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2116 Commits

Author SHA1 Message Date
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
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
James Agnew 731be21c9f Exclude commons-logging from dependencies 2019-09-30 18:58:25 -04:00
jamesagnew f373abf74c License header updates 2019-09-30 15:32:49 -04:00
James Agnew 066c9a7fb7 Improvements to AutohrizationInterceptor create handling 2019-09-30 15:07:23 -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
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
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