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Author SHA1 Message Date
ianmarshall f7db280099 Merge remote-tracking branch 'remotes/origin/master' into im_20200131_remove_circular_dependency_forcedid 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
 2020-02-18 12:13:00 -05:00
James Agnew 60f16dd91d
Update to 4.3.x core JAR (#1715) 
* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Start working on converter

* Account for compile errors

* Test fix

* Work no validator

* Work on getting core working

* Add some test coverage

* Many test fixes

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
 2020-02-17 14:28:29 -05:00
Ken Stevens da11d3d89e
remove distinct from search (#1712) 
* it works now

* oops

* add successful migration message

* add successful migration message

* Add fix for #1300

* Remove FIXME

* Test fix

* Test fix

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-02-15 12:45:59 -05:00
jamesagnew 1d1aadb813 Work on multitenancy 2020-02-09 20:57:50 -05:00
James Agnew ebf395bee9 Merge branch 'master' into ja_20200206_multitenancy 2020-02-09 08:40:29 -05:00
jamesagnew f7ec41ffc5 Work on multitenancy 2020-02-09 08:40:15 -05:00
James Agnew c5c1e3196b Resolve FIXMEs (#1705) 
* Resolve FIXMEs

* Test fixes

* Test fixes

* Clean up unused code

* Add some test coverage

* Test fix

* Test fix

* Avoid intermittent
 2020-02-09 08:39:46 -05:00
James Agnew b2d2346228 Work on multitenancy 2020-02-07 15:18:06 -05:00
Ken Stevens da54d3443e
fix noisy logs (#1701) 2020-02-04 11:29:09 -05:00
James Agnew 4229645602 Fix to code delta CSV encoding 2020-02-03 20:56:48 -05:00
James Agnew 5d4f34d67c Intermittent test fix (yes again...) 2020-02-03 19:21:12 -05:00
James Agnew 26589e61c3 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-02-03 18:06:46 -05:00
James Agnew b06105d970 Intermittent test fix 2020-02-03 18:06:29 -05:00
Ken Stevens a31e90da2e
Merge pull request #1698 from jamesagnew/ks-20200203-remove-search-lastused 
Remove searchLastReturned column
 2020-02-03 16:53:27 -05:00
James Agnew d7b45ff65c Test fix 2020-02-03 16:48:27 -05:00
Ken Stevens 2e96d6bc2d fix test 2020-02-03 15:49:37 -05:00
Ken Stevens 3c46595e81 Merge remote-tracking branch 'remotes/origin/master' into ks-20200203-remove-search-lastused 2020-02-03 11:33:15 -05:00
Ken Stevens b4325199cf review feedback 2020-02-03 11:20:18 -05:00
Ken Stevens 7faf8932cf
Merge pull request #1695 from jamesagnew/ks-20200131-near-search-http 
Ks 20200131 near search http
 2020-02-03 10:38:29 -05:00
James Agnew 709aeb4ae8
Drop unnecessary index (#1696) 2020-02-03 10:29:39 -05:00
Ken Stevens cda906d7b8 Column removed. Time to run tests. 2020-02-03 09:44:10 -05:00
jamesagnew 38eb12234d Merge branch 'master' into ks-20200131-near-search-http 2020-02-03 05:27:50 -05:00
James Agnew 218f344945 Test fix working 2020-02-03 05:24:02 -05:00
jamesagnew 9d59de14a9 Unit test fix 2020-02-03 05:24:02 -05:00
Ken Stevens 63f2f38689 reinstate near param count validation 2020-02-02 21:21:37 -05:00
Ken Stevens decb47dfc2 remove unused block 2020-02-02 16:56:25 -05:00
Ken Stevens ffcf617659 pre-review cleanup 2020-02-01 20:27:21 -05:00
Ken Stevens 74948737a7 pre-review cleanup 2020-02-01 20:18:42 -05:00
Ken Stevens c375c66f15 test passes 2020-02-01 20:15:58 -05:00
Ken Stevens fb1eb7ca8f parking wip 2020-02-01 13:58:27 -05:00
Ken Stevens cd617389c6 create failing test 2020-01-31 18:07:17 -05:00
Ken Stevens 868ef9590d started writing test 2020-01-31 17:14:37 -05:00
ianmarshall 5d5b3d7639 Changes to schema to loosen dependencies between Forced ID table and the Resource and Resource History tables. 2020-01-31 11:16:01 -05:00
jamesagnew f38370fbf7 Drop half-written test 2020-01-31 05:50:30 -05:00
jamesagnew d4295124f1 Reduce verbosity of scheduler logging 2020-01-30 16:28:56 -05:00
James Agnew 6985f3e5f3 Rework how IDs are calculated for quartz jobs 2020-01-30 08:49:40 -05:00
James Agnew e6d3897700 Add tests 2020-01-30 08:49:40 -05:00
jamesagnew 578f2b7aef License header updates 2020-01-30 05:26:10 -05:00
Ken Stevens 2545fc6e3d Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
 2020-01-29 17:06:02 -05:00
James Agnew a6f3ee8319 Add a unit test 2020-01-29 09:35:22 -05:00
James Agnew 9548e74b17 Fix a test i missed 2020-01-28 15:46:46 -05:00
James Agnew 471073103f Further reduce memory usage in the terminology delta operations 2020-01-28 14:36:15 -05:00
Ken Stevens eff4b294df Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search 
# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
 2020-01-25 18:40:55 -05:00
James Agnew ba0048aade
Resolve memory leak (#1685) 
* Work on memory leak

