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3143 Commits

Author SHA1 Message Date
Nick Goupinets 2a3b72db17 Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-11-27 16:54:04 -05:00
Nick Goupinets dc2a9e55c5 Renamed sourceResource to goldenResource 2020-11-27 16:53:47 -05:00
jamesagnew fbbba11417 Formatting only 2020-11-27 16:16:01 -05:00
IanMMarshall 722e24d80c
Merge pull request #2175 from jamesagnew/ft-fix-expend-filter-contains-issue 
Fixed expand filter issue
 2020-11-27 14:47:05 -05:00
ianmarshall bbba4428ee Changed name for new tokenFilter to make it unique. 2020-11-27 11:38:24 -05:00
ianmarshall be88a256d0 Changed name for new tokenFilter to make it unique. 2020-11-27 11:32:08 -05:00
Frank Tao 014e2ba9cb Rework on the expand issue replaced the EdgeAnalyzer 2020-11-26 20:37:51 -05:00
Frank Tao a511543e77 Merge branch 'master' into ft-fix-expend-filter-contains-issue 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
 2020-11-26 18:47:10 -05:00
swagers cb693afe25
Changed the names URIs and IDs of a few LOINC concept maps (#2197) 
Changed to match what LOINC uses for these concept maps

Co-authored-by: Steven Wagers <swagers@regenstrief.org>
 2020-11-26 10:06:17 -05:00
James Agnew fb8658da70
Always apply vs filters correctly (#2195) 
* Always apply valueset filters correctly

* Test fix

* Testfix

* Test fix

* Add changelog

* Test fix
 2020-11-24 18:12:02 -05:00
Frank Tao 3d9e0aeac1 Added more test cases 2020-11-23 21:32:46 -05:00
Frank Tao 5a05513250 Revoked filter op to EQUAL and enabled NGramAnalyzer 2020-11-21 14:46:26 -05:00
Frank Tao 5b471602c6 Merge branch 'master' into ft-fix-expend-filter-contains-issue 2020-11-20 10:29:58 -05:00
James Agnew a01f5ae906
Fix subsumption test direction (#2183) 
* Fix subsumption test direction

* Add changelog

* Test fixes
 2020-11-19 21:48:54 -05:00
James Agnew 8b65db0c98
Improve error message on unique constraint violation (#2182) 
* Improve error message on unique constraint violation

* Add changelog

* Test fixes

* Test fix
 2020-11-19 21:20:59 -05:00
Frank Tao e551f1837e Updated based on review 2020-11-19 20:22:13 -05:00
Tadgh 953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
ianmarshall d99db2dbcc Fixed NPE in package loader when package description is null. Also renamed tests that would have caught this problem sooner. 2020-11-18 22:37:35 -05:00
Frank Tao 878c22192e Added expand filter impl for R5 and dstu3, changed the filter logic 2020-11-18 22:26:21 -05:00
Frank Tao f65fdb0d52 Merge branch 'master' into ft-fix-expend-filter-contains-issue 2020-11-18 19:54:01 -05:00
Tadgh 75c0c25d7b remove references to EMPI 2020-11-18 19:50:00 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
Tadgh 805d5b1d6c Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-17 09:28:37 -05:00
IanMMarshall 7532313c0f
Change to not set ValueSet expansion component parameter id HibernateSearch not enabled. (#2178) 
Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-17 07:46:55 -05:00
Frank Tao 78f730c4ca Fixed expend filter issue 2020-11-15 22:39:14 -05:00
jamesagnew 1db0944243 Improve logging for terminology ingestion 2020-11-13 17:25:14 -05:00
IanMMarshall ed953d82f8
Rename index that was recently changed. (#2173) 
* Restoring name of index that was changed in migration task.

