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3777 Commits

Author SHA1 Message Date
James Agnew 9e057574a6
Allow multi-resource Subscription criteria (#3110) 
* Allow start criteria subscriptions

* Rework subscription tests

* Subscription cleanup

* Add changelog

* Test fixes

* Test fix
 2021-10-26 16:48:13 -04:00
michaelabuckley 2cf8e74414
Introduce standard date search test cases (#3096) 
* Introduce standard date search test cases
 2021-10-26 19:15:06 +00:00
JasonRoberts-smile 20f31e4854
Jr 20211021 chained references 3 (#3107) 
* 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

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

* adding some failing test cases to illustrate the limitations of qualified searches

* clean up merge cruft

* changelog

* create recursive resource links

* add test coverage for a more complicated case

* changelog

* remove unnecessary check for _contained flag

* fix broken tests
 2021-10-25 10:16:10 -04:00
JasonRoberts-smile b267fdb752
Jr 20211018 chained references 2 (#3099) 
* 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

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

* adding some failing test cases to illustrate the limitations of qualified searches

* clean up merge cruft

* changelog
 2021-10-22 12:41:05 +00:00
Tadgh 2d55af1ec4
Fix postgresql regression (#3101) 
* Bump elastic version

* Fix broken types for sql builder in postgres

* Add changelog

* Fix changelog
 2021-10-21 16:23:41 -04:00
michaelabuckley f98f3cdaa9
Extend ordinal date search to year and month precision (#3102) 
* added eq and gt test cases

* added missing gt search param tests

* added lt tests

* Add some high-bound test cases

* More test cases and new compressed format

* More test cases

* More test cases

* Re-order columns for easier reading

* Comments

* Cleanup and comments

* Fixed incomplete date issue

* Set to the last millisecond 23:59:59.999

* Disabled 4 failed JVM/TZ related test cases

* Added changelog

Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
 2021-10-21 15:32:26 -04:00
jmarchionatto 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
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
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
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
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
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
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 b2a4ff2f29 Try to avoid intermittent 2021-10-11 19:14:01 -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 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 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
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
Tadgh cd1a4154c1 Merge branch 'remove-parallel-non-gets' of github.com:hapifhir/hapi-fhir into remove-parallel-non-gets 2021-09-28 09:55:13 -04:00
Tadgh 072c030c2d Remove modifications, defaults work 2021-09-28 09:55:06 -04:00
Tadgh ad05a5ec09
Merge branch 'master' into remove-parallel-non-gets 2021-09-28 09:43:01 -04:00
Tadgh dde0529b07 Remove extra semicolon 2021-09-27 15:36:17 -04:00
Tadgh 0c123384c7 add test for failing batch bug, remove bounding on queue 2021-09-27 15:34:19 -04:00
katie_smilecdr d121f6eff1 Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition 2021-09-27 15:10:19 -04:00
juan.marchionatto 2dec5f0821 Add explicit brackets 2021-09-27 13:47:23 -04:00
juan.marchionatto b4343a9823 Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-09-27 09:48:15 -04:00
juan.marchionatto 00ceb3f35d Add tests 2021-09-27 09:47:05 -04:00
michaelabuckley 5ee5b08b50
Merge branch 'master' into mb-fix-NoFt-tests 2021-09-24 16:38:05 -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 d03f9cb35b Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-09-24 15:40:22 -04:00
juan.marchionatto eb9f29b3f3 Simplify code 2021-09-24 15:05:06 -04:00
katie_smilecdr d067586607 [3020] add documentation/changelog 2021-09-24 14:49:07 -04:00
Michael Buckley 11c5f7ee87 Some configs don't publish and FullText service at all. Make it optional. 2021-09-24 14:32:34 -04:00
Michael Buckley 79e2800f3e Fix cut-n-paste glitch in dstu2 NoFt 2021-09-24 13:48:01 -04:00
katie_smilecdr 8c145d1212 Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition 2021-09-24 13:01:38 -04:00
katie_smilecdr 6431ae4401 [3020] fix implementation/add tests 2021-09-24 13:00:05 -04:00
Michael Buckley db55837c3c Make our NoFt tests actually run without Ft. 
Hibernate search was always configured with a lucene heap engine in all JPA tests.
Added a new config param - hapi_test.enable_lucene - to disable with config params on the NoFt tests.
 2021-09-24 12:05:16 -04:00
jmarchionatto 4ab60e2f9b
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology 2021-09-24 08:59:15 -04:00
Ken Stevens 0db40c6118 support non-jpa batch 2021-09-24 00:39:15 -04:00
Ken Stevens 53c7476dae
hapi storage (#3024) 
* first pass moving core storage classes to storage-api

