01-29 11:05:05 -05:00
James Agnew 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
vedion 99b646eed7
Mapping noExtensibleWarnings and noBindingMsgSuppressed between FhirInstanceValidator and InstanceValidator (#2054) 
Co-authored-by: ahn <anders.havn@systematic.com>
 2021-01-17 09:21:08 -05:00
James Agnew 8f8c5c31f1
Add validation rules interceptor (#2264) 
* Start work on validation rules interceptor

* Work on interceptor

* Add tests

* Work on validation interceptor

* Work on interceptor

* Test fix

* Documentation tweaks
 2021-01-01 14:29:10 -05:00
James Agnew 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
ianmarshall 7899837fe0 Replaced references to SystemIdentifier with SystemUrlAndVersion. 2020-09-30 22:04:08 -04:00
ianmarshall 90f1981817 Updated tests for missed dstu2 code coverage. 2020-09-30 18:10:57 -04:00
ianmarshall dc3443665c Changes per code review. 2020-09-29 21:12:27 -04:00
ianmarshall 8e7b4e8437 Changes per code review. 2020-09-29 21:05:28 -04:00
ianmarshall 732624bfaf Fix broken JUnit test. 2020-09-25 22:55:01 -04:00
ianmarshall 47244c54dc Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support 
# Conflicts:
#	hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
 2020-09-25 09:10:07 -04:00
ianmarshall 5fe46be41c Validate code changes and new tests. 2020-09-24 18:51:47 -04:00
ianmarshall ceb5ec6384 Use canonical identifiers for code systems rather than specifying version separately. 2020-09-23 16:42:29 -04:00
Frank Tao e6a669444d Added invalid test cases for DSTU3 2020-09-22 20:51:20 -04:00
ianmarshall b32c4f01a8 Fixed lookupCode implementation in InMemoryTerminologyServerValidationSupport. 2020-09-22 18:46:16 -04:00
Frank Tao 64f2bae2e7 Impl CodeSystem $validate-code for R4 with basic test cases 2020-09-18 22:30:59 -04:00
ianmarshall 7b15f85fa1 Merge remote-tracking branch 'remotes/origin/feature_20200830_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:35:31 -04:00
ianmarshall d00db11586 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-09 17:38:24 -04:00
jamesagnew f3a5433c06 Set reference validation policy on hapi.fhir.org 2020-09-08 05:51:10 -04:00
ianmarshall 29b293f179 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-21 10:16:49 -04:00
James Agnew 03cde8c53f
Don't use remote termsvc on implied system validation (#2045) 
* Don't use remote termsvc on implied system validation

* Add changelog
 2020-08-18 13:56:37 -04:00
ianmarshall 4db00fa604 Fix broken test and cleanup. 2020-08-17 18:14:37 -04:00
ianmarshall bd94ff96cc Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-16 21:38:41 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew f0ed640e24 Upgrade core library dependency version 2020-08-10 09:05:04 -04:00
ianmarshall d39348d7bd Initial changes to support multiple versions for code system. 2020-08-09 11:49:04 -04:00
James Agnew 6a8e09addf
Ensure that parent structuredefinitions are snapshotted before (#2005) 
* Ensure that parent structuredefinitions are snapshotted before
snapshotting child

* Add changelog
 2020-07-28 11:46:58 -04:00
James Agnew 077ee02771
Fix validation for enumerated ValueSets (#1982) 
* Allow code validation against enumerated VS

* Work on validation

* Work on this

* Work on tests

* Work on validation

* Work on tests

* Work on validation

* Test fixes

* Add changelog

* For a change

* Test fixes
 2020-07-15 13:38:14 -04:00
James Agnew 29bf6b8171
Fix a bug validating ValueSets (#1981) 
* Fix a buig validating ValueSets

* Test fix
 2020-07-15 09:25:34 -04:00
James Agnew c949349a41
Correctly validate ISO 3166 codes (#1967 update) (#1973) 
* Add tests

* Test fixes

* Fix tests

* Test fix

* One more test fix
 2020-07-09 18:34:26 -04:00
James Agnew 4b1546f002
Add support for ISO 3166 to validator (#1967) 
* Add ISO 3166 support

* Add support for ISO-3166

* Add changelog

* Test fixes
 2020-07-06 05:29:48 -04:00
James Agnew 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
James Agnew 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
James Agnew f88298a1fb
Remote terminology service enhancements (#1934) 
* Remote terminology service enhancements

* Add changelog
 2020-06-23 11:35:26 -04:00
James Agnew 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
Diederik Muylwyk 314df43091 BaseValidationSupportWrapper.expandValueSet(...) and ValidationSupportChain.expandValueSet(...) were incorrectly replacing expansion options (i.e. offset and count) with null. 2020-06-22 16:52:52 -04:00
James Agnew b6540064ea
Improve TX scoping for validation (#1925) 
* Improve TX scoping for validation

* Test fix

* Test fix

* Some cleanup

* Test fixes

* Test fix
 2020-06-17 14:04:12 -04:00
jamesagnew 0c100f1aca Test fixes 2020-06-10 08:09:10 -04:00
James Agnew 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
jamesagnew d2f018919c Add test 2020-06-03 15:16:38 -04:00
James Agnew 6899604ae4
Correct validation of fragment codesystems (#1865) 
* Update validation for fragment codesystem

* Test fixes

* Add changelog

* Test fix
 2020-05-25 20:44:09 -04:00
James Agnew e780a8402e
Use R5 snapshot generator (#1862) 
* Use R5 snapshot generator

* Snapshot generator reworking
 2020-05-23 12:54:19 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
James Agnew 63ff0ede9c
Make diff operation work securely (#1859) 
* Make diff operation work securely

* Build tweak

* FIx tests
 2020-05-21 19:20:48 -04:00
jamesagnew b044d05332 Add a disabled test 2020-05-20 17:26:24 -04:00
James Agnew 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
James Agnew 9d8bd0d51e
Bump R4 definitions to 4.0.1 (#1837) 
* Bump R4 definitions to 4.0.1

* Add changelog

* Test fixes
 2020-05-08 19:34:13 -04:00
James Agnew a77aa6a28e
Multitenancy Ticket 2 - #1813 (#1821) 
* Work on multitenancy

* Second ticket started

* More multitenancy work

* Work on tenancy security

* Work on multitenancy

* Test fixes

* Add docs

* cs tweak

* Multitenancy fixes

* Add debug log

* Fix build

* Add headers

* Add partition selection interceptor hook

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Account for review comments

* Resolve FIXMES

* Work on tests

* Test fixes

* A bit more cleanup

* Work on multitenancy

* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Allow disabling text modifier indexing

* Add changelog

* Docs fixes

* Address review comment

* Resolve merge conflicts

* Merge master

* Compile fix

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-05 15:12:15 -04:00
James Agnew 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
jamesagnew 371cda280a Test fix 2020-04-23 08:50:22 -04:00
jamesagnew 4978a5de21 Add test 2020-04-23 05:30:08 -04:00
James Agnew 1a3a40b3c9
Merge pull request #1796 from jamesagnew/ja_20200409_report_json_error_attr_name 
Improve error message reporting for invalid json - Fix #1793
 2020-04-09 15:11:57 -04:00
jamesagnew ac29073b72 Test fixes 2020-04-09 14:22:04 -04:00
James Agnew fdf6633145
Add validation for currencies to validator (#1797) 
* Add validation for currencies to validator

* Add changelog
 2020-04-09 11:39:30 -04:00
jamesagnew 300c4e66ba Fix broken test 2020-03-23 19:09:03 -04:00