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2544 Commits

Author SHA1 Message Date
Tadgh d91cb7524c Fix up whitespace 2020-03-13 15:30:49 -07:00
Tadgh 03567c5831 Add perftrace. Remove regex 2020-03-13 15:29:48 -07:00
Ken Stevens 6b019492fe
Merge pull request #1758 from jamesagnew/ks-20200312-json-annotation 
moved common Json annotations out into an interface
 2020-03-13 15:58:21 -04:00
Tadgh 74fd2c1519 wip 2020-03-13 11:28:44 -07:00
jamesagnew 72b9d9a350 FIx spelling mistake 2020-03-13 09:19:45 -04:00
James Agnew 1dc5d89013
Optmize forced ID resolution (#1754) 
* Add forced ID caching

* Work on id optimization

* Test fixes

* More optimization work

* Add some docs

* Work on docs

* Test fixes

* Test fixes

* Test fixes

* Address review comments

* Compile fix
 2020-03-12 17:12:50 -04:00
Ken Stevens ecf5284c87 moved common Json annotations out into an interface 2020-03-12 13:36:34 -04:00
Tadgh c3ceffbd72 wip 2020-03-09 16:05:41 -07:00
Tadgh e38ec3e3dd Fix typo 2020-03-09 14:57:53 -07:00
Tadgh 12412a7be9 Add query capturing to query 2020-03-09 13:58:59 -07:00
Tadgh 59d1603597 Some variable renaming. Adds some questions. 2020-03-09 13:51:47 -07:00
Tadgh aca4bcfaad Minor refactoring for readability 2020-03-06 14:22:31 -08:00
Tadgh b299d0b63f Fix Typos, reduce code duplication 
* Change Two streams into one.
* Fix typos.
* Begin Writing docstrings
* Rename variables for clarity
 2020-03-06 11:39:39 -08:00
Tadgh 0acfc51082 Split test into two tests, one of which passes, one of which fails, showing the missing functionality 2020-03-05 16:38:42 -08:00
James Agnew 58ee76549c Merge branch 'master' into ja_20200206_multitenancy 2020-03-04 08:19:22 -05:00
Ken Stevens 9b37ba35d0
Merge pull request #1747 from jamesagnew/ks-20200303-bulk-export-filter 
fixed a copy/paste error in bulk export with test
 2020-03-03 19:54:26 -05:00
Ken Stevens e819d40414 fix near searching for R4 2020-03-03 18:33:19 -05:00
Tadgh a510543933 Fix log conditional 2020-03-03 14:03:55 -08:00
Tadgh df7a9916c3 Swap from trace to info logging 2020-03-03 14:01:12 -08:00
Ken Stevens d104fbdf7d fixed a copy/paste error in bulk export with test 2020-03-03 16:40:31 -05:00
Ken Stevens 705735b9c0 review feedback: javadoc 2020-03-03 13:29:10 -05:00
Ken Stevens 5b5ef08500 Merge remote-tracking branch 'remotes/origin/master' into ks-20200302-near-chain 2020-03-03 09:44:52 -05:00
James Agnew 4a160a2df3 Merge branch 'master' into ja_20200206_multitenancy 2020-03-03 09:25:19 -05:00
James Agnew 58b5bd9664
Limit type on _has query (#1743) 
* Limit type on _has query

* Add changelog
 2020-03-03 08:28:38 -05:00
James Agnew 3c2c1dab2e
Error on missing profile validation (#1742) 
* Error on missing profile validation

* Add changelog

* Test fixes
 2020-03-03 08:28:26 -05:00
Ken Stevens a56df03055 restrict near-distance extraction to DSTU3 2020-03-02 21:50:57 -05:00
Ken Stevens 4e1be80525 fixme 2020-03-02 21:39:28 -05:00
Ken Stevens d1b54a9668 pre-review cleanup 2020-03-02 21:32:27 -05:00
Ken Stevens 27dcafe4f2 all but unit tests 2020-03-02 21:27:50 -05:00
Ken Stevens 24acb57f3b began with failing test. 
test now passes.
 2020-03-02 17:56:25 -05:00
Tadgh 8d9119faef Rework span name 2020-03-02 14:37:09 -08:00
Gary Graham 6123e4b189 rework based on PR comments 2020-02-28 16:31:16 -05:00
Gary Graham ed7b9fc6b6 Initial attempt at integrating elastic APM for search performance 2020-02-28 16:09:16 -05:00
James Agnew 8c78e465b1
Defer large term delta adds (#1736) 
* Defer large term delta adds

