honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
3,969 Commits 660 Branches 129 Tags 1.2 GiB
Commit Graph

1527 Commits

Author SHA1 Message Date
jamesagnew 116b9e335d Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-07-15 15:23:11 -04:00
jamesagnew 43ac912033 Clean up terminology uploading 2018-07-15 15:22:52 -04:00
jamesagnew 84b57f04d3 Fixed tests 2018-07-14 13:51:11 -04:00
James Agnew 738abc415c Disable scheduled tasks during unit tests 2018-07-14 13:24:51 -04:00
jamesagnew 36b4ed28e4 Header updates 2018-07-14 10:16:53 -04:00
James Agnew 81e8f77232 Work on indexes 2018-07-13 09:58:54 -04:00
James Agnew e6ca408f67 Permissions for operations 2018-07-12 18:40:15 -04:00
James Agnew 03e7b018a6 Add skeleton for the $process-message operation in JPA erver 2018-07-12 17:52:24 -04:00
patrick-werner b275d20aba added R4 document operation & merge master 2018-07-11 16:21:13 +02:00
patrick-werner 68772f1e3a removed unnecessary test 2018-07-10 16:02:39 +02:00
patrick-werner df7a9322e9 Merge branch 'master' into documentOperation 2018-07-10 14:35:51 +02:00
James Agnew e992043a22 Fix ID 2018-07-06 09:43:43 -04:00
James Agnew f03b1dec8e Remove warning 2018-07-06 09:40:23 -04:00
James Agnew 60f57f2a6f Fix property handler 2018-07-06 09:36:04 -04:00
James Agnew 1533746bbe Add tests 2018-07-06 09:29:51 -04:00
James Agnew c8f0e0047f Test fixes 2018-07-05 19:17:06 -04:00
James Agnew c9d7b88cab Loinc updates 2018-07-05 18:52:19 -04:00
James Agnew 3b794a4f39 Fix a crash when reindexing deleted resources 2018-07-02 09:17:48 -04:00
jamesagnew 6d83edabb6 License header updates 2018-07-01 20:59:04 -04:00
James Agnew 328541f537 Test fix 2018-07-01 12:57:05 -04:00
James Agnew b929864873 Merge branch 'improve_jpa_indexes' 2018-07-01 12:08:03 -04:00
James Agnew 6ef34a8c5f
Merge pull request #1018 from jamesagnew/jpa_view 
Jpa view
 2018-07-01 11:47:17 -04:00
James Agnew 495fd9f68e Add support for patch in AuthorizationInterceptor 2018-07-01 11:46:11 -04:00
frankjtao 2c06a1437b merged master to jpa_view 2018-06-30 22:16:30 -04:00
frankjtao 0ab15a05d6 Merge branch 'jpa_view' of https://github.com/jamesagnew/hapi-fhir.git into jpa_view 
Conflicts:
	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceSearchView.java
 2018-06-29 22:18:22 -04:00
frankjtao ccf3c17f59 impl ResourceSearchView, reduce sql to db 2018-06-29 21:24:43 -04:00
frankjtao af4b9f1c7b impl ResourceSearchView, reduce sql to db 2018-06-29 21:24:02 -04:00
James Agnew 6afc2a7296 Improve indexing 2018-06-29 16:25:11 -04:00
James Agnew bb637c5433 Work on presence API 2018-06-29 14:32:08 -04:00
James Agnew 03fc593cb9 Fix broken test 2018-06-28 18:11:19 -04:00
James Agnew 32fefefcd8 Allw successful deletion of concept maps 2018-06-28 18:01:00 -04:00
James Agnew 7b809f059a Terminology updates 2018-06-27 18:48:36 -04:00
James Agnew 32ddfff191 Improve indexing 2018-06-27 18:33:04 -04:00
James Agnew 24beebe32f Fix valueset URI for loinc groups 2018-06-27 13:15:37 -04:00
James Agnew 79ede4c5ee Remove orphanremoval 2018-06-27 11:31:53 -04:00
James Agnew 4dca271735 Clean up concept deletion 2018-06-27 11:19:11 -04:00
James Agnew 050f9939ac Merge branch 'master' into improve_jpa_indexes 2018-06-27 10:44:18 -04:00
James Agnew 2b992cfb3b Fix compile issue 2018-06-27 10:34:06 -04:00
James Agnew 8c849b16a4
Merge pull request #1015 from jschneid-nmdp/resolve-term-upload-deferred-short-circuit 
avoid potential short circuit during saveDeferred processing of uploaded (e.g. LOINC) terminology
 2018-06-27 10:33:06 -04:00
James Agnew fb2976d0d2 Improve code system deletion from terminology service 2018-06-27 10:22:13 -04:00
Joel Schneider b2853b3f9d modify BaseHapiTerminologySvcImpl saveDeferred method to avoid short circuit that could potentially prevent processing of some deferred value sets and concept maps 2018-06-27 02:20:12 -05:00
