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2465 Commits

Author SHA1 Message Date
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
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
jamesagnew 89aa37ea6a Add a test 2019-08-17 15:16:11 -04:00
jamesagnew 81adc5c99e Merge master 2019-08-17 14:31:30 -04:00
Ken Stevens 970c421311 allow urls in batch transactions to start with / 2019-08-17 14:31:30 -04:00
jamesagnew f252cda126 Test fixes 2019-08-17 14:15:28 -04:00
James Agnew 74c83f6148 Test fixes 2019-08-17 12:01:04 -04:00
James Agnew 9e8af58e81 Fix reference params via filter 2019-08-16 14:56:36 -04:00
James Agnew 4490c9ca09 Correct the eq operator on the _filter parameter 2019-08-14 14:39:40 -04:00
Sean McIlvenna b37c4b5ae7 Fixing broken unit tests 2019-08-14 14:35:18 -04:00
Sean McIlvenna d92be90789 Changes to subscriptions to include the resource that triggered the subscription in the payload, serialized as JSON or XML depending on the Subscription.channel.payload property's value 2019-08-14 14:35:18 -04:00
jamesagnew e1b43d811f Version bump to 4.1.0-SNAPSHOT 2019-08-14 14:06:06 -04:00
jamesagnew 3f22456b0f Bump version to 4.0.0 2019-08-14 11:06:26 -04:00
James Agnew b4fece0ae9 Add interceptor hook for graphql calls 2019-08-13 14:46:50 -04:00
jamesagnew e2f0f4ed8b License header updates 2019-08-13 05:28:35 -04:00
James Agnew 301a8f8432
Merge #1146 - Filter implementation (#1220) 
* Initial commit of _filter keyword implementation.

* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.

* - Changes to support "ne" matching on resource ID for _filter

* Implemented language

* Commit/push before creation of pull request

* Ongoing merge work

* Ongoing merge work

* Merge master in

* Test fix
 2019-08-12 11:59:33 -04:00
James Agnew 0c9e5ec1ea
Support GraphQL for R3/4/5 (#1424) 
* Work on grpahql enhanbcements

* Add some more chars to the sanitizer function

* Add changelog
 2019-08-12 08:24:32 -04:00
jamesagnew 2999a292e6 Get subscriptions working for R5 2019-08-11 18:32:47 -04:00
jamesagnew d316ec1146 Fix NPE 2019-08-11 18:25:02 -04:00
James Agnew 2518d4e0be Add some tests 2019-08-08 15:23:55 -04:00
jamesagnew 4e1bbe681a Bump supported PGSQL driver 2019-08-08 15:12:29 -04:00
James Agnew dd0cb10dbb
validate operation ignores parameter profile (#1417) 
* This should be working now - need to check tests

* Add a changelog and some docs

* One more test fix

* Tests should be passing

* Fix compile

* Test fixes

* Ignore outdated DSTU2 validation test
 2019-08-07 15:31:59 -04:00
James Agnew b0eb19cf2f A few fixes resulting from the R5 merge 2019-08-06 17:55:51 -04:00
James Agnew 60eab3ad70
Add support for R5 resources (#1416) 
* Work so far on R5 support

* Add support for R5

* Docs changes
 2019-08-06 17:30:31 -04:00
Diederik Muylwyk 8475aa4cc8 Add TRM_CODESYSTEM_VER.CS_DISPLAY to migration tool. 2019-08-01 14:44:03 -04:00
Diederik Muylwyk d67de13708 Syncing master into working branch. 2019-08-01 13:51:26 -04:00
Diederik Muylwyk 78842164fd Addressing review comments. 2019-08-01 13:37:46 -04:00
jamesagnew 46c8c61932 Restore build - May need to roll back the RDF changes 2019-08-01 10:14:56 -04:00
Diederik Muylwyk ffda92514a Incremental work on large ValueSet expansion support; still need to actually use the terminology tables when expanding. 2019-07-31 16:33:50 -04:00
Diederik Muylwyk 0e2dcce841 Incremental work on large ValueSet expansion support; still need to fix asynchronous tests and actually use the terminology tables when expanding. 2019-07-31 15:52:25 -04:00
James Agnew 3196bc370f Add a default implementation to new terminology service loader method 2019-07-31 10:07:51 -04:00
James Agnew b956b7552e Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-30 17:52:47 -04:00
James Agnew 04ce9cfc1a Add support for uploading custom terminology using the 
$upload-external-code-system operation
 2019-07-30 17:30:18 -04:00
Diederik Muylwyk d1cba9f928 Syncing master into working branch. 2019-07-29 19:39:29 -04:00
jamesagnew cf5201c67b Add a constructor 2019-07-29 19:31:47 -04:00
Diederik Muylwyk a8489f4331 Added TRM_VALUESET.EXPANSION_STATUS column, index, fields to entity, and migration tasks. 2019-07-29 19:30:46 -04:00
jamesagnew a3cbdf0956 Make terminologyuploaderprovider not abstract 2019-07-29 19:02:51 -04:00
James Agnew b030d1af31 Test fixes 2019-07-29 18:17:40 -04:00