* Rename TermValueSetConcept index that was recently changed.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-13 14:12:25 -05:00
Tadgh f648d8ec2b renaming in personsvc 2020-11-13 09:44:15 -05:00
Nick Goupinets 2bbfb6dfaa WIP 2020-11-11 15:27:57 -05:00
Nick Goupinets b0f449ff5e MergerSvcTest WIP 2020-11-11 10:17:03 -05:00
IanMMarshall bf9e02bc16
Merge pull request #2164 from jamesagnew/im_20201029_ig_package_long_description 
Truncate package descriptions that are longer than 200 characters.
 2020-11-10 12:01:53 -05:00
James Agnew 63b7b379c2
Improve ValueSet filtering (#2162) 
* Improve filter search

* Filter improvements

* Tests passing

* Test fixes

* Fix transaction filter

* Add changelog

* Test fix

* Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Resolve FIXME

* Test fix

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-11-10 11:01:13 -05:00
ianmarshall 881193cf24 Truncate package descriptions that are longer than 200 characters. 2020-11-09 16:19:05 -05:00
jamesagnew 4f6be9d9a7 Reduce test timeout 2020-11-09 14:46:15 -05:00
Nick Goupinets 4c0fab8cec Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-11-09 09:06:50 -05:00
jamesagnew 22fe9420ac Add tests 2020-11-06 09:10:47 -05:00
Tadgh 5797cd0682 * Add source_resource_id column 
* Add source_resource columm
Still need to depracate the old columns.
Reworked a Matcher to ignore Person
 2020-11-05 13:07:45 -05:00
Frank Tao ce1caee9fa
Feature 2020 10 28 reverse chain (#2160) 
* Added test cases for multiple '_has'

* Fixed composite search for the new SearchBuilder

* Added more test cases
 2020-11-05 05:27:11 -05:00
IanMMarshall 38a975f09d
Im 20201028 fix versioned valueset expansions (#2151) 
* Fixes to ValueSet expansion for cases where CodeSystem is versioned.

* Fixes to ValueSet expansion for case where URL and filter parameters specified.

* Restore maven-wrapper.properties file inadvertently deleted from GitHub.

* Fix JUnit tests and ValueSet exclude.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-04 16:36:43 -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
jamesagnew 783cbb3cf8 Bump postgres driver version 2020-10-26 19:34:50 -04:00
James Agnew 72294fc0a0
Suport typeFilter parameter for bulk export (#2147) 
* Cleanup

* Fix tests

* Work on bulk export

* Work on export

* Test fixes

* Add changelog

* Address review comments

* Address review comments
 2020-10-26 12:28:07 -04:00
James Agnew 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
James Agnew 4a5f5199b5
Add custom partition interceptor examples (#2145) 
* Add custom partition interceptor examples

* Add documentation

* Test fixes

* Remove outdated test

* Test modification
 2020-10-25 19:19:40 -04:00
blangley28 d468183edd
Validate theSearchParamRegistry is not null (#2142) 2020-10-23 10:29:55 -04:00
IanMMarshall 1c9e4dcc81
Merge pull request #2135 from jamesagnew/im_20201015_loinc_versioned_resourceids 
Im 20201015 loinc versioned resourceids
 2020-10-22 19:01:31 -04:00
IanMMarshall fd46d0965f
Merge pull request #2141 from jamesagnew/im_20201020_package_installer_enhancements 
Enable package installer to load non-Conformance resources
 2020-10-21 18:28:15 -04:00
ianmarshall 115b09e4d4 Throw exception if any resources in package have no url and no identifier. 2020-10-21 17:23:40 -04:00
ianmarshall 756432e61a Enable package installer to load resources other than conformance resources. 2020-10-21 15:47:31 -04:00
jamesagnew 9b4c1a58a6 License header updates 2020-10-21 12:58:29 -04:00
Ken Stevens 3b91873b7c
delete expunge (#2131) 
Added delete _expunge=true
 2020-10-20 17:21:50 -04:00
James Agnew 9e8e98b6fb
Rework scheduler to use Spring factory (#2134) 
* Rework scheduler to use Spring factory

* Add test
 2020-10-19 10:33:12 -04:00
ianmarshall f3639ee1ce Changes to terminology loader to support preserving the original resource IDs for LOINC even when multiple versions are loaded. 2020-10-16 16:30:37 -04:00
Tuomo Ala-Vannesluoma 1435540320
Improve synchronous searching by providing offset & limit support (#2059) 
* Improve synchronous searching by providing offset & limit support

Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)

* Review and test fixes

Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)

* Remove temporary count querying fix for synchronous loads

* Fix offsetting of everything operations, do not drop zero offset

* Fix jpa test default and maximum page size, add some fixmes to tests before resolved

