Commit Graph

3628 Commits

Author SHA1 Message Date
katiesmilecdr 5ee823e829
[3109] fix bug (#3112)
* [3109] fix bug

* [3109] add unit tests for BinaryAccessProvider
2021-10-27 19:52:57 +00:00
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