James Agnew 52e3c9496e Fix slow upload 2018-06-26 21:59:01 -04:00
James Agnew 74bca0562e Merge branch 'improve_jpa_indexes' of github.com:jamesagnew/hapi-fhir into improve_jpa_indexes 2018-06-26 21:54:32 -04:00
James Agnew a63205ecff Merge branch 'master' into improve_jpa_indexes 2018-06-26 21:54:12 -04:00
James Agnew f7029b9a0f Update part code url for loinc 2018-06-26 17:17:31 -04:00
jamesagnew a77896ff2d Add callback for resource deletion 2018-06-26 07:54:21 -04:00
James Agnew f0da7a33de Fix expunge transaction boundaries 2018-06-25 10:22:49 -04:00
jamesagnew e5cb609f4d Performance improvements 2018-06-24 20:02:27 -04:00
jamesagnew 9a880361b6 Merge branch 'master' into improve_jpa_indexes 2018-06-24 15:15:31 -04:00
jamesagnew 2d57699066 Work on index improvements 2018-06-24 15:09:53 -04:00
frankjtao f38f71cf0a Merge remote-tracking branch 'origin/master' into 
1008_fix_jpa_sql_loop_issue
 2018-06-22 15:34:56 -04:00
James Agnew 60ed0dab48 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-06-22 11:22:36 -04:00
James Agnew e9fffd3cdc Allow indexing in custom search params to descend into contained 
resources
 2018-06-22 11:22:07 -04:00
James Agnew d46b9b00be Liinc updates 2018-06-22 09:59:54 -04:00
Frank Tao 103b587ab5 #1008: Fixed sql looping issue 2018-06-21 22:32:08 -04:00
James Agnew cef4596211 Loinc updates 2018-06-21 19:23:23 -04:00
James Agnew d6bfce4a1d Make all loinc files mandatory 2018-06-21 18:30:57 -04:00
James Agnew 1b40188aab FIx missing import 2018-06-21 14:48:39 -04:00
jamesagnew b3f7ab274d License header updates 2018-06-21 14:44:34 -04:00
James Agnew b9a4e1ae0f Merge branch 'improve_jpa_indexes' of github.com:jamesagnew/hapi-fhir into improve_jpa_indexes 2018-06-21 13:48:27 -04:00
James Agnew 5b6cde8a9f Merge branch 'master' into improve_jpa_indexes 2018-06-21 13:48:04 -04:00
jamesagnew ecc8e1eda0 More work on indexes 2018-06-21 13:42:34 -04:00
James Agnew cc98f65500 Merge branch 'master' into valueset_expansion_fixes 2018-06-21 10:20:24 -04:00
James Agnew 2dc445fd10 ValueSet enhancements 2018-06-21 10:19:14 -04:00
James Agnew e63604afc9
Merge pull request #1000 from rhausam/update-filenames 
Updated LOINC filenames to match 2.64 and future releases.
 2018-06-21 10:18:36 -04:00
patrick-werner f9a19c4b1f starting implementing check if only one Composition is returned 2018-06-20 16:12:58 +02:00
James Agnew 218937e425 Several fixes 2018-06-20 05:53:32 -04:00
frankjtao 6e7d67ba70 Update due to Spring version change 2018-06-19 20:16:27 -04:00
patrick-werner b76ad6870f Merge remote-tracking branch 'origin/master' into documentOperation 2018-06-19 16:57:54 +02:00
patrick-werner 0a8afb38ba moved the BundleProvider -> DocumentBundle code from DAO to Service Layer 2018-06-19 15:20:35 +02:00
patrick-werner 627491ad95 fixed Test if maxThreads >= 2 2018-06-19 14:50:04 +02:00
James Agnew 127efd55b0
Merge branch 'master' into 963_jpa_performance 2018-06-19 06:50:05 -04:00
frankjtao 299cf5b230 Changed retval to resource id instead of SearchResult in SearchResultDao 2018-06-16 22:37:12 -04:00
jamesagnew 24ad8870cf Add to indexes 2018-06-16 18:23:05 -04:00
James Agnew d13d53c8ef Add a bit of logging 2018-06-15 14:01:07 -04:00
Rob Hausam 215e224e3d Updated terminology upload tests and artifacts to the new LOINC filenames. 2018-06-14 20:30:32 -05:00
James Agnew 99f80eef88 Performance enhancements to JPA searching 2018-06-15 01:13:44 +08:00
Rob Hausam 75c1b7baa8 Updated LOINC filenames to match 2.64 and future releases. 2018-06-14 11:33:35 -05:00
James Agnew a46b4a4637 Reindexing shouldn't stop unexpectedly 2018-06-13 22:03:15 +08:00
patrick-werner c2b2a7eaa7 added missing CORS Headers for Test Setup 2018-06-11 11:09:23 +02:00
James Agnew cc0e836680
Auth interceptor early checks (#995) 
* Validator fix