* move term service apis

* nearly done

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor

* create new SearchConstants class to store platform independent search constants

* move a couple of subscription services

* move transaction processor adapter to storage

* version bump

* move searchparam

* fix test

* fix compile includes

* fix text

* fix docs
 2021-09-23 22:04:46 -04:00
katie_smilecdr 8bd14ae024 [3020] add $partition-management-lists-partitions 2021-09-23 16:08:56 -04:00
juan.marchionatto 91d9101785 Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology 2021-09-23 13:45:28 -04:00
juan.marchionatto d1e9c23c13 Remove loinc.xml file from application. Now it required as input for loinc upload. 2021-09-23 13:43:27 -04:00
juan.marchionatto 9c8fd26692 Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-09-23 11:56:44 -04:00
juan.marchionatto 751c5d0d05 Implement revision suggestions. Add changelog. 2021-09-23 11:55:50 -04:00
Tadgh ad9e0f1c9a
Merge branch 'master' into 3014-prevent-delete-expunge-cascade 2021-09-23 09:33:04 -04:00
Jimmy Deng 2436f748aa fix test 2021-09-22 14:38:53 -04:00
Jimmy Deng f9796b9e2a fix test 2021-09-22 12:52:28 -04:00
Jimmy Deng 26ac649946 changelog 2021-09-22 11:11:10 -04:00
Jimmy Deng 9a18422173 fix review 2021-09-22 11:09:50 -04:00
Jimmy Deng 48f73fa1d1 typo 2021-09-22 10:25:57 -04:00
Jimmy Deng c913707599 added header check 2021-09-22 10:15:22 -04:00
juan.marchionatto 81a4f0c78f Rename method for clarity. Increase test coverage. 2021-09-22 09:40:25 -04:00
juan.marchionatto fdf639d353 Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-09-22 09:25:48 -04:00
Justin Dar ad5297b714 fix for issue #3014 2021-09-21 13:09:08 -07:00
Ken Stevens 060791aeb4
hapi-fhir-storage-api (#3006) 
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence

* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api

* move bulk import apis

* create hapi-fhir-jpa

* create hapi-fhir-jpa

* move CircularQueueCaptureQueriesListener to japi-fhir-jpa

* move mdm logs to storage-api

* move gziputil to storage-api

* move quartz scheduling to hapi-fhir-jpa

* move default subscription channel factory to storage-api

* consolidated batch constants

* correct accidental Logs change

* remove dependency of cdr-api on cdr-persistence

* fix javadoc

* pom descriptions

* review feedback
 2021-09-21 15:36:08 +00:00
juan.marchionatto 371484a4ea Fix test to add now required id to loinc CodeSystem creation 2021-09-20 17:19:31 -04:00
juan.marchionatto 3d5c863276 Revert creation of test utility class finally not needed 2021-09-20 17:18:45 -04:00
juan.marchionatto 9c790a7374 Revert creation of test utility class finally not needed 2021-09-20 17:18:11 -04:00
juan.marchionatto 8a1d95f348 Add service to get CodeSystem from its forcedId without forcing rollback by ResourceNotFoundException in case not found 2021-09-20 17:14:42 -04:00
Johnson Lu f1f9c672ad
3110 zh disallow unknown extensions (#3009) 
* Added allowKnownExtensionsOnly() method such which calls setAnyExtensionsAllowed() to set myAnyExtensionsAllowed to false and modified changelogs to add entry for this ticket.