* Ignore one failing test, fix others

* Fix Dereferenced variable may be null

* Fix everything paging in R4 by adding DISTINCT if synchronous load is used

Also fix assertion of size when hitting fetchSizeDefaultMaximum

* Add documentation about offset annotation and paging

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-10-12 17:42:03 -04:00
vedion e4214a4cbe
Exposing hasIncludes PersistedJpaBundleProvider (#2047) 
Co-authored-by: ahn <anders.havn@systematic.com>
 2020-10-12 17:37:12 -04:00
James Agnew 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
IanMMarshall a44037daf3
Merge pull request #2122 from jamesagnew/im_20201007_conceptmap_sourcesystemversion 
Fixed loader so that it now sets source system version for ConceptMap…
 2020-10-08 14:04:49 -04:00
James Agnew d2aae361bf
Rewrite deferred interceptor callback framework (#2121) 
* Rewrite deferred interceptor callback framework

* Improve deferred handling

* Null guard

* Test fix
 2020-10-07 20:08:18 -04:00
ianmarshall 476eba676e Fixed loader so that it now sets source system version for ConceptMap resources. 2020-10-07 15:07:25 -04:00
ianmarshall 46b2fde1db Fixed tests to accommodate suggested changes from code review. 2020-10-07 11:07:34 -04:00
IanMMarshall 1bac646dc3
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/LoadedFileDescriptors.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-10-07 11:01:54 -04:00
IanMMarshall e24e233ec6
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/LoadedFileDescriptors.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-10-07 11:01:47 -04:00
ianmarshall 0f39eeb0e9 Bug fix and test improvements. 2020-10-06 21:22:09 -04:00
ianmarshall d9841e59ac Restore ability to load LOINC PartLink data from a single file for pre-2.68 versions. 2020-10-06 14:36:23 -04:00
IanMMarshall 5ec1284b8a
Apply suggestions from code review 
Edits per code review.

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-10-05 15:14:39 -04:00
ianmarshall 2258d37283 Documentation for terminology. 2020-10-05 09:02:00 -04:00
IanMMarshall f1710fd0be
Merge pull request #2081 from jamesagnew/feature_2020_09_02_term_multi_version_support 
Feature 2020 09 02 term multi version support
 2020-10-01 12:24:40 -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
Ken Stevens 09d09233ff
empi bugfixes and enhancements (#2104) 2020-09-29 17:27:43 -04:00
IanMMarshall c593958d2c
Apply suggestions from code review 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 15:16:46 -04:00
IanMMarshall d63c15ef09
Apply suggestions from code review 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:27:57 -04:00
IanMMarshall 43c16e1737
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:27:03 -04:00
IanMMarshall 43b6bd38ff
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:26:30 -04:00
IanMMarshall 2be47b5567
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:18:21 -04:00
IanMMarshall b8531e599f
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:18:00 -04:00
IanMMarshall 3940e7526f
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:17:36 -04:00
IanMMarshall 6aa1a5ec3f
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:17:19 -04:00
IanMMarshall ebb3fa0ca1
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:16:56 -04:00
IanMMarshall 10620a8bb4
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:16:13 -04:00
ianmarshall 9d8664ccd8 Additional tests and updates. 2020-09-27 21:09:06 -04:00
ianmarshall e86d9deaac Additional tests. 2020-09-27 17:45:15 -04:00
ianmarshall 732624bfaf Fix broken JUnit test. 2020-09-25 22:55:01 -04:00
ianmarshall 1dc4a533d6 Fixes to terminology loader. 2020-09-25 21:43:15 -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 6f9874468a Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-25 08:54:17 -04:00
ianmarshall 2bceacd9a6 Update loader to ensure that ConceptMap and ValueSet Ids are unique for each version loaded. 2020-09-25 08:51:53 -04:00
ianmarshall 5fe46be41c Validate code changes and new tests. 2020-09-24 18:51:47 -04:00
ianmarshall e5daea17b7 Additional cleanup and migration tasks. 2020-09-23 17:17:07 -04:00
ianmarshall dffc02a126 Missing fixes for DSTU3 and R5. 2020-09-23 16:51:18 -04:00
ianmarshall 640ee94c5c Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support 2020-09-23 16:43:22 -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 3d3d013d72 Changed import of IdType to r5. 2020-09-23 09:19:06 -04:00
Frank Tao b6d86dc5f2 Added fail(); in the invalid test cases 2020-09-22 20:39:20 -04:00
Frank Tao 20661c7a2b Removed unused import 2020-09-22 20:19:43 -04:00
Frank Tao 673274a966 Added invalid test cases for CodeSystem/$validate-code R3 2020-09-22 20:18:18 -04:00
ianmarshall b32c4f01a8 Fixed lookupCode implementation in InMemoryTerminologyServerValidationSupport. 2020-09-22 18:46:16 -04:00
ianmarshall 4216cee8c6 Added and enhanced tests plus fixes arising from tests. 2020-09-22 14:44:32 -04:00
James Agnew ef4f3df945
Don't install draft package contents (#2099) 
* Don't install draft package contents