* Enhance AuthorizationInterceptor so that it tries to deny access earlier
for compartment searches that are outside the allowable compartment.

* FIx DSTU2 test that wasn't updated

* More test fixes
 2018-06-10 17:48:20 -04:00
frankjtao 35991cd21b #963: renamed the parameter to 'the*' 2018-06-07 14:19:44 -04:00
Diederik Muylwyk 903df68d2a
978 cli tools for importing exporting terminology mappings need to be fixed (#988) 
* Fixed export issue.

* Fixed import issue.

* Fixed tests.

* Fixed tests.
 2018-06-07 10:22:41 -04:00
patrick-werner 6bcddea416 Merge branch 'master' into documentOperation 2018-06-07 09:17:58 +02:00
James Agnew 6feb23896f Hopefully fix #983 2018-06-06 15:51:23 -04:00
James Agnew e7804b881c Fix CI issue 2018-06-06 11:39:06 -04:00
jamesagnew 583437d656 Prevent a crash if the application context has been set incorrectly in 
embedded deployments
 2018-06-06 08:37:25 -04:00
patrick-werner 49bdff1862 current state of $document 2018-06-05 18:32:59 +02:00
patrick-werner 38b7b00f52 Merge branch 'master' into documentOperation 2018-06-04 17:34:39 +02:00
patrick-werner bd0682c2b2 Merge remote-tracking branch 'origin/master' into documentOperation 2018-06-04 13:53:02 +02:00
jamesagnew 987679483a Version bumps 2018-06-03 15:29:10 -04:00
James Agnew e36bc3889c
Merge pull request #974 from Romanow88/master 
Fixes #972 Update Spring Data 1.11.6.RELEASE to 2.0.7.RELEASE
 2018-06-03 15:28:05 -04:00
James Agnew 30dd3c00b9 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-06-02 08:59:48 -04:00
Roman Doboni 8f1effe5e3
Merge branch 'master' into master 2018-06-02 09:37:56 +02:00
James Agnew d52c1ed090 Add a bit more logging for occasional failing test 2018-06-01 17:43:29 -04:00
jamesagnew fedf4a870a License header updates 2018-06-01 07:41:01 -04:00
James Agnew 7f87def432 Fix tests 2018-06-01 07:40:33 -04:00
James Agnew a9cb4dae2f Allow storage of messages 2018-06-01 07:07:24 -04:00
frankjtao 73f12744ae #963 Improved performance for tag loading 2018-05-31 21:30:46 -04:00
jamesagnew abcf7852b1 Tests pasing locally 2018-05-31 09:10:34 -04:00
Romanow a336f33b4b Update Spring Data 1.11.6.RELEASE to 2.0.7.RELEASE 2018-05-31 14:42:15 +02:00
James Agnew 7e0584af2f Merge branch 'java9' of github.com:jamesagnew/hapi-fhir into java9 2018-05-30 21:59:51 -04:00
James Agnew 2f07066c59 Test fixes 2018-05-30 21:59:41 -04:00
James Agnew c2afd9728d More test fixes 2018-05-30 21:57:17 -04:00
jamesagnew 432bc66208 Merge branch 'java9' of github.com:jamesagnew/hapi-fhir into java9 2018-05-30 21:24:01 -04:00
James Agnew bb5d4110a2 Test fixes 2018-05-30 21:23:20 -04:00