* Work on term delta uploading

* Resolve memoery leak in terminology service

* Fix cache key
 2020-01-25 17:48:26 -05:00
Ken Stevens 78ab01f00b Change log and check in-memory search for location 2020-01-24 21:56:14 -05:00
Ken Stevens c87f8e0f4a tested near anti-meridian 2020-01-24 18:55:32 -05:00
Ken Stevens 72ccd76ed0 prepping for antimeridian test 2020-01-24 14:37:28 -05:00
Ken Stevens 11dc087750 code review 2020-01-24 13:08:47 -05:00
Ken Stevens 672902486a optimize imports 2020-01-24 13:07:19 -05:00
Ken Stevens 4ba91e0797 remove getDao() from Dao 2020-01-24 13:01:58 -05:00
Ken Stevens 9b0f850cf4 remove newSearchBuilder from dao 2020-01-24 13:01:35 -05:00
Ken Stevens 16cb9a74e4 Remove newSearchBuilder() from BaseHapiFhirDao 2020-01-24 12:19:08 -05:00
Ken Stevens b465a7b781 final cleanup 2020-01-23 19:20:51 -05:00
Ken Stevens 01bc941f5f Optimize imports 2020-01-23 19:15:30 -05:00
Ken Stevens e031ad203e FIXME 2020-01-23 19:12:05 -05:00
Ken Stevens 99949629a8 FIXME 2020-01-23 18:49:09 -05:00
Ken Stevens 3e28047f78 fix tests 2020-01-23 18:27:35 -05:00
Ken Stevens a687d7c9c1 testSearchResourceLinkWithChain is failing 2020-01-23 17:38:59 -05:00
Ken Stevens 6ca97df1c9 fix npe 2020-01-23 16:20:53 -05:00
Ken Stevens 8114419110 fix npe 2020-01-23 16:06:15 -05:00
Ken Stevens 48a71d6649 fix npe 2020-01-23 15:58:13 -05:00
Ken Stevens d2ef5555fe app context loads 2020-01-23 15:48:25 -05:00
Ken Stevens ab74e66870 compiles. now to run the tests... 2020-01-23 15:43:41 -05:00
Ken Stevens 49743352a6 remove unused enum 2020-01-23 14:28:10 -05:00
Ken Stevens c9fe68c5ab inlined single use methods 2020-01-23 14:21:07 -05:00
Ken Stevens e99402bd38 Almost done refactor. Just need to separate state from service. 2020-01-23 14:06:09 -05:00
Ken Stevens 4c53333539 started to refactor predicates out of SearchBuilder 2020-01-23 12:00:12 -05:00
Ken Stevens e6f5af01ed convert degrees to kilometers for near calculation 2020-01-22 16:55:19 -05:00
Ken Stevens 8b8088a3a2 begin with failing test 2020-01-22 15:06:39 -05:00
Ken Stevens b07b87954d r4 works. But distance calculation still needs to be fixed. 2020-01-22 12:00:09 -05:00
Ken Stevens 9413e8f198 r4 works. But distance calculation still needs to be fixed. 2020-01-22 11:59:03 -05:00
Ken Stevens 5da2823553 add negative test 2020-01-22 09:25:43 -05:00
Ken Stevens 6cebb56f13 testing complete. Now just need pre-review cleanup. 2020-01-21 17:06:19 -05:00
Ken Stevens 12dfac927e moar tests 2020-01-21 16:53:20 -05:00
Ken Stevens 04b60a4a16 no distance and zero distance tested 2020-01-21 16:18:42 -05:00
Ken Stevens 992b62151b yay box search works! 2020-01-21 16:04:34 -05:00
Ken Stevens 3cb9a9f4a2 added asserts 2020-01-21 15:45:41 -05:00
Ken Stevens b463929c28 parse nearDistance into a special search parameter field so it's available when we're adding the near parameter 2020-01-21 15:38:25 -05:00
Ken Stevens a961a7c022 begin with failing test 2020-01-21 14:39:00 -05:00
Ken Stevens eca21bec3e exact coord matching works now 2020-01-21 14:30:51 -05:00
Ken Stevens 299e1e35e1 removed coordextractor and moved to token (looks cleaner and more in line with how the other ones are parsed) 2020-01-21 11:06:40 -05:00
Ken Stevens dd137a0a30 Coord extraction implemented 2020-01-21 10:17:49 -05:00
James Agnew c0e929dacb
Copy identifiers to placeholder resources (#1675) 
* Copy identifiers to placeholder resources