* Add changelog

* Add changelog
 2020-09-22 09:44:36 -04:00
James Agnew 072e63be5a
Avoid a crash on double date chains (#2097) 
* Avoid a crash on double date chains

* Add changelog

* Address coverage warning
 2020-09-21 15:43:07 -04:00
ianmarshall f9f8bf6515 Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support 2020-09-20 22:02:08 -04:00
ianmarshall 302bbca8fd Changes to support multi-versioning in ValueSet $expand operation. 2020-09-20 22:01:21 -04:00
Frank Tao 8f692a4776 CodeSystem/$validate-code not supported for DSTU2, DSTU3 2020-09-19 22:54:39 -04:00
Frank Tao a3a032584b Made Transactional 2020-09-19 15:18:28 -04:00
Frank Tao 01d88a665d Added CodeSystem/$validate-code for R5 2020-09-19 14:13:07 -04:00
Frank Tao 7db9f7475b Changed fetch size to 1 for CodeSystem $validate-code 2020-09-19 12:52:18 -04:00
Frank Tao 05de0c5031 Added more test cases for R4 2020-09-19 12:36:14 -04:00
Frank Tao 64f2bae2e7 Impl CodeSystem $validate-code for R4 with basic test cases 2020-09-18 22:30:59 -04:00
Ken Stevens 3189819dd5
limit transaction size config (#2087) 2020-09-16 14:13:03 -04:00
jamesagnew b64e982ec3 Credit for #2083 2020-09-16 09:07:33 -04:00
Tue Toft Nørgård c884f29112
SearchCoordinatorSvcImpl gets ExecutorService from injected ThreadPoolTaskExecutor (#2083) 
* Get ExecutorService from injected ThreadPoolTaskExecutor which enables support of TaskDecorators (e.g. to add/clear ThreadLocal logging context (MDC) variables)

* Properly initialize ThreadPoolTaskExecutor
 2020-09-16 09:05:28 -04:00
ianmarshall 7f7e1f39bc Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 22:06:43 -04:00
ianmarshall b2b63cbb02 Fixed JUnit tests. 2020-09-15 22:05:46 -04:00
ianmarshall 3add1320b7 Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:52:02 -04:00
ianmarshall ca0bdc8e4c Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-15 16:49:06 -04:00
ianmarshall 539ef63fc0 Merge branch 'im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:24:47 -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 087c9e3c3b Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:34:11 -04:00
ianmarshall b4cd09a5b6 Further cleanup 2020-09-15 12:30:26 -04:00
ianmarshall fe684ee4c0 Further cleanup 2020-09-15 12:26:17 -04:00
ianmarshall cd104ad635 Revised approach for versioning of ValueSet. 2020-09-15 10:21:42 -04:00
James Agnew 9711b5ed18
Update resources on package reinstall (#2078) 
* Start testing

