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3818 Commits

Author SHA1 Message Date
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 8da38d1a9eb6a07601721f8143cf544fbb9e9a63
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Oct 11 21:31:42 2021 -0400

    Test fixes

commit c73fd288f00855178c3bd31567c56c3fbc62e513
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