* Add tests

* Maven cleanup

* Still messing around with azure

* Adding to logging

* More azure work

* One more attempt

* More messing around with azure

* Test fix

* Another caching attempt

* More work on azure pipeline

* Fix pipeline file

* Keep working on pipeline

* More work on azure

* More azure

* More azure work

* More azure
 2020-01-21 06:09:06 +09:00
James Agnew 63c310c168 Make a constant public 2020-01-17 13:16:23 +08:00
James Agnew aad5a30a3d
Support count=0 (#1670) 
* Support count=0

* Fix LGTM issue
 2020-01-15 14:52:32 +08:00
James Agnew 201ec34db4
Fix expunge issue when no tags present (#1671) 
* Fix expunge issue when no tags present

* Add changelog

* Try to clean up POMs that are failing CI

* Rework dependencies

* Roll back change that did not work
 2020-01-15 14:47:22 +08:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665) 
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
 2020-01-14 10:27:01 +08:00
James Agnew a19d246432 License header version bump, and add the ability for "add column" 
migration tasks to fail gracefully
 2020-01-12 11:01:21 +08:00
James Agnew b30de00ea1 Add parser stress test 2020-01-08 09:12:17 -05:00
jamesagnew 1720144cfb Test fix 2020-01-08 05:39:44 -05:00
James Agnew 49ed374d2f Remove test code that accudentally got committed 2020-01-06 14:26:30 -05:00
James Agnew 23ca94d3c5 Add example interceptor 2020-01-06 14:26:03 -05:00
James Agnew e42acef66b Test fix 2020-01-03 14:23:19 -05:00
James Agnew ca3b4297e1 FIx #1649 - Account for LOINC file format changes in 2.67 2020-01-03 14:19:22 -05:00
James Agnew 5cfc75eac2 Test fixes 2019-12-25 13:05:33 -05:00
James Agnew 536f46c89e Test fix 2019-12-21 12:24:15 -05:00
James Agnew a3ac893635
Merge branch 'master' into master 2019-12-21 11:32:45 -05:00
James Agnew 5187ddf7a2 One more fix 2019-12-19 15:21:12 -05:00
Ken Stevens ec4d7d1e99 Log a message if subscriptions are disabled on the server. 2019-12-18 15:18:16 -05:00
James Agnew f9b8567a3a Fix compile error 2019-12-17 19:28:07 -05:00
James Agnew d9be281fff Fix intermittent 2019-12-17 17:00:01 -05:00
jamesagnew 6fc0bdb88f Add licene headers 2019-12-16 11:14:17 -05:00
Ken Stevens 68a7613f9e Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseFlywayMigrateDatabaseCommand.java
 2019-12-16 08:58:26 -05:00
jamesagnew f2221bcc69 Restore errorprone to the build 2019-12-15 19:11:27 -05:00
jamesagnew 5f4355017d More test logging 2019-12-15 07:45:29 -05:00
James Agnew 10deea4967
Merge pull request #1610 from jasmdk/MissingMandatoryStatusOnSnomed 
Missing mandatory status on created Snomed CodeSystem
 2019-12-11 19:27:47 -05:00
Ken Stevens 9e4f57836f Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-05 21:45:31 -05:00
jamesagnew cafb6424f1 Test fix 2019-12-05 21:33:06 -05:00
Ken Stevens 6c432733d5 Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-05 18:03:02 -05:00
James Agnew 67b53e5326 Prevent ConcurrentModificationException during cascading delete 2019-12-05 18:00:40 -05:00
Ken Stevens a939dab894 fake change to trigger CI 2019-12-05 11:53:41 -05:00
Ken Stevens 334daddf33 fake change to trigger CI 2019-12-05 10:32:53 -05:00
Ken Stevens 676a443cf2 NPEs 2019-12-04 21:20:09 -05:00
Ken Stevens c516ab8a75 fake change 2019-12-04 18:02:10 -05:00
Ken Stevens 2f89f10c64 allow users to set default group 2019-12-04 17:23:51 -05:00
Ken Stevens b171ff97ea improve logging 2019-12-03 22:02:00 -05:00
Ken Stevens 09d2599ce5 fix test 2019-12-03 16:01:52 -05:00
Ken Stevens 5588da5ff8 Merge remote-tracking branch 'origin/master' into ks-20191119-scheduler 2019-12-03 08:51:50 -05:00
Ken Stevens 993d8220d1 review feedback 2019-12-02 11:18:52 -05:00
James Agnew f58fba6f04
Some test cleanup (#1616) 
* Some test cleanup

* Add test

* More test logging

* More docs cleanup

* Add test logging
 2019-12-02 11:00:18 -05:00
Ken Stevens 63218e560d Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-12-02 08:59:17 -05:00
James Agnew 86bd9a28fe
Fix to valueset expansion logic (#1613) 
* Fox to valueset expansion logic

