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2301 Commits

Author SHA1 Message Date
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
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
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
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
Ken Stevens b1421b1d60 @NotNull (hope I picked the right one!) 2019-09-05 16:20:24 -04:00
Ken Stevens 2a08808935 final PR cleanup 2019-09-05 16:11:58 -04:00
Diederik Muylwyk 6fa9658b24 Incremental progress on large ValueSet expansion. 2019-09-05 15:54:45 -04:00
Diederik Muylwyk 655222fcac Merging master into working branch. 2019-09-05 11:59:44 -04:00
Diederik Muylwyk 91cfecd257 Incremental progress on large ValueSet expansion. 2019-09-05 11:43:31 -04:00
Ken Stevens 01015bc435 added list stresstest 2019-09-04 21:15:08 -04:00
Ken Stevens 1f60d85517 Merge branch 'ks-anylist-enhancement' into ja_20190822_1440_infinispan_query_cache 2019-09-04 13:31:19 -04:00
Ken Stevens fa62ab9c9e Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
 2019-09-04 13:31:00 -04:00
Ken Stevens 0a5c52122e added list stresstest 2019-09-04 08:49:18 -04:00
Diederik Muylwyk b00b1d2278 Toggle pre-expansion config. 2019-09-03 20:36:54 -04:00
Diederik Muylwyk ea19b46f60 Added an indexed order column to TermValueSetConcept for improved fetching. 2019-09-03 20:36:16 -04:00
Diederik Muylwyk aa9a984075 Don't trust stored total when determining whether or not to expand. 2019-09-03 18:44:52 -04:00
Diederik Muylwyk 358f649d1f Minor tweaks following review. 2019-09-03 17:14:31 -04:00
Diederik Muylwyk 3e522a7414 Address review comments. 2019-09-03 16:37:28 -04:00
Diederik Muylwyk 6ebc9572ac Adjust concept and designation totals as we process. 2019-09-03 16:23:20 -04:00
Diederik Muylwyk b42b598d01 Added pre-fetch for concept designations, improved paging for expanded ValueSets, and columns on TermValueSet for number of concepts and designations. 2019-09-03 16:02:28 -04:00
jamesagnew 1ef70a0fca Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-03 07:02:09 -04:00
jamesagnew 8b09b3f3eb Rename config enum for consistency 2019-09-03 07:01:36 -04:00
Diederik Muylwyk 02a896f31e Fix NPE for ValueSet operation validate-code when Coding and/or CodeableConcept is null for DSTU3/R5. 2019-09-02 21:28:51 -04:00
Diederik Muylwyk c34d8458ef Refactor getting resource PIDs with utility methods. 2019-09-02 18:16:46 -04:00
Diederik Muylwyk 16963881b0 Reset pre-expansion schedule. 2019-08-30 19:36:34 -04:00
Diederik Muylwyk 548647defe Toggle pre-expansion config. 2019-08-30 19:31:45 -04:00
Diederik Muylwyk f29abd7167 Fixed ResourceTable lookups for pre-expansion and code validation. 2019-08-30 19:31:05 -04:00
Diederik Muylwyk 9f7cf3923b
Merge pull request #1458 from jamesagnew/1457-valueset-pre-expansion-need-to-account-for-existing-valuesets-and-user-assigned-ids 
Resolve "ValueSet pre-expansion - need to account for existing ValueSets and user-assigned IDs."
 2019-08-30 10:48:39 -04:00
Diederik Muylwyk 8ef9c61b83 Address review comments; improve logging. 2019-08-30 10:47:21 -04:00
James Agnew 8700088c67 Missed a keyword 2019-08-29 22:06:43 -04:00
James Agnew 668af76514 Make method static again 2019-08-29 22:03:58 -04:00
James Agnew 347aada62e Add a setter for unit tests 2019-08-29 21:43:29 -04:00
James Agnew dbe86c8669 One more test fix 2019-08-29 21:35:07 -04:00
James Agnew 1b1d80b850 Test fix 2019-08-29 21:02:19 -04:00
Diederik Muylwyk e03d6a5d47 Fixed handling of pre-expansion in light of pre-existing, non-pre-expanded ValueSets. 2019-08-29 18:09:30 -04:00
James Agnew c5a88444b6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-08-29 14:00:37 -04:00
James Agnew 956bb39327 Resolve an inefficient regex expression 2019-08-29 13:59:31 -04:00
Diederik Muylwyk c22bf8b09f Fixed handling of client-assigned IDs throughout terminology services. 2019-08-29 10:48:54 -04:00
Diederik Muylwyk e67a750c4f validate-code operation now works with client-assigned IDs; added a bunch of failing tests to work on tomorrow. 2019-08-28 18:49:18 -04:00
Ken Stevens d2ae3c24a1 FIXME 2019-08-28 16:26:56 -04:00
Ken Stevens 3e58962ac1 Split search cache api from search result cache api. 2019-08-28 16:24:56 -04:00
Ken Stevens eab589bcac fixed intermittently failing test 2019-08-28 13:11:44 -04:00
Ken Stevens 259426b0dd Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
 2019-08-28 10:37:17 -04:00
Diederik Muylwyk 9ef0519b4c validate-code operation has been optimized for large ValueSets; submitting pull request. 2019-08-27 21:15:12 -04:00
Diederik Muylwyk 6b0084fc3b
Merge pull request #1448 from jamesagnew/1447-loinc-filenames-should-be-configurable 
Resolve "LOINC filenames should be configurable."
 2019-08-27 13:47:40 -04:00
Diederik Muylwyk 94c7fc49fd Making LOINC filenames configurable; fix implicit ValueSet URL for loinc-all. 2019-08-27 13:46:42 -04:00
Diederik Muylwyk 1adfda44d9 Making LOINC filenames configurable; ready for review. 2019-08-27 11:19:01 -04:00
James Agnew 70d0a8aa8f
Get patch working (#1449) 2019-08-27 05:42:15 -04:00
Diederik Muylwyk f4789247b2 Making LOINC filenames configurable; fix IEEE medical device code property key. 2019-08-26 18:46:57 -04:00
Diederik Muylwyk 0765254024 Making LOINC filenames configurable; initial commit. 2019-08-26 18:32:21 -04:00
Diederik Muylwyk 0ee15874ca loinc-all ValueSet is now created automatically when loading LOINC terminology. 2019-08-26 16:42:37 -04:00
Diederik Muylwyk 073d2a45a4 Multiaxial hierarchy support is implemented; we not populated parent and child properties. 2019-08-26 14:26:38 -04:00
Ken Stevens 17f58a61c3 Revert "add accessor to search hash" 
This reverts commit 2dc70c92
 2019-08-24 14:13:06 -04:00
Ken Stevens 2dc70c92f1 add accessor to search hash 2019-08-24 14:10:17 -04:00
Diederik Muylwyk b41926307c Completed work on large ValueSet expansion support; ready for review. 2019-08-23 17:40:45 -04:00
James Agnew 10958a8e4d I think this might work now.. 2019-08-23 12:22:27 -04:00
James Agnew c564052b15 One more test fix 2019-08-23 11:46:56 -04:00
Diederik Muylwyk 890555a77d Incremental work on large ValueSet expansion support; transaction boundaries need to be broken up. 2019-08-23 11:46:32 -04:00
James Agnew c346ba92c8 Revert accidental commit 2019-08-23 11:17:02 -04:00
James Agnew abc894ce90 A few refactors based on ken's suggestions 2019-08-23 10:57:58 -04:00
James Agnew 6fa27934a8 Tests all seem to be working 2019-08-23 10:14:13 -04:00
Diederik Muylwyk 97a235ddfc Merging master into working branch. 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
 2019-08-22 14:02:56 -04:00
Diederik Muylwyk 72dd6b2922 Incremental work on large ValueSet expansion support; fixed broken deletion for TermValueSetConceptDesignation. 2019-08-22 14:00:08 -04:00
James Agnew 4afa55ea26 Initial commit - Not yet compiling 2019-08-22 08:49:34 -04:00
Ken Stevens 37c1ba44fe Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump 2019-08-21 15:04:16 -04:00
James Agnew 9428430822
Add support for Resource.meta.source (#1438) 
* Work on indexing source