jamesagnew 2684e2b030 Build fixes 2018-05-30 16:17:36 -04:00
jamesagnew d127a89047 Some test fixes 2018-05-30 11:01:43 -04:00
jamesagnew 833a46d07e Work on test compilation 2018-05-30 08:27:09 -04:00
jamesagnew 5a96482860 More work o JDK9 tests 2018-05-30 08:04:01 -04:00
James Agnew a52805e504 Work on JDK9 support 2018-05-30 05:45:08 -04:00
James Agnew 7951d883d0 Merge branch 'master' into java9 2018-05-29 08:43:21 -04:00
patrick-werner 83c8718c2a Merge branch 'v3.4.4' into documentOperation 2018-05-29 10:06:30 +02:00
Frank Tao 404d37cedc Fixed #963 : load history table once instead of one by one in the loop 
in the SearchBuilder class.
 2018-05-28 22:45:45 -04:00
Diederik Muylwyk 0e2c57fa60 Bumping version. 2018-05-28 17:44:38 -04:00
patrick-werner 8872fc94c5 Merge remote-tracking branch 'origin/master' into documentOperation 
# Conflicts:
#	hapi-tinder-plugin/src/main/resources/vm/jpa_resource_provider.vm
#	hapi-tinder-plugin/src/main/resources/vm/jpa_spring_beans.vm
#	hapi-tinder-plugin/src/main/resources/vm/jpa_spring_beans_java.vm
 2018-05-28 17:05:50 +02:00
Diederik Muylwyk 2871920734 Preparing release. 2018-05-28 10:45:47 -04:00
James Agnew a7eac969d9 Site enhancements for release 2018-05-28 08:53:36 -04:00
jamesagnew 67f21426cb Disable content header on response for non-create operations 2018-05-25 07:28:01 -04:00
jamesagnew 49aaa01db8 Fix compile issues 2018-05-23 17:42:48 -04:00
James Agnew 850aa99ddb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-05-23 16:28:35 -04:00
James Agnew ed6609e414 One more test fix 2018-05-23 16:28:13 -04:00
jamesagnew b146a80502 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-05-23 16:09:34 -04:00
jamesagnew 92dc258c6e Update license headers 2018-05-23 16:09:23 -04:00
James Agnew ba8827091a Reindexing fixes 2018-05-23 16:07:48 -04:00
James Agnew a3687e446e Correctly handle missing search params with new indexing infrastructure 2018-05-23 11:42:38 -04:00
James Agnew 0c5c347db7 FIx broken reindex process 2018-05-23 10:48:07 -04:00
James Agnew 2f2900e837 Improve indexing on JPA server in anticipation of a new indexing 
strategy in HAPI FHIR 3.5.0
 2018-05-23 08:09:57 -04:00
jamesagnew e8139192e0 FIx test issues 2018-05-21 13:07:11 -04:00
James Agnew c588e01a4d Handle invalid paths in Consent resource 2018-05-16 21:45:23 -04:00
jamesagnew 4d62120a18 Fix issues reported by errorprone 2018-05-15 08:44:15 -04:00
jamesagnew f9946fee61 Fixes to get the build passing once more 2018-05-15 07:34:44 -04:00
James Agnew a3ff08d9ec
Replace phloc with ph for #775 (#930) 
* Replace phloc with ph