* Work on docs

* Docs tweaks

* Docs tweaks

* Fix test

* Remove unused class

* Add changelog
 2019-12-01 21:21:19 -05:00
Ken Stevens 959dba7611 pre review cleanup 2019-12-01 16:51:01 -05:00
Ken Stevens 0c728a27df remove unused mystery class 2019-11-29 16:07:38 -05:00
Ken Stevens f92c2bb5f9 ensure only one @PostConstruct method to make order explicit 2019-11-29 11:46:03 -05:00
Ken Stevens 37eef4e3e4 rename schedule interface methods 2019-11-29 11:04:35 -05:00
Ken Stevens 321790f6bf standardized job names and how they're scheduled 2019-11-29 10:12:13 -05:00
Ken Stevens a0e363171d replace FireAtInterval class with an interface for now 2019-11-29 09:21:20 -05:00
Ken Stevens 319eead414 Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-11-27 14:20:15 -05:00
ahn 29b08e7308 Missing mandatory status on created Snomed CodeSystem 2019-11-27 12:21:02 +01:00
James Agnew f4fc19502b Fix intermittent failure 2019-11-26 22:24:50 -03:00
Ken Stevens a89bb6c411 simplified api 2019-11-25 20:59:40 -05:00
Ken Stevens 4c7c574eef first pass scheduler working 2019-11-25 20:12:45 -05:00
Ken Stevens 8c4ffc024d Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler 2019-11-25 16:40:40 -05:00
James Agnew ca620d652f
Add tests (#1606) 
* Support chained HAS

* Add some tests

* Add some cleanup

* Work on intermittent tests
 2019-11-24 10:11:49 +01:00
James Agnew 27749f4e23
Support chained HAS (#1605) 2019-11-24 06:29:56 +01:00
James Agnew a2f77b23d2
Fix #1583 - Index local refs in canonical types (#1593) 
* Fix #1583 - Index local refs in canonical types

* Add fix to pre-expansion

* Test fix

* Rework ID handling

* Test fixes

* Fix test
 2019-11-23 16:32:37 +01:00
Ken Stevens b36670377f fix circular reference merge to master 2019-11-22 11:02:05 -05:00
Ken Stevens a71eb039e3 merge two beans into one 2019-11-21 21:19:56 -05:00
Ken Stevens 6f9cd56c81 moved scheduler up to hapi-server 2019-11-20 14:30:24 -05:00
Ken Stevens b73cdbcaf5 add factory 2019-11-19 17:23:06 -05:00
Ken Stevens f3535a2bef split scheduler from service 2019-11-19 13:32:20 -05:00
Ken Stevens 8fca468e1f remove boolean from scheduling API 2019-11-19 10:13:22 -05:00
James Agnew 3173af31ae Try to avoid intermittent test failure 2019-11-17 15:28:50 -05:00
James Agnew 74159dcb26
Work on refactoring how PIDs work (#1580) 
* Start work on refactoring how PIDs work

* Some test fixes

* Test fixes

* Test fixes

* Restore accidentally deleted line

* One more tweak

* Rework resource link extraction

* Test fix

* Split out transaction processor

* Updates

* Test fix

* Test fixes

* Test fixes

* Clean up LGTM warning

* Fix compile failure

* One more test fix

* Fix LGTM issue

* Add spot for metadata

* Add test logging

* Remove testing code

* More test logging

* Add some test logging

* Attempty to fix intermittent test failure

* Improve exception tracking

* Work on simplifying search param registry

* Fix compile

* Fix compile errors

* Fix two test bugs
 2019-11-17 14:35:19 -05:00
James Agnew fba134853c Remove unused code 2019-11-15 16:44:17 -05:00
Anthony Sute a3ee2c1923 Unit tests for _filter-based URI matching 2019-11-14 19:04:23 -05:00
Anthony Sute d2c0b21773 (1) Changes to equal and not-equal operator logic for numerics to use exact values per discussions with Grahame and James 
(2) Additional unit tests
(3) Changes to tests affected by (1) above
 2019-11-14 15:05:23 -05:00
Ken Stevens 995bda0623 update comment 2019-11-14 14:55:02 -05:00
Ken Stevens ad39b319f8 fix test 2019-11-14 14:55:02 -05:00
Ken Stevens 1fff132f8e fix test 2019-11-14 14:55:02 -05:00
Ken Stevens ad8930fdba handle paging case 2019-11-14 14:55:02 -05:00
Ken Stevens f11d939131 oops 2019-11-14 14:55:02 -05:00
Ken Stevens 25c094e38a skip trying to populate resources in search result bundle if no resources were found 2019-11-14 14:55:02 -05:00
Anthony Sute 2c22b9d7ef Added _filter unit tests for date type values. 2019-11-12 17:58:29 -05:00
Anthony Sute bed0cc4d61 New unit tests to support _filter gt, lt, ge, and le operators for string types. 2019-11-12 15:06:17 -05:00
James Agnew aa0301084b
Don't succeed validation on unknown codesystem (#1575) 
* Don't succeed validation on unknown codesystem