* Modified docs to remove description for .allowAnyExtensions() and included it within a description for .allowKnownExtensionsOnly() and also added test for .allowKnownExtensionsOnly()

* refactored allowKnownExtensionsOnly() to rejectUnknownExtensions()
 2021-09-20 15:40:56 -04:00
juan.marchionatto 1492b9220a Add test comment 2021-09-20 11:15:53 -04:00
juan.marchionatto d706caf949 merge master in 2021-09-20 11:08:17 -04:00
juan.marchionatto d372371f36 Make sure a loinc CodeSystem always has a ForcedId 2021-09-20 08:51:51 -04:00
Tadgh 3b1bf7aa09
Merge branch 'master' into 2849_add_new_mdm_param 2021-09-17 13:27:09 -04:00
Jaison B 8bb9aca8df Merge branch 'master' into 2849_add_new_mdm_param 2021-09-17 10:18:24 -06:00
jmarchionatto 115056800c
Merge branch 'master' into issue-2995-valuesetcomposeincludeversion-is-not-set-when-uploading-terminology 2021-09-17 11:32:18 -04:00
juan.marchionatto 18e3ed68eb Revert loinc.xml deletion until current work gets completed 2021-09-16 15:14:43 -04:00
juan.marchionatto fbd23498fc Adjust test data and fix all test cases implemented so far 2021-09-16 13:41:05 -04:00
juan.marchionatto c9162cba6d Merge in fix for ISSUE-2995 2021-09-16 13:20:00 -04:00
juan.marchionatto 0dfc716a82 Adjust code validation to properly obtain CodeSystem's current version 2021-09-16 13:18:49 -04:00
James Agnew a56c85f780
Eliminate Search Coordinator ThreadPool (#2991) 
* Add test

* Remove search coordinator thread pool

* Add changelog

* Add docs

* Test fixes

* Test fixes

* Test fixes

* Test fix
 2021-09-16 16:37:34 +00:00
juan.marchionatto 3d3bab5102 merge master into branch 2021-09-16 11:02:17 -04:00
juan.marchionatto 16e329e40c Add version to ValueSet.compose.include when uploading terminology 2021-09-15 14:40:21 -04:00
Tadgh 724e4b37da Fix up test to actually match 2021-09-15 11:24:01 -04:00
Tadgh 171f0f8724 fix rulebuilder 2021-09-15 09:04:45 -04:00
Tadgh a0c8cc4279 fix test 2021-09-15 01:23:43 -04:00
Tadgh 8f0e8b9e51 remove useless DB calls 2021-09-14 18:44:55 -04:00
Tadgh 9bb1558b71 Update query count ttest 2021-09-14 17:45:09 -04:00
Tadgh bb5e04e706 Fix broken test 2021-09-14 17:22:25 -04:00
Tadgh b25bdc1169 Remove crazy double encoding 2021-09-14 13:48:37 -04:00
Tadgh 9771210553 Prefer non-lazy outcomes in map 2021-09-14 13:40:53 -04:00
Tadgh 49debec36a Fix problem with null conditionals 2021-09-14 10:48:56 -04:00
juan.marchionatto bd456dfff2 Enhance test by adding operations use cases. Improve test data with more version differentiators. 2021-09-14 10:00:15 -04:00
juan.marchionatto 8288d12e97 Obtain current CodeSystem from null-pointed ForcedId, as done for ValueSet 2021-09-14 09:58:32 -04:00
Tadgh 9d982c5e08
Merge branch 'master' into conditional-bug 2021-09-14 08:51:58 -04:00
Tadgh 1ca313f8ad lower logging 2021-09-13 21:27:05 -04:00
Tadgh b4e2679872 Remove jetbrains 2021-09-13 21:15:23 -04:00
Tadgh a0cd83398b Bump test java to 16 2021-09-13 20:52:14 -04:00
Tadgh 3ccadd636e
Merge branch 'master' into 2958-consistent-error-handling 2021-09-13 19:38:57 -04:00
Justin Dar 876768718d Remove log 2021-09-13 11:29:36 -07:00
Justin Dar 3ca73f1067 Merge remote-tracking branch 'origin/2958-consistent-error-handling' into 2958-consistent-error-handling 2021-09-13 11:26:39 -07:00
Justin Dar 46936e1704 Fixed code formatting and better way of fixing issue 2021-09-13 11:26:21 -07:00
Tadgh 5f86370c98 Merge branch 'master' into conditional-bug 2021-09-13 13:04:10 -04:00
Tadgh 59c8765e6a Add implementation to validate conditional URLs post-transaction 2021-09-13 13:03:44 -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
James Agnew 5554431146
Avoid dead SearchParameter links in CapabilityStatement (#2790) 
* Avoid dead SearchParameter links in CapabilityStatement