* Update resources on package install

* Add changelog
 2020-09-15 08:46:43 -04:00
Frank Tao 0d929d4d19 Updated based on review comments 2020-09-14 09:30:03 -04:00
Frank Tao 8551b33e8a Merge branch 'feature_2020_09_02_term_multi_version_support' into ft_2020_09_11_term_multi_version_support_loader 2020-09-14 09:15:12 -04:00
Frank Tao 701fe81acf
Merge pull request #2072 from jamesagnew/ft_2020_09_10_term_multi_version_support_db_migration 
Term multi version support db migration - ConceptMap table change
 2020-09-14 09:13:12 -04:00
Frank Tao 91c1df7ce4 Supported ConceptMap Version from the properties 2020-09-11 21:38:42 -04:00
Frank Tao 750cbf4ba3 @Deprecated the old findTermConceptMapByUrl method 2020-09-11 09:20:01 -04:00
Frank Tao 16a5f57ae9 Added for ConceptMap DB migration 2020-09-10 21:41:06 -04:00
Frank Tao 972bdbd87d Updated based on code review 2020-09-10 21:17:41 -04:00
Frank Tao c873b6d6dd Fixed ConceptMap $translation without conceptMapVersion issue. 2020-09-09 22:24:02 -04:00
ianmarshall b4a87adc64 Suggested test that includes case where ConceptVersion is not specified in $translate operation. 2020-09-09 16:53:14 -04:00
Frank Tao 2fd692f5bb Updated R5 reverse $translate test case for more coverage 2020-09-07 20:54:35 -04:00
Frank Tao 5e17625a1b Fixed NullPointerException for reverse $translate operation. 2020-09-07 18:09:01 -04:00
Frank Tao 5410042643 Multi-version supported for ConceptMap $translate operation 2020-09-07 10:43:58 -04:00
Frank Tao 81cd73f820 Added test cases to for duplicate url and version of ConceptMap 2020-09-06 15:27:29 -04:00
Frank Tao 1ecec0abc9 Fixed duplicate ConceptMap URL only 2020-09-06 15:23:26 -04:00
Frank Tao 45b88de3b6 Fixed typo 2020-09-06 11:47:07 -04:00
Frank Tao ed2801dbaf ConceptMap multi-version supported 2020-09-06 11:33:55 -04:00
ianmarshall 5b707f97a9 Missing commits 2020-09-04 09:25:35 -04:00
ianmarshall 019d08a064 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-03 22:37:39 -04:00
ianmarshall 5f005120c9 Initial changes to support multi-version ValueSets 2020-09-03 22:36:15 -04:00
jamesagnew 5b7e6b593b Avoid startup retry loop 2020-09-02 19:56:57 -04:00
James Agnew d8542899e5
Don't lazy load DAOs (#2061) 
* Don't lazy load DAOs

* More tweaks
 2020-09-01 09:54:50 -04:00
James Agnew c6777578a8
Avoid DB binary storage deadlock (#2062) 
* Avoid DB binary storage deadlock

* Add changelog

* Rework
 2020-09-01 09:52:38 -04:00
ianmarshall 94440c849f Ensure that LOINC loader assigns a distinct ID for each version. 2020-08-30 21:53:38 -04:00
ianmarshall 1c55d87b10 Problem found in LOINC loader. 2020-08-30 17:11:48 -04:00
ianmarshall 3fef8f7bef Back out changes relating to validate operations. Cleanup of code 2020-08-30 15:29:57 -04:00
ianmarshall 92313cd770 Tests and fixes to support versioned CodeSystem lookup and subsume operations 2020-08-26 16:23:17 -04:00
ianmarshall 5a0bce9155 Changes to enable request delete of specific Code System version. 2020-08-25 12:45:53 -04:00
ianmarshall 796d2923e0 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-25 12:07:13 -04:00
ianmarshall 749c2bc4be Changes to enable request delete of specific Code System version. 2020-08-25 12:06:07 -04:00
James Agnew 437e81fc65
Support multiple updates of one resource in a transaction (#2050) 
* Support multiple updates of one resource in a transaction

* Test update

* Add changelog

* Test fix
 2020-08-25 05:55:54 -04:00
vedion 31d736915f
- Adding missing null guard (#2049) 
* - Adding missing null guard. Guard needed when reference can't be resolved.

* Adding test for INCLUDE_ALL null guard fix

Co-authored-by: ahn <anders.havn@systematic.com>
 2020-08-22 16:59:36 -04:00
ianmarshall dc786eaff9 Refine model for storing multiple code versions. 2020-08-21 10:16:10 -04:00
ianmarshall 2126c5c556 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-18 11:15:09 -04:00
jamesagnew 30ac44974d Add JPA Starter to componentscan exclusions 2020-08-18 08:06:21 -04:00
ianmarshall c1dcf0442c Fix broken tests. 2020-08-17 21:52:16 -04:00
ianmarshall 4db00fa604 Fix broken test and cleanup. 2020-08-17 18:14:37 -04:00
James Agnew 1fadaeeff5
Reject nvalid SearchParameter wiith no path expression (#2043) 
* Fix some changelog typos

* Reject SearchParameter with invalid path

* Add changelog

* Test fix

* Test fixes

* Test fixes

* Test fix

* One more test fix
 2020-08-17 11:21:55 -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
Ken Stevens 7dd7f2b923
resource pid userdata fix (#2044) 
* fixed resource UserData RESOURCE_PID for expunge hook (was incorrectly pointing to ResourceHistoryTable pid instead of ResourceTable pid.