* Test fixes

* Work on error messages

* Work on code validation API

* work on tests

* Work on validation

* Test fix

* Update DSTU3 validation reources

* Upgrade structures

* Test fixes
 2019-11-12 14:35:49 -05:00
Anthony Sute 49ed6b48dc Merged James' most recent changes. 2019-11-12 13:57:02 -05:00
Anthony Sute 09daf7aacc Implemented changes/fixes and associated unit tests for following _filter operators for strings: 
- eq
- ne
- co
- sw
- ew
 2019-11-11 21:58:49 -05:00
James Agnew 1a348abaf5 Try to fix 2 intermittent test failures 2019-11-08 08:45:08 -05:00
jamesagnew 3b1d8d1bc0 Add test logging sort 2019-11-08 07:27:25 -05:00
jamesagnew 7c8342dcc1 Add some test logging 2019-11-08 05:53:59 -05:00
James Agnew c027ff27c3 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-11-07 21:52:31 -05:00
James Agnew d4aea82460 Add some test logging 2019-11-07 21:50:06 -05:00
James Agnew 056756dbab
Fix paging issue #1300 (#1584) 
* Fix paging issue

* Add changelog with credit

* Add a test
 2019-11-07 18:17:09 -05:00
James Agnew ebc52e6b48 Correctly handle below expansion with missing system 2019-11-07 09:28:24 -05:00
Anthony Sute 92de268f32 Fixes for LGTM warnings 2019-11-06 08:47:53 -05:00
Anthony Sute 3cf8254625 (1) Fixes to address _filter-based _id retrievals not being restricted to the specified resource type 
(2) Import fix for FhirServerConfig.java in hapi-fhir-jpaserver-example
 2019-11-06 08:47:53 -05:00
jamesagnew 9c93d5d7f7 Test fixes 2019-11-04 07:04:26 -05:00
James Agnew 78a323f105 Test fixes 2019-11-03 21:20:22 -05:00
James Agnew f481e11ad5 Update migration tasks 2019-11-03 18:49:47 -05:00
James Agnew 60628356a8 Version bump spring 2019-11-03 11:29:22 -05:00
jamesagnew 2bf578879a One more bit of extensibility 2019-11-02 19:03:46 -04:00
jamesagnew f7ad82d7a8 Add a test 2019-11-02 18:47:02 -04:00
jamesagnew 5ad57d9ea9 Add some API to subscriptionactivating interceptor to make it more 
extendible
 2019-11-02 18:14:50 -04:00
jamesagnew 89b25ce828 License updates 2019-11-02 17:34:05 -04:00
James Agnew 3b6709e1d1
Merge pull request #1566 from jamesagnew/ja_20190928_rationalize_search_param_extractor 
Rationalize search param extractors across FHIR versions
 2019-11-02 16:18:23 -04:00
James Agnew 33a3ea8fca Fix compile error 2019-10-30 16:23:24 -04:00
James Agnew cacd243a44
Correctly Expand ValueSets in non-lucene mode (#1573) 2019-10-30 16:21:44 -04:00
Ken Stevens 1fd3948b12
Merge pull request #1572 from jamesagnew/ks-source-subscriptions 
fixed in-memory search by _source for Dstu3
 2019-10-30 16:20:14 -04:00
James Agnew e96500d54f Add a test 2019-10-30 15:51:46 -04:00
James Agnew 7f62d60c4e Correctly Expand ValueSets in non-lucene mode 2019-10-30 14:26:31 -04:00
Ken Stevens 21c591eaf2 ready for review 2019-10-30 13:49:10 -04:00
James Agnew d3e66680f0 Add some testing 2019-10-30 09:49:40 -04:00
James Agnew b90f285218 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-30 08:41:14 -04:00
James Agnew 007cfaf00e
Don't error out on missing CS (#1570) 
* Don't error out on mi9ssing CS

* Add tests

* Add a bit of test coverage

* One more test
 2019-10-30 08:38:39 -04:00
James Agnew 9c852283e9
Correctly handle "special" search params in CS (#1569) 
* Correctly handle "special" search params in CS

* Add another test
 2019-10-30 05:31:25 -04:00
James Agnew 84803a02ef
Preserve line numbers in XML validation (#1567) 
* Preserve line numbers in XML validation

* Test fixes
 2019-10-29 15:54:49 -04:00
James Agnew c5f48b6b47 Add tests 2019-10-29 13:24:43 -04:00
James Agnew 3dfb6959c1 Don't reload terminology resources when nothing has changed 2019-10-29 11:35:26 -04:00
James Agnew 2b8426114f Test fixes 2019-10-28 10:58:14 -04:00
James Agnew d321a8276a Fix intermittent 2019-10-28 10:45:39 -04:00
jamesagnew 75ad205bd5 Try to fix intermittent 2019-10-28 07:23:49 -04:00
jamesagnew 51a0006548 Work on rationalizing search param extractor 2019-10-27 20:04:33 -04:00
jamesagnew ac4d108126 Merge branch 'ja_20190928_rationalize_search_param_extractor' of github.com:jamesagnew/hapi-fhir into ja_20190928_rationalize_search_param_extractor 2019-10-27 18:17:29 -04:00
James Agnew 817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -04:00
jamesagnew 5a300d2d8e Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-10-26 10:32:16 -04:00
James Agnew 403a3d1889
Correct URI loading in testpage-overlay (#1565) 
* Clean up tests