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
 2021-09-11 18:27:18 -04:00
Tadgh 94f157a4ac Start refactoring of basetransactionprocessor 2021-09-11 15:13:05 -04:00
Tadgh b224463d35 add broken test 2021-09-10 22:46:35 -04:00
jdar8 a02a9e0254
Merge branch 'master' into 2958-consistent-error-handling 2021-09-10 17:02:31 -07:00
Justin Dar 2163e6e548 Fixed error that previous fix caused 2021-09-10 12:36:11 -07:00
Justin Dar 77845d66f7 Improved code formatting 2021-09-10 10:54:33 -07:00
juan.marchionatto 5b6ac3e6d6 Refactor to eliminate duplication 2021-09-10 11:22:04 -04:00
Dušan Markovič d6d862015b Address concerns in review for issue 2975 2021-09-10 15:46:27 +02:00
juan.marchionatto d7fde3f984 Simplify implementation. Add tests. 2021-09-10 09:32:47 -04:00
Dušan Markovič cfc0c7e6b3 Add test for validation of multiple hosts in ElasticsearchHibernatePropertiesBuilder 2021-09-10 11:44:15 +02:00
Dušan Markovič 032a9155f0 Merge branch 'master' of https://github.com/hapifhir/hapi-fhir into issue_2975 2021-09-10 09:11:06 +02:00
Justin Dar 836948010f Fixes issue (#2958) where Procedure?patient caused inconsistent results and ensured that such requests gave http 400 2021-09-09 16:10:09 -07:00
Dušan Markovič ed325e9e11 Enable multiple hosts in ElasticsearchHibernatePropertiesBuilder 2021-09-10 00:14:21 +02:00
Tadgh a4ba65a9fd Don't wrap known errors 2021-09-09 12:27:34 -04:00
Tadgh d5f3b5db18 Merge branch 'master' into fix-batch-pool-breaking 2021-09-09 11:28:44 -04:00
Tadgh 41d5e2b8e7 Add failing test, implementation 2021-09-09 10:50:54 -04:00
Ken Stevens 661ca02a6a revert clobbered code 2021-09-09 09:28:01 -04:00
Dušan Markovič c6aa21b915 Enable empty username and password in ElasticsearchHibernatePropertiesBuilder 2021-09-09 12:55:04 +02:00
Ken Stevens 5bc571d97d fix test 2021-09-09 01:00:12 -04:00
Ken Stevens 519244a2ea unit test passes 2021-09-08 19:14:50 -04:00
Tadgh 0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index 
Custom elastic index
 2021-09-08 14:29:58 -04:00
Tadgh fbf6b35d2e
Merge branch 'master' into custom-elastic-index 2021-09-08 08:49:26 -04:00
Tadgh 5d5c45e357 Add whitespace 2021-09-08 08:49:19 -04:00
Tadgh f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-08 08:45:47 -04:00
Tadgh c2414d2cae Throw error if misconfigured 2021-09-07 18:35:59 -04:00
Tadgh 436c74616b
Merge branch 'master' into custom-elastic-index 2021-09-07 18:19:35 -04:00
Jason Roberts 34075911ce Merge branch 'master' into jr-20210831-contained-chained-search 2021-09-07 17:28:24 -04:00
Jason Roberts 207558dba3 code review feedback 2021-09-07 17:27:22 -04:00
Kevin Dougan SmileCDR 2dcc4f534f
Resolve Search Causing JOINs on HFJ_RESOURCE Checking RES_TYPE and RES_DELETED_AT Columns (#2964) 2021-09-07 19:38:08 +00:00
jamesagnew a3743fbcca Add utility method 2021-09-07 14:21:50 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Tadgh 6a2a5d5097 Merge branch 'master' into custom-elastic-index 2021-09-07 13:56:56 -04:00
Tadgh eabe3e7c74 Merge branch 'master' into custom-elastic-index 2021-09-07 13:56:44 -04:00
Tadgh ecd93c9e8a Add changelog 2021-09-07 13:54:28 -04:00
Tadgh 16752f393c Finalize implementation 2021-09-07 13:33:03 -04:00
leif stawnyczy 4d7f53851c issue-2901 cleanup of code/imports 2021-09-07 12:08:32 -04:00
leif stawnyczy 69287b6bc3 issue-2901 review fixes - moving methods to idhelperservice 2021-09-07 11:52:11 -04:00
Jari Maijenburg d3d7c6e97e
Merge branch 'master' into npe_fix 2021-09-07 17:36:05 +02:00
Nick Goupinets 35aaa98431 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-07 11:27:49 -04:00
Tadgh ca2a1ff9df Add HsTest replicating boot failure 2021-09-07 10:08:17 -04:00
Jason Roberts 190ca7a2b5 tests for longer chains 2021-09-07 09:40:49 -04:00
Tadgh ad5d56172a Return 2 unused beans 2021-09-07 09:11:48 -04:00
Ken Stevens a1733ed3eb cleanup 2021-09-06 13:55:19 -04:00
Ken Stevens 4281648a33 extract some methods for readability 2021-09-06 13:52:10 -04:00
Ken Stevens ea153334fb extract some methods for readability 2021-09-06 13:50:09 -04:00
Tadgh 710fb3bd89 wip 2021-09-05 00:04:13 -04:00
Tadgh f0a8659653 Fix template and setup static prefix as sample 2021-09-04 23:55:03 -04:00
Jari Maijenburg cdb7ffb0d3 Fixed NPE in PidToIBaseResourceProcessor 2021-09-04 01:44:07 +02:00
Nick Goupinets c63a503841 Updated link processing for MDM events 2021-09-03 16:29:26 -04:00
leif stawnyczy 64270a51e0 issue-2901 review fixes 2021-09-03 15:36:42 -04:00
Jason Roberts 0dad28fb33 tidy up 2021-09-03 15:02:19 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929) 
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