* fix merge
 2020-08-16 20:48:39 -04:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew 90ebaf8549 Add one more test for #2023 2020-08-11 08:54:03 -04:00
jamesagnew f3fbad63e7 Avoid a LOB error when expanding a valueset on Postgres 2020-08-11 08:30:48 -04:00
jamesagnew f0ed640e24 Upgrade core library dependency version 2020-08-10 09:05:04 -04:00
James Agnew e61b39fc30
Force a flush of the SearchParameter cache sooner when SPs change (#2030) 
* Force a flush of the SearchParameter cache sooner when SPs change

* Add changelog

* Test fixes
 2020-08-09 19:30:59 -04:00
jamesagnew 096f310cae Increase visibility 2020-08-09 14:23:06 -04:00
James Agnew 8f6d08dd58
Fix #2022 - Invalidate caches on expunge (#2029) 
* Fix #2022 - Invalidate caches on expunge

* Rename changelog file
 2020-08-09 14:14:28 -04:00
jamesagnew 49f4f3ef62 Add license headers 2020-08-09 13:23:45 -04:00
ianmarshall d39348d7bd Initial changes to support multiple versions for code system. 2020-08-09 11:49:04 -04:00
James Agnew 8e0023c385
Disable referential integrity for some paths (#2025) 
* Disable referential integrity for some paths

* Add changelog

* Remove unneeded file
 2020-08-09 07:09:37 -04:00
James Agnew 63ef2ce006
Fix #2012 - Always filter total from search results when consent interceptor in use (#2020) 
* consent bug test

* Fix #2012 - Always filter total from search results when consent
interceptor in use

* Add changelog

* Address coverage issues

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
Co-authored-by: jvi <jvi@trifork.com>
 2020-08-07 09:16:02 -04:00
James Agnew 5d9d4070fb
Fix an issue with binary storage not updating correctly if a retry (#2014) 
interceptor is present
 2020-08-05 09:14:40 -04:00
Tadgh 750d693fc3
Merge pull request #1984 from jamesagnew/batch-empi-job 2020-08-04 13:21:25 -07:00
jamesagnew 03f7289ac8 Add test for #2012 2020-08-04 09:16:47 -04:00
Tadgh 2cf48eb9b9 Move field length into constants 2020-08-01 13:11:33 -07:00
Tadgh 995c188305 implement function for all concrete classe 2020-08-01 13:03:37 -07:00
Tadgh 0a4d81eb85 Move getNextBatch into IResultIterator 2020-08-01 13:00:55 -07:00
Tadgh efaf09fbfa Fix java.lang.string in empiLink entity 2020-08-01 11:47:00 -07:00
Tadgh 48bf78e972 Rename service interface name 2020-07-30 12:17:14 -07:00
Tadgh 102f936156 Rework into new person deleting service 2020-07-29 12:17:07 -07:00
Tadgh 0e88f359f5 Merge remote-tracking branch 'remotes/origin/master' into batch-empi-job 2020-07-29 09:42:12 -07:00
James Agnew 3098affccb
Update path when updating resource links (#2007) 
* fix resource link index reuse bug

* Resolve merge conflicts

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-07-28 21:40:56 -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
Tadgh 82dcc395ec Merge branch 'master' into batch-empi-job 2020-07-27 14:59:27 -07:00
James Agnew 3a7ac0debc
Correct invalid decimal numbers stored in DB (#2003) 
* Correct invalid decimal numbers stored in DB

* Add changelog
 2020-07-27 13:33:27 -04:00
jamesagnew c6769ef075 Add test for #1999 2020-07-25 15:17:25 -04:00
James Agnew a6fd6254db
Speed up loinc ingestion (#1991) 
* Speed up loinc ingestion