* Try to fix intermittent

* Fix URI issue

* Add changelog
 2019-10-25 16:14:06 -04:00
jamesagnew cd84af30b1 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-25 05:56:39 -04:00
jamesagnew 935ec9ebc2 License headers 2019-10-25 05:44:51 -04:00
Ken Stevens f19100cbb3 final cleanup 2019-10-24 20:29:45 -04:00
Ken Stevens 4a2ed62357 review feedback 2019-10-24 20:25:16 -04:00
Ken Stevens 08472c1e3f ready to merge 2019-10-24 17:56:15 -04:00
Ken Stevens 4fa849a3e5 pre-review cleanup 2019-10-24 16:43:47 -04:00
Ken Stevens 43f17534bb commiting with FIXMEs so James can review 2019-10-24 16:40:53 -04:00
James Agnew df4376606d
Validation cleanup (#1561) 
* Validation cleanup

* Test fix

* Fix build

* Test tweaks
 2019-10-24 13:09:18 -05:00
James Agnew 385a885abf Add ability for resource source to be specified by header 2019-10-24 08:32:52 -04:00
James Agnew 0d3f7d4a03 Correctly handle searching by source in JPA server 2019-10-23 06:58:16 -04:00
James Agnew 19247ffb46
Allow updating externalized binary (#1556) 
* Add non working test

* Add a test

* FIx test

* Allow updating existing externalized binary data

* Add test

* Remove unneeded test

* Fix test
 2019-10-22 18:10:03 -04:00
James Agnew 371bf2e5cf Disable unit test SQL logging 2019-10-22 17:27:36 -04:00
James Agnew 9b94e4e26d
Allow uploading term deltas using CS resource (#1555) 
* Work on accepting codesystem reources for delta operations

* Ongoing work on term uploader

* Restore the ability to use CodeSystem resources for the delta

* Add tests

* Fix NPE

* Test fixes
 2019-10-22 17:11:39 -04:00
James Agnew 464c6c5b45
Upgrade dependencies and addess Semmle issues (#1554) 
* Version bumps

* FIx build issues

* Address a few Semmle issues

* Work on tests

* Some test fixes

* Test fix

* Fix deletions

* Test fix

* Fix intermittent test failure

* One more dependency bump

* Add some test logging

* Remove bad import

* Add some tests

* Test updates
 2019-10-22 17:10:58 -04:00
Ken Stevens d0704269d7 ready for rereview 2019-10-22 10:13:49 -04:00
Ken Stevens 427f7397da ready for rereview 2019-10-22 10:13:49 -04:00
Ken Stevens 0f40b2c48f npe check for binary storage interceptor 2019-10-22 10:13:49 -04:00
James Agnew 73961072a6
Handle invalid chains on custom search params (#1553) 
* Handle invalid chains on custom search params

* Add some more tests

* One more test fix
 2019-10-21 21:21:33 -04:00
James Agnew 0af79b84d9
Use webjars instead of including JS deps (#1551) 
* Use webjars instead of including JS deps

* Add changelog
 2019-10-21 07:22:55 -04:00
James Agnew bfbc73caaf
Auto externalize binary contents (#1550) 
* Auto externaliZe binary attachments

* Work on externalization

* Auto externalize binary content

* Work on tests

* Fix alert
 2019-10-19 09:01:00 -04:00
James Agnew 985cd49892 Test fixes 2019-10-18 16:36:05 -04:00
James Agnew 0cddb54476 Remove accidental commit 2019-10-18 15:52:03 -04:00
James Agnew c455a46160 Add missing class 2019-10-18 15:51:20 -04:00
James Agnew a71d969ba1 Add line numbers to validation failures 2019-10-18 14:10:47 -04:00
James Agnew 50af4bfb19 Merge latest changes 2019-10-18 13:36:26 -04:00
James Agnew 13b80a294a Test fix 2019-10-18 07:13:11 -04:00
James Agnew 0971998f57 Fix #848 - Pass raw JSON to the validator 2019-10-17 11:28:48 -04:00
James Agnew 12a74e6cbc
Fix term uploads and validate against valueset recalculation (#1540) 
* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Work on upload command

* Test fixes

* Work on validation fixes

* Work on validation against pre-expansion

* Work on direct validation

* A bit of cleanup

* Add some javadoc

* Force another build

* Test fixes

* Fix tests

* Fix tests
 2019-10-15 21:31:29 -04:00
James Agnew 8b2ab51bc6
Handle canonical questionnaire refs in validator (#1544) 
* Handle canonical questionnaire refs in validator

* FIx changelog

* Fix canonical reference

* Build tweak

* Change to trigger a build
 2019-10-15 20:27:53 -04:00
James Agnew 839f935401 remove unnecessary index 2019-10-15 19:07:37 -04:00
James Agnew fdcf5f5d73 Add a test 2019-10-15 18:16:22 -04:00
James Agnew bf476b9c32 Handle null returns from search cache methods 2019-10-15 16:25:21 -05:00
James Agnew 9c23959b38 Licene header updates 2019-10-15 15:08:13 -04:00
James Agnew 9a050461a8 Make cache timeout configurable 2019-10-15 09:34:48 -04:00
James Agnew 2725797610
Implement Terminology Delta Operations (#1536) 
* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Test fixes
 2019-10-14 19:14:41 -04:00
James Agnew e656863a73
Correct bugs reported by LGTM (#1533) 
* Correct bugs reported by LGTM