* rearrange method calls so persistence module can perform clear operation on its own

* 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>

* review feedback

* review feedback

* Remove inheritance

* fix beans

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
 2021-09-03 14:58:19 -04:00
Jason Roberts 8a9e4e4328 force the resource table to be the root of the query if we might be traversing a contained reference 2021-09-03 11:26:46 -04:00
Vadim Karantayer b29a61df40 update TestUtil to test Embeddable classes, not just Entity classes 2021-09-03 10:40:54 -04:00
leif stawnyczy 78c71ce761 issue-2901 fix tests 2021-09-03 08:38:19 -04:00
Jason Roberts 5604cabbe8 add tests for qualifiers 2021-09-03 07:45:57 -04:00
Jason Roberts 0edf77d214 clean up a bit 2021-09-03 07:31:49 -04:00
Kevin Dougan SmileCDR fed755523f
Resolve - Avoid JOINs on HFJ_RESOURCE Checking RES_TYPE and RES_DELETED_AT Columns (#2944) 
* Added the start of a new Unit Test.

* Renamed the Unit Test.

* Fleshed out the Unit Test with additional Resource properties.

* Tweaked the Unit Test more but it is still not working as desired so more changes will be needed to replicate the specific scenario...

* More Unit Test tweaks...

* More Unit Test tweaks.

* More tweaks...

* Reproduced the problem.

* Finally, a Failing Unit Test that exposes the problem.

* Fixed the Unit Test by changing how SearchBuilder manipulates underscore params.

* Added another test scenario.

* Added a third search test.

* Removed the third search example since it was not effective.

