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2173 Commits

Author SHA1 Message Date
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 731be21c9f Exclude commons-logging from dependencies 2019-09-30 18:58:25 -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
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
Diederik Muylwyk bf5d6acef4 More troubleshooting. 2019-09-24 15:36:06 -04:00
Diederik Muylwyk 46a6b7aaef Troubleshooting lack of ValueSet pre-expansion when updating a ValueSet via transaction bundle. 2019-09-24 15:30:40 -04:00
James Agnew bd763d728b Merge branch 'master' into ks-source-request-id-append-bug 2019-09-24 14:49:39 -04:00
James Agnew 5f563057c0
Set up CI with Azure Pipelines (#1502) 
* Set up CI with Azure Pipelines

[skip ci]

* Update azure-pipelines.yml for Azure Pipelines

* Skip tests for a build

* Work on pipeline

* Update azure-pipelines.yml for Azure Pipelines

* Interceptors docs

* Test fix

* Disable releases from snapshot repo

* Try disabling jitpack

* Fix dependency issue

* A couple of test fixes

* Change to trigger a build

* Force a change to trigger a build

* Force a build

* FIx test
 2019-09-24 14:38:38 -04:00
Ken Stevens 0e90867a65 fixed meta.source request append bug 2019-09-24 14:35:34 -04:00
James Agnew 9b2826f3c6
Handle searches with chained slash value (#1503) 
* Work on test case for bug with searches

* Work on tests

* Fix issue with slashes in reference chain parameter for JPA server
 2019-09-24 14:31:05 -04:00
Diederik Muylwyk df4b6c798c Modified LOINC Terms to RadLex RPIDs ID and URL; pattern is mappings of main LOINC terms to say 'loinc' but parts and other codes are specified. 2019-09-24 09:21:42 -04:00
Diederik Muylwyk 2a2e8e0ab8
Merge pull request #1501 from jamesagnew/1483-need-consistent-assignment-of-fullurl-id-and-url-for-loinc 
Fixed inconsistent IDs and URLs for LOINC.
 2019-09-23 15:59:21 -04:00
James Agnew 6f44d7c360
Fix issue deleting CodeSystem resources (#1316) 
* Fix deleting CodeSystem resources

* Test fixes

* Address review comments
 2019-09-23 15:58:57 -04:00
James Agnew 004f42cdcc Clean up docs 2019-09-23 15:56:02 -04:00
Diederik Muylwyk 59d7ccb99e Fixed inconsistent IDs and URLs for LOING. 2019-09-23 15:49:58 -04:00
Diederik Muylwyk 56e2904029 Removing my name. Whoops! 2019-09-20 18:48:47 -04:00
Diederik Muylwyk 0cc35699b8 Specify full path for LOINC filenames to avoid duplicates. 2019-09-20 18:43:38 -04:00
Diederik Muylwyk e1e8ec981b Replaced migration task column length constants with literals because they are not necessarily constant across schema versions. 2019-09-20 12:31:54 -04:00
jamesagnew 6475146bc9 Add license headers 2019-09-19 18:08:21 -04:00
James Agnew eddb98084d Move PreferReturnEnum back to original location to avoid regressions 2019-09-19 15:48:58 -04:00
James Agnew 6fde2879ef Fix one more intermittent test 2019-09-19 14:53:29 -04:00
James Agnew 47805bceff Test fixes 2019-09-19 14:42:27 -04:00
James Agnew a5a0fca065 Test fixes 2019-09-19 11:33:33 -04:00
James Agnew 2be63a1650 Test fixes 2019-09-19 09:45:07 -04:00
jamesagnew 170698562a Bump to current org.hl7.fhir.core 2019-09-19 08:11:30 -04:00
James Agnew 30dfde645b Upgrade to Fontawesdome 5 and prevent uploading resources with binary 
storage extensions
 2019-09-19 05:28:05 -04:00
James Agnew 6b21e8cd90 Add some testing to the bulk export service 2019-09-18 14:43:00 -04:00
James Agnew 4a751cbfc5
Integrate Bulk Export (#1487) 
* Start working on subscription processor