* Add some tests

* A few more updates

* YAML update

* Test fixes

* One more test fix

* Test fix
 2019-10-09 19:26:57 -05:00
James Agnew 861ed36f00
Allow patches to be authorized for DSTU3 transactions (#1529) 
* Allow patches to be authorized for DSTU3 transactions

* Add changelog
 2019-10-08 14:29:27 -05:00
jamesagnew 150c865f68 License header updates 2019-10-03 21:20:08 -04:00
James Agnew 069db501ee
Fix _has parameter (#1525) 
* Fix _has parameter

* Bug fixes

* Add a comment

* Test fixes
 2019-10-03 21:19:31 -04:00
James Agnew 836fac9a30 Ensure that JPA PRESHOW interceptor broadcasts don't include expunged 
resources
 2019-10-03 15:49:03 -04:00
Ken Stevens 38ad11be64
Merge pull request #1513 from jamesagnew/ks-subscription-delivery-queue-configurable-name 
subscription delivery queue configurable name
 2019-10-03 15:19:12 -04:00
James Agnew 1b5528a998 Fix compile error 2019-10-03 15:06:14 -04:00
James Agnew a3b9db1363 Clean up a few unused methods and move test classes into test project 2019-10-03 14:58:02 -04:00
Ken Stevens f6db6ff068 Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name 2019-10-03 13:35:05 -04:00
Ken Stevens 53f47fbb1e Merge remote-tracking branch 'remotes/origin/master' into ks-narrow-search-pointcut 2019-10-03 12:20:20 -04:00
Ken Stevens d1deedf247 pre-review cleanup 2019-10-03 12:14:11 -04:00
Ken Stevens 566443d0fe move BundleUtil back 2019-10-03 12:05:26 -04:00
Ken Stevens 98c76a4d49 Test passes 2019-10-03 12:03:38 -04:00
Ken Stevens 29e7cdc476 Added ability to modify URLs in BundleUtil 2019-10-03 09:46:32 -04:00
James Agnew db668d96b9 Add a few tests and remove some dead code 2019-10-03 09:00:14 -04:00
James Agnew 2193a30b45
CodeSystem Delta Uploader (#1520) 
* Terminology Delta Uploading

* Add delta operations

* Fix up tests

* Improve test coverage a bit

* Improve test coverage reporting

* fix yaml

* A couple of test enhancements

* FIx intermittent test failure
 2019-10-03 07:19:00 -04:00
Ken Stevens 53f949c2d0 pre-review cleanup 2019-10-02 08:36:54 -04:00
Ken Stevens 5aa4f88da3 Remove ISubscribableChannel interface. We don't need it after all. 2019-10-02 06:35:39 -04:00
Ken Stevens ed195f8dab Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name 2019-10-02 06:21:12 -04:00
Clayton Bodendein 08825a81d9 Add missing @Override annotations 
Added missing @Override annotations so that if/when methods in superclasses change
there will be a compile-time error if subclasses haven't been changed accordingly.

This was done using IntelliJ IDEA's "Missing @Override annotation" inspection.
 2019-10-02 05:45:59 -04:00
Ken Stevens f0b2bb8309 fixed triggering subscriptions 2019-10-01 14:57:25 -04:00
Ken Stevens ca95791d2e fix test 2019-10-01 10:52:00 -04:00
Ken Stevens ade9e0316e Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name 2019-10-01 09:20:00 -04:00
James Agnew b028337d8f Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-09-30 21:11:41 -04:00
Ken Stevens 6867a57625 null check 2019-09-30 17:15:35 -04:00
jamesagnew f373abf74c License header updates 2019-09-30 15:32:49 -04:00
Ken Stevens a9f83a8c43 Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name 2019-09-30 15:19:15 -04:00
James Agnew 066c9a7fb7 Improvements to AutohrizationInterceptor create handling 2019-09-30 15:07:23 -04:00
Ken Stevens fd8b5206e7 Separated ChannelRegistry from ActiveSubscriptionRegistry so we can support a many-to-one relationship there 
All tests pass
 2019-09-30 15:01:47 -04:00
Diederik Muylwyk 396f358f2d Support for long concept property values has been added. 2019-09-30 14:40:31 -04:00
Diederik Muylwyk a324e51efa
Merge pull request #1516 from jamesagnew/1512-need-to-implement-the-ancestor-filter-with-in-operator-for-loinc 
Resolve "Need to implement the ancestor filter with IN operator for LOINC"
 2019-09-30 10:37:25 -04:00
Diederik Muylwyk dbd5331f5a Support for ancestor filter with IN operator for LOINC has been added. 2019-09-30 10:25:29 -04:00
James Agnew 0bee7a7b53 Test fix 2019-09-30 10:12:49 -04:00
Diederik Muylwyk 7eaa5d5574 Merging master into working branch. 2019-09-30 09:41:43 -04:00
Diederik Muylwyk 1b2892f475
Merge pull request #1505 from jamesagnew/1454-need-to-implement-the-ancestor-and-descendant-filters-for-loinc 
Resolve "Need to implement the ancestor and descendant filters for LOINC."
 2019-09-30 09:39:32 -04:00
James Agnew 557a8ccc66
Add top level support for ElasticSearch (#1514) 
* ElasticSearch work