* Add some logging
 2020-07-23 09:20:33 -04:00
Tadgh bbe6d5600e Address review comments 2020-07-22 11:58:08 -07:00
jamesagnew 5f1078ac13 Cleanup of package installer 2020-07-21 11:43:57 -04:00
Tadgh 4ec2be4ff5 Merge branch 'master' into batch-empi-job 2020-07-21 07:54:18 -07:00
Tadgh e82451533f Move provider logic. Fix tests to reflect. Remove now-dead methods 2020-07-21 07:52:51 -07:00
jamesagnew c44c1ff11f Wrap NPM loader in a try-catch 2020-07-21 09:57:10 -04:00
Tadgh de9621602b Update provider and create test skeletons for empi batch run 2020-07-18 18:18:21 -07:00
Tadgh 62b5221c3f Move Empi Batch work to the BaseHapiResourceProvider, allowing manual EMPI runs on a server/type/ID basis. 2020-07-18 13:36:14 -07:00
Tadgh 4fa4dd1c48 Update Javadocs 2020-07-17 13:39:39 -07:00
James Agnew 5db90d3e6e
Address issues when importing US Core (#1986) 
* Work on US Core import

* Work on US Core

* Resolve issues with US Core import

* Test fix
 2020-07-17 15:28:16 -04:00
Tadgh e540e4b0a2 Minor addition to PointcutLatch to support an inline runnable 2020-07-17 12:06:19 -07:00
Tadgh 1e12c740f6 Merge branch 'master' into batch-empi-job 2020-07-17 09:28:10 -07:00
Tadgh 92461b6346 wip 2020-07-17 09:00:15 -07:00
jamesagnew b57681da59 License header updates 2020-07-17 08:54:20 -04:00
Ken Stevens ebd6ca4b64
Empi 3 ruleset version (#1978) 
* add rule version

* add rule version

* Rough in model for Golden Record.

* Test Link Rule Version

* add eid match boolean

* added new fields to EmpiLink to provide more information about how the link was created

* add logging to check an edge case

* all tests pass

* wip with failing tests

* tests pass

* FIXME

* optimize imports

* test score in provider output

* FIXME

* FIXME

* Fix jpa test app context

* fix migration string length

* review feedback param name

* review feedback javadoc

* review feedback javadoc

* bean config reorganization for cdr

* add more tests
 2020-07-17 08:31:15 -04:00
Tadgh 6bb92717f5 Merge branch 'master' into batch-empi-job 2020-07-16 11:00:32 -07:00
Ibrohim Kholilul Islam 5a79304893
Implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation (#1896) 
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports
 2020-07-16 09:25:26 -04:00
jamesagnew 962055e092 Undo extra logging in tests 2020-07-15 13:47:19 -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 063bf4237c
Allow ConceptMap with no explicit group source/target (#1983) 
* Allow ConceptMap with no explicit group source/target

* Add changelog
 2020-07-15 12:57:10 -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
jamesagnew addcdc9269 Make method transactional 2020-07-14 19:12:40 -04:00
jamesagnew d6f6ec2d66 License headers 2020-07-13 16:57:24 -04:00
Tadgh 677bc5577b wip 2020-07-13 12:00:19 -07:00
James Agnew 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
James Agnew 5c14a6c217
Revert pointless SQL optimization (#1977) 
* Revert pointless SQL optimization

* Fix tests
 2020-07-09 22:14:25 -04:00
James Agnew 1449b9cb0a
Install NPM resources correctly (#1972) 
* Install NPM resources correctly

* Fix tests
 2020-07-09 18:37:55 -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
Ibrohim Kholilul Islam 7a44fa3eb3
Fix GraphQL Array of Argument should be ORed (#1966) 
* provide IQueryParameterOr instead of IQueryParameterType to params.add

* add tests
 2020-07-08 10:38:50 -04:00
Tadgh 86f2761580 Merge branch 'master' into batch-empi-job 2020-07-07 07:52:42 -07:00
Tadgh 5b402de581 Add EmpiTargetType to link 2020-07-07 07:51:41 -07:00
Tadgh f82a53e6f9 Merge branch 'master' into batch-empi-job 2020-07-06 13:12:20 -07:00
Tadgh 3081df3cbd
Merge pull request #1969 from jamesagnew/empi-interceptor-bug 
EMPI Storage interceptor bug fix
 2020-07-06 13:10:39 -07:00
jamesagnew 489bd77dd4 Make constraint name comparisons case insensitive 2020-07-06 14:58:03 -04:00
Tadgh 84da932187 fix test 2020-07-06 11:36:47 -07:00
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
Tadgh 25d8668f55 Add Basic provider method, skeleton of tests 2020-07-03 15:21:32 -07:00
James Agnew 290577ff3e
Remove unnecessary type predicate (#1963) 
* Remove unnecessary type predicate