* Work on new scheduler

* Test fixes

* Scheduler refactoring

* Fix test failure

* One more test fix

* Updates to scheduler

* More scheduler work

* Tests now all passing

* Ongoing work on export

* Ongoing scheduler work

* Ongoing testing

* Work on export task

* Sync master

* Ongoing work

* Bump xml patch version

* Work on provider

* Work on bulk

* Work on export scheduler

* More test fies

* More test fixes

* Compile fix

* Reduce logging

* Improve logging

* Reuse bulk export jobs

* Export provider

* Improve logging in bulk export

* Work on bulk export service

* One more bugfix

* Ongoing work on Bulk Data

* Add changelog
 2019-09-17 16:01:35 -04:00
James Agnew 882e0853df Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-16 15:55:49 -04:00
James Agnew 38cf830384 Accurately reflect codesystem URL 2019-09-16 15:55:32 -04:00
Diederik Muylwyk 3a9342913c Address review comments. Added tests. 2019-09-16 11:54:34 -04:00
Diederik Muylwyk b05c5f3f71 Implement the parent and child filters for LOINC. #1453 2019-09-15 21:52:33 -04:00
Diederik Muylwyk 9b1af6b207 Implement both a copyright property and a copyright filter for LOINC. #1451 2019-09-13 16:18:51 -04:00
Diederik Muylwyk 678d58ab90 Only manually add EXTERNAL_COPYRIGHT_NOTICE to LOINC uploader if it doesn't already exist in loinc.xml 2019-09-13 11:57:19 -04:00
Diederik Muylwyk 75ddba7f2d Add EXTERNAL_COPYRIGHT_NOTICE property for LOINC uploader. 2019-09-13 11:49:01 -04:00
Diederik Muylwyk 7dce29b86e
Merge pull request #1468 from jamesagnew/dm-more-performance-tuning-on-valueset-expansion 
More performance tuning on ValueSet expansion.
 2019-09-10 17:57:13 -04:00
Diederik Muylwyk 65e029458c Test fixes. 2019-09-10 17:50:49 -04:00
Diederik Muylwyk d4feb5d0b1 Final cleanup before review. 2019-09-10 14:21:42 -04:00
James Agnew 9420bca341
Merge branch 'master' into ks-in-memory-date-compare 2019-09-10 13:25:29 -04:00
Diederik Muylwyk 57d4cc23ee More bug-hunting. DSTU3 was missing a null check. 2019-09-10 11:56:07 -04:00
James Agnew 0843a2b02d Avoid leaking details when canSeeReource rejects a resource from consent 
service
 2019-09-10 11:14:44 -04:00
Ken Stevens c974e9283b added search % now test 2019-09-10 10:11:09 -04:00
Diederik Muylwyk 67d24eedff Merging master into working branch. 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
 2019-09-09 19:01:29 -04:00
Diederik Muylwyk dbe5a36f26 Reset schedule for pre-expansions. Ready for review. 2019-09-09 18:44:25 -04:00
Diederik Muylwyk 7e76c1893f Fixed bug for large ValueSet expansion with URL parameter; return 404 for unknown ValueSets. 2019-09-09 18:41:00 -04:00
James Agnew 2052df3152 Error with a 404 on invalid valueset 2019-09-09 18:01:41 -04:00
Diederik Muylwyk 19676a01b7 Incremental progress on large ValueSet expansion with URL parameter. 2019-09-09 17:24:01 -04:00
Diederik Muylwyk c82c3a093f Removing gaps from concept order when pre-expanding ValueSets. 2019-09-09 15:24:37 -04:00
jamesagnew 95e75d0a7d Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-09 15:02:55 -04:00
Diederik Muylwyk 4fc0ad6f0a Cleanup following paired programming with JA. 2019-09-06 17:56:56 -04:00
James Agnew 6ec991cd39 Finally this is fast! 2019-09-06 16:29:09 -04:00
James Agnew 718fcb28a5 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-06 14:58:03 -04:00
Diederik Muylwyk 0cabc0392f Incremental progress on large ValueSet expansion. 2019-09-06 14:57:34 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
jamesagnew 362c658f9a License headers 2019-09-06 10:23:36 -04:00
Ken Stevens c88e6a6fa7
Merge pull request #1442 from jamesagnew/ja_20190822_1440_infinispan_query_cache 
Externalize query cache into its own service
 2019-09-06 08:28:12 -04:00
James Agnew 785d40a777 Accuont for a few schema changes 2019-09-05 21:29:47 -04:00