* Add ElasticSearch properties builder

* Clean up POM

* Remove redundant project

* Try to troubleshoot embedded elasticsearch

* Another test attempt

* Add credentials to elasticsearch config

* Work on lastn

* Address review comments

* A couple of test fixes
 2019-09-30 09:30:39 -04:00
Diederik Muylwyk 0386448b3f Initial commit for work on ancestor filter with IN operator for LOINC. 2019-09-30 09:21:32 -04:00
James Agnew c0eb662a21 Rationalize search param extractor 2019-09-28 19:23:21 -04:00
Diederik Muylwyk 3e173bb07c Merging master into working branch to resolve conflicts. 
# Conflicts:
#	src/changes/changes.xml
 2019-09-26 20:19:22 -04:00
Diederik Muylwyk 5f17fb30b4 Address review comments. 2019-09-26 20:15:55 -04:00
Ken Stevens 07286e3b3f Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name 2019-09-26 17:50:14 -04:00
James Agnew ed78a5f06d Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-26 16:56:42 -04:00
James Agnew 77d15a1836
Fix failing tests due to race conditions 
* Work on failing tests

* Temporary downgrade of fhir core

* Work on failing build

* Fix pom

* Don't upload codecov

* Restore codecov

* Restore all tests

* Keep hammering away at intermittent test failures

* More test fixes

* Keep chipping away at these...

* Add some extra checks

* Work on tests

* More test logging

* More logging

* This might be it!

* Final build fixes?

* Address some review comments

* A couple more corrections
 2019-09-26 16:11:15 -04:00
Ken Stevens 392d7ab000 Extend SubscribableChannel with SubscribableChannelManagement so we can get a handler count so we know when to destroy a channel 2019-09-26 15:46:40 -04:00
James Agnew cc0df9850c Make sure the validator can get at codes defined in notpresent 
codesystems
 2019-09-26 14:44:09 -04:00
James Agnew 94f87e7282 Allow term service to return codes 2019-09-26 12:46:41 -04:00
Diederik Muylwyk b6400764c4 Removed scratch notes. 2019-09-26 11:42:26 -04:00
Diederik Muylwyk efae77a330 Added changelog entries. 2019-09-26 11:36:55 -04:00
Diederik Muylwyk a4f9894104 Merging master into working branch. 2019-09-26 10:41:34 -04:00
Diederik Muylwyk e098cea07f Throw UnsupportedOperationException for LOINC ancestor filter with IN operator; ignore tests. See #1512 in GitHub. 2019-09-26 10:39:55 -04:00
James Agnew ddb5605830 Improve test logging 2019-09-25 22:17:47 -04:00
Diederik Muylwyk 4f7db37d8e Additional progress for ancestor/descendant filters; only ancestor/in remains. 2019-09-25 21:36:36 -04:00
James Agnew 99787d14f1 Add some test logging 2019-09-25 21:20:36 -04:00
James Agnew 8657afb01e
Fix intermittent test failures regarding search (#1509) 
* Add some logging

* Add more test logging

* Work on some test logging

* Fix compile error

* Work on codecov

* Work on codecov

* Remove test debug messages
 2019-09-25 20:15:21 -04:00
Diederik Muylwyk 7c5cf9f1f4 Incremental progress for ancestor/descendant filters. 2019-09-25 17:33:45 -04:00
Diederik Muylwyk 9b4671c05e Added a bunch of tests for ancestor/descendant filters. 2019-09-25 16:52:08 -04:00
Diederik Muylwyk 729d3a3d3b Fix intermittent test failure. 2019-09-25 15:32:39 -04:00
James Agnew 4570e50c03 Fix nullability on one column 2019-09-25 15:31:26 -04:00
James Agnew cddaf058a2 Add some extra test logging 2019-09-25 15:27:17 -04:00
Diederik Muylwyk 30588bf8ee Completed fixing tests after enabling pre-expansion by default. 2019-09-25 14:29:50 -04:00
jamesagnew b2c13f3018 Work on codecov integration 2019-09-25 13:25:59 -04:00
Diederik Muylwyk 6b22d705c7 Incremental progress fixing tests after enabling pre-expansion by default. 2019-09-25 13:24:50 -04:00
jamesagnew 2efef13528 Another test fix 2019-09-25 05:43:58 -04:00
jamesagnew 4c064186a9 Try to fix intermittent testfailure 2019-09-25 05:39:00 -04:00
Diederik Muylwyk 799848291f Merging master into working branch. 2019-09-24 16:47:19 -04:00
Diederik Muylwyk 5743efa066 Minor tweak to test. 2019-09-24 16:46:05 -04:00
James Agnew 21b91ac0e7 Make sure we call the updateEntity method on the correct DAO type when 
processing inside a transaction
 2019-09-24 16:16:13 -04:00