* Test fix

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-09-03 05:28:04 -04:00
Tadgh 2ed7019a6c Add another test 2021-09-03 00:08:12 -04:00
Frank Tao 8651990cac Fixed class cast issue 2021-09-02 23:04:30 -04:00
Frank Tao 56890dba93 Reformatted the code 2021-09-02 22:26:55 -04:00
Frank Tao be96adb694 Merge branch 'poc-chained-not-bug' into ft-search-with-not-modifier 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderSearchModifierR4Test.java
 2021-09-02 22:07:22 -04:00
Frank Tao b81a61e465 Fixed :not modifier issue for the resource 2021-09-02 21:52:37 -04:00
VK-SMILECDR 39f18e1897
Merge branch 'master' into 2948 2021-09-02 17:24:15 -04:00
Vadim Karantayer c28f5e75b3 update TestUtil to recursively scan down into subpackages 2021-09-02 15:35:40 -04:00
Jason Roberts 9fd2746113 fixed the double chain with contained resource second case 2021-09-02 14:38:30 -04:00
Tadgh 26ff15f939
Revert "Fix search of :not modifier" 2021-09-02 14:33:30 -04:00
Tadgh 6c700f9432 Add POC for failure 2021-09-02 13:33:27 -04:00
leif stawnyczy 6f82e3568c issue-2901 remove debug code 2021-09-02 13:20:38 -04:00
leif stawnyczy 49124c298d issue-2901 fixing test 2021-09-02 13:15:24 -04:00
leif stawnyczy ff7433edd7 issue-2901 cleaning up test contexts 2021-09-02 11:43:12 -04:00
leif stawnyczy cbfcc02a92 issue-2901 removing cruft and cleaning up 2021-09-02 11:07:06 -04:00
leif stawnyczy 1a7b101d03 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-02 10:13:04 -04:00
leif stawnyczy 0286eb5278 issue-2901 updated some documentation and added support for autocreated placeholder / autoversioned references at paths when in transactios and have not been created yet 2021-09-02 09:15:39 -04:00
Tadgh b1d192637d
Merge pull request #2928 from hapifhir/ft-search-with-not-modifier 
Fix search of :not modifier
 2021-09-02 08:41:16 -04:00
Ben Li-Sauerwine 6e389d6f59 Merge branch 'memorycacheservicefix' of https://github.com/theGOTOguy/hapi-fhir into memorycacheservicefix 2021-09-01 15:05:32 -04:00
Ben Li-Sauerwine 0724e652bb Refactor to prevent adding additional signatures to expungeEverythingByType. 2021-09-01 15:04:31 -04:00
Ben Li-Sauerwine 3789bc0f75
Merge branch 'master' into memorycacheservicefix 2021-09-01 13:55:03 -04:00
Jason Roberts 2e2048ce52 Add more test cases, not passing 2021-09-01 13:37:45 -04:00
katie_smilecdr 453ef7ec1c Merge branch 'master' into 2935_Search_with_trailing_percent_sign 2021-09-01 11:33:26 -04:00
Ben Li-Sauerwine 7001272e4b Clear out the memory cache whenever we call the ExpungeEverythingService. 2021-09-01 01:26:47 -04:00
Ben Li-Sauerwine 444bc5f330
Merge branch 'master' into memorycacheservicefix 2021-08-31 20:26:31 -04:00
Ben Li-Sauerwine 51fe5ec5e7 Remove extra update from test. 2021-08-31 20:16:22 -04:00
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
juan.marchionatto 28e3265b6c Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-08-31 15:52:24 -04:00
katie_smilecdr a1fbeeacaa [2935] Escape "%" in like expression 2021-08-31 15:11:06 -04:00
Ken Stevens c1dc342659 more logs 2021-08-31 15:06:51 -04:00
Ken Stevens ef4adda527 failing tests 2021-08-31 14:53:05 -04:00
Tadgh d75af14d29 Merge branch 'master' into double-conditionalCreateIssue 2021-08-31 14:25:51 -04:00
Tadgh 765b18013c
Merge branch 'master' into fix-intermittent-in-tests 2021-08-31 14:22:22 -04:00
juan.marchionatto 710343a599 Use ForcedId to get current ValueSet version 2021-08-31 13:33:39 -04:00
Tadgh 825ac1e81c Chnge privacy 2021-08-31 12:58:00 -04:00
Tadgh b1515b5963 Lazy load executor so that tests work safely. 2021-08-31 12:57:45 -04:00
Tadgh c9f5dfd6d3 Swap to SyncTaskExecutor 2021-08-31 11:33:06 -04:00
Tadgh 2f6d8c7b35 Revert logging 2021-08-31 10:56:31 -04:00
Tadgh 0f6ae50105 Fix bug in hashToSearchMap 2021-08-31 10:47:23 -04:00