* fix handling of common search parameters
* Revert "fix handling of common search parameters"
This reverts commit 89c45eebdc.
* Fix implementation, add test (#3378)
* Fix implementation, add test
* Tighten test
* Rip out dead modules
* Add changelog
* Jr 20220210 handle common search params in contained searches (#3377)
* fix handling of common search parameters
* add support for reference search parameters with multiple paths
* Issue 3357
* Version bump
* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests
* added changelogs for this fix
* Fix broken changelog file
* Can't specify specific resource type permissions for bulk export (#3376)
* deny user from exporting without perms
* add unit tests
* add changelog
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
* Make migration donothing as it was added in error
* Remove ehcache
* Add version.yaml:
* Add to sources/javadocs for dist
* Fix typo
* fix up pom
* wip test removing checkstyle plugin from deployable pom
* remove test pom changes, instead just dont deploy to sonatype
* typo
* Remove ehcache
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
* Initial design of adding exception codes to exceptions
* Initial design of adding exception codes to exceptions
* change int module name to string
* add comment
* shorten message
* shorten message
* added checkstyle
* developing checker
* completed checkstyle plugin and unit test for it
* fix NPE
* fix checker so it ignores throws on exceptions that aren't new
* change parameter order in InvalidResponseException
* accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter
* exclude generated files
* BIG COMMIT added error codes to all exception throws
* example test fix
* Modified tests such that the assert statements would better match the message responses.
* Modified additional tests such that the assert statements would better match the message responses.
* fix test
* merge master
* merge master
* Fourth commit of modified tests such that the assert statements would better match the message response
* Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages.
* Modified assert messages to better match new error codes
* Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install
* Modified assert messages to better match new error codes
* Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed.
* Reverted changes on azure-pipelines.yml
* updated hapi-fhir version for checkstyle module
* changes to azure-pipelines.yml
* changes to azure-pipelines.yml
* change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES
* changes to azure-piplines (these changes are to be reverted after testing)
* reverted changes to azure-piplines
* reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir)
* Attempted fix on checkstyle build error
* modified azure-piplines.yml to change maven repository for checkstyle build
* Attempted fix on checkstyle build error
* checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work)
* attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work)
* reverted changes for hapi-deployable-pom
* add javadoc
* update last code
* Attempted fix on checkstyle build error
* Finished adding in missing error codes to pass Checkstyle checks
* Test pipelining
* Fixing errors and bumping version (as suggested by Gary)
* Merge
* Fixing Checkstyle error
* Attempted fix for date error
* Add error code onto assert statement
* Add in a couple more error codes
* Fixing assert statements
* Bump to static version for dependency
* Adding error code to message
* Adding error codes to exceptions
* Adding error codes to exceptions
* Change to work with cdr branch