* Work on tests

* Refactor query count tests

* Unit test fixes

* Add some tests

* DAO fix

* Fix compile error

* Unit test fix

* Cleanup

* Test fix

* Fix compile error

* One more test fix
 2019-08-21 11:17:43 -04:00
Diederik Muylwyk 3218bd7853 Incremental work on large ValueSet expansion support; implemented paging when reading concepts from the terminology tables. Switched from Derby to H2. 2019-08-20 18:11:53 -04:00
Ken Stevens 5703b55e88 Merge remote-tracking branch 'remotes/origin/master' into ks-awaitility-version-bump 2019-08-20 15:08:25 -04:00
Ken Stevens df7469731b turn of sql queries 2019-08-20 15:02:02 -04:00
James Agnew ce44115152
Handle cascading deletes correctly with circular references (#1435) 
* Handle cascading deletes correctly with circular references

* A bit of cleanup

* Address review comments

* FIx some javadocs

* Fix an incorrect message
 2019-08-20 10:08:34 -04:00
Ken Stevens daf45db2be fixed a test and removed awaitility excludes 
mvn install completed successfully
 2019-08-20 09:14:21 -04:00
Diederik Muylwyk 70aef7fbbb Incremental work on large ValueSet expansion support; need pageable results while querying TRM_VALUESET_CONCEPT. 2019-08-19 18:43:43 -04:00
Diederik Muylwyk 53364a3af1 Downgraded FIXMEs to TODOs regarding -code for large ValueSets. 2019-08-19 02:50:01 -04:00
Diederik Muylwyk 8590e0ca4d Merging master into working branch. 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
 2019-08-19 02:28:30 -04:00
Diederik Muylwyk dfd098c374 Incremental work on large ValueSet expansion support; added use of terminology tables when expanding. 2019-08-19 02:26:12 -04:00
jamesagnew 54657214de FIx issue uploading US Core resources 2019-08-17 18:11:52 -04:00