* Add changelog
 2020-02-28 14:41:15 -05:00
James Agnew 5bc554949b
Remove deleted resources from cached search results (#1732) 
* Remove deleted resources from cached search results

* Add changelog

* Add tests
 2020-02-28 10:57:26 -05:00
Gary Graham f86a4c9fa1 Add date ordinals to subscription matching checker 2020-02-26 17:05:23 -05:00
Gary Graham 2dc94de6bb roll back change to inmemory matcher test 2020-02-26 14:31:35 -05:00
Gary Graham 077f9df814 I keep finding more tests 2020-02-26 12:04:33 -05:00
Gary Graham a97443b1ed Fix test failures. One caused by invalid test. One caused by granularity need LT not LTE 2020-02-26 11:12:27 -05:00
James Agnew cb9906580e
Index canonical references (#1728) 
* Index canonical references

* Add changelog

* Fix compile error

* Add whitespace
 2020-02-25 21:45:46 -05:00
Gary Graham df9e86ec66 Merge branch 'master' into date-match-bug 2020-02-25 17:26:53 -05:00
James Agnew b2b0ff22b4
Collapse date joins (#1726) 
* Collapse date joins

* Add changelog

* Address review comments

* Add whitespace

* fix test

Co-authored-by: Ken Stevens <ken.stevens@sympatico.ca>
 2020-02-25 17:17:13 -05:00
Gary Graham 2204fbeabd Adding some comments 2020-02-25 17:08:11 -05:00
Gary Graham 1e833af5f0 Variable reuse 2020-02-25 17:06:38 -05:00
Gary Graham f56e38148b Add flag to DaoConfig controlling behaviour 2020-02-25 16:43:17 -05:00
Gary Graham 512af5b87d Add changelog entry 2020-02-25 14:09:51 -05:00
Gary Graham da7224ff89 update broken test to reflect new reality of business logic of ordinal date comparison 2020-02-25 14:07:03 -05:00
Gary Graham 3ec772b527 rework ResourceIndexedSearchParamDate constructor to support incoming string values 2020-02-25 14:06:36 -05:00
Gary Graham 3b41b5b960 Type migration to boxed integer to avoid int defaulting to 0 2020-02-25 11:18:39 -05:00
Gary Graham 34d5925393 Move common work to DateUtils. Rename function for clarity. 2020-02-25 09:37:57 -05:00
Gary Graham 7f5b3394e0 Hacky first-pass of adding ordinal date field to ResourceIndexedSearchParamDate and using it for search 2020-02-24 19:34:16 -05:00
Ken Stevens b33ad73d46 switch subscriptionchannelfactory to autowire 2020-02-24 14:28:14 -05:00
Ken Stevens 18d859281e Merge remote-tracking branch 'remotes/origin/master' into date-match-bug 2020-02-24 11:47:43 -05:00
Ken Stevens 41b5eb2484 Switching cdrsubscribablefactory from @ComponentScan to @Bean 2020-02-23 15:43:30 -05:00
j-chan c0811376b7
Moved TranslateRawParameters method from BaseHapiFhirResourceDao to BaseStorageDao (#1722) 2020-02-20 10:52:43 -05:00
James Agnew 6200cd2ddc Add test asserts 2020-02-19 21:21:22 -05:00
James Agnew 79ad0aebb5 Add a test 2020-02-19 18:01:35 -05:00
James Agnew a05c4ce9eb
Don't thrash delta links (#1721) 
* Don't thrash delta links

* Add changelog

* Remove commented out code
 2020-02-19 17:46:54 -05:00
James Agnew ab8dfa5a03
Avoid multi-term for ElasticSearch (#1717) 
* Avoid multi-term for ElasticSearch

* Add changelog

* Remove redundant code
 2020-02-18 16:40:44 -05:00
IanMMarshall fba28950ec
Merge pull request #1693 from jamesagnew/im_20200131_remove_circular_dependency_forcedid 
Changes to schema to loosen dependencies involving Forced ID table
 2020-02-18 14:16:09 -05:00
James Agnew 64f07e4dc0
Includes performance enhancement (#1702) 
* Includes performance enhancement

* Add changelog

* Test fix

* Fix typo

* A few coverage cleanups

* Test fix

* Fix changelog
 2020-02-18 14:11:48 -05:00
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
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -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