* Enable schematron tests

* Make HAPI-FHIR ph-schematron on OSGI

* Work on getting tests passing

* Another test fix

* Fix up transaction handling for DSTU2

* Add changelog

* Avoid double transaction

* Dont use readonly

* One more test fix

* Update to snapshow build

* Resolve a circular dependency

* Try to fix tests

* Solve recurring NPE in DSTU2 tests

* Fix one more test

* Test fix

* More test threading fixes

* One more attempt to get tests passing

* Refactoring for tests

* Refactoring for tests
 2018-05-14 17:38:40 -04:00
jamesagnew ccb859fdbe FIxes to get the synced build working 2018-05-13 08:08:34 -04:00
jamesagnew 150f27a9ca Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-05-12 19:40:31 -04:00
jamesagnew 3d762b984b Sync to R4 definitions 2018-05-12 19:35:42 -04:00
James Agnew 9d24e8b040 Use HTTP 409 for conflict when two threds update the same resource 2018-05-11 17:41:07 -04:00
James Agnew f1ba0016b2 Improve the error message thrown by JPA server 2018-05-11 17:03:48 -04:00
James Agnew b17eebd8d2 Squashed commit of the following: 
commit 2be11651c2
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 11:50:53 2018 -0400

    Update changelog

commit b3bb5f9052
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 11:19:28 2018 -0400

    Parameter updates

commit f6b1082ba4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 07:24:30 2018 -0400

    More test fixes

commit 81a69c265f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:26:48 2018 -0400

    Fix compile error

commit 935938e92c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:25:18 2018 -0400

    Another test fix

commit 43568a1f8d
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:18:06 2018 -0400

    Fix compile error

commit e95894e643
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 06:13:50 2018 -0400

    More work on tests

commit 9393fb8f4f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu May 10 05:36:27 2018 -0400

    One more fix

commit 437f5051e4
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 21:32:10 2018 -0400

    Work on validator

commit 20c51add4f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 19:34:10 2018 -0400

    Validator fix

commit 7bf2b0a0e9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 18:44:04 2018 -0400

    Fix test

commit adc73e75c9
Author: James Agnew <jamesagnew@gmail.com>
Date:   Wed May 9 17:22:34 2018 -0400

    Merge validator
 2018-05-10 11:53:32 -04:00
Diederik Muylwyk d97fb8f5cf
709 the conceptmap operation called translate needs to be implemented (#923) 
The ConceptMap operation $translate has been implemented.
 2018-05-10 10:52:56 -04:00
patrick-werner cbd3ddbbd7 $document operation on Composition working (1st draft) 2018-05-10 15:05:06 +02:00
James Agnew a0c40cf98a Move a few more constants around 2018-05-05 12:21:56 -04:00
James Agnew 5c505b7cd7 Refactor operations to use constants for their names 2018-05-05 08:27:45 -04:00
James Agnew 7688be1231 Work on getting java9 building 2018-05-03 18:34:29 -04:00
jamesagnew f66e6d055e Add license header 2018-05-02 14:54:11 -04:00
James Agnew bb25a97e66 FIx up logging rule 2018-05-02 14:34:55 -04:00
James Agnew 220cb1716f Add a new rule 2018-05-02 14:28:01 -04:00
James Agnew 45360d80cb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2018-05-02 14:19:28 -04:00
James Agnew 87666a1622 Use a direct subclass for the resource cache 2018-05-02 14:18:53 -04:00
jamesagnew 34d9646d8b Headers 2018-05-02 06:18:16 -04:00