* Add changelog
 2020-07-03 17:54:25 -04:00
IanMMarshall e23e222f80
Merge pull request #1960 from jamesagnew/im_20200630_code_system_load 
Accidentally merged pull request before pushing changes from code review
 2020-07-03 16:29:34 -04:00
Tadgh 6259eada3c Fix parameter names. These are not partitions 2020-07-03 13:18:48 -07:00
ianmarshall b1ff6cbe37 Changes from code review 2020-07-03 14:25:24 -04:00
Tadgh 63bf9cca1b
Merge pull request #1961 from jamesagnew/bulk-intermittent 
Bulk intermittent bug
 2020-07-03 11:19:51 -07:00
Tadgh 4ff63e2493 Remove unnecessary logging. Spring batch already logs this 2020-07-03 10:21:04 -07:00
Tadgh d09f410b4d Tidy logging, increase timeout to 120 because clocks 2020-07-03 10:15:57 -07:00
Tadgh a84a41643d Increase awaitility timeout for bulk export of ALL resources 2020-07-03 10:08:34 -07:00
ianmarshall 4e5ca2ee15 Changes from code review 2020-07-03 13:08:11 -04:00
Tadgh 38cb526696 Add logging 2020-07-03 09:40:52 -07:00
ianmarshall 46abdfafe0 Merge remote-tracking branch 'remotes/origin/master' into im_20200630_code_system_load 2020-07-02 13:29:17 -04:00
ianmarshall 557f732e17 Cleanup and improved Unit tests. 2020-07-02 12:03:15 -04:00
Ken Stevens 714bd6216e
Empi 70 phonetic indexing (#1941) 
* start with failing test

* test passes with fixmes

* javadoc and config

* pre-review cleanup

* generalize encoding

* test passes, but indexing needs to be optimized

* test passes, but indexing needs to be optimized

* step 1 of optimization.  big refactor of all predicates

* step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation

* integrated new phonetic encoders into empi

* phonetic search implemented

* IT passes

* pre-review cleanup

* final pre-review cleanup

* final pre-review cleanup

* Fix compile error

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-06-30 17:36:54 -04:00
jamesagnew bb17688680 Add test for #1780 2020-06-30 17:03:16 -04:00
ianmarshall 0788e79d51 Fix to address deferred save of TermConcept when code system version changes prior to save. 2020-06-30 15:07:14 -04:00
jamesagnew 2cdef055aa Missed commit on #1951 
Squashed commit of the following:

commit f820135996
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 14:29:24 2020 -0400

    Address review comments

commit 11c4f9defb
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:38:16 2020 -0400

    Fix LGTM warning

commit b650fdb9ea
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:20:52 2020 -0400

    Test fix

commit 6ebcceeb5c
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:49:01 2020 -0400

    Add changelog

commit 4a1d7383b0
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:46:52 2020 -0400

    Bundle transmission

commit 88bd4abf0c
Merge: 7cde945281 25fc747b9f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:31:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 7cde945281
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:10:33 2020 -0400

    Work on seed bundles

commit ed2e62752e
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 09:39:10 2020 -0400

    Work on subscriptions

commit 52addcff59
Merge: 64a9eaa4de bf8de84801
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Sat Jun 27 18:09:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 64a9eaa4de
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:32:17 2020 -0400

    Start work

commit f74eba5397
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:28:18 2020 -0400

    Terser should create correct Enumeration on create
 2020-06-30 14:31:40 -04:00
James Agnew fa4bbe3685
Allow search criteria as subscription delivery mechanism (#1951) 
* Terser should create correct Enumeration on create

* Start work

* Work on subscriptions

* Work on seed bundles

* Bundle transmission

* Add changelog

* Test fix

* Fix LGTM warning
 2020-06-30 14:29:09 -04:00
James Agnew 072f3a422a
Use read partition for finding update candidate on upsert (#1945) 
* Use read partition for finding update candidate on upsert

* Add changelog
 2020-06-29 18:22:27 -04:00
Tadgh 8df0448f88 Fix import 2020-06-29 11:04:03 -07:00
Tadgh 4e789fbf42 Fix import error 2020-06-29 11:01:38 -07:00
Tadgh e365e643ba
Merge pull request #1906 from jamesagnew/spring-batch-integration 
Spring batch integration
 2020-06-28 16:10:43 -07:00
jamesagnew be23eb3cfc Move the flush into the existing transaction 2020-06-27 18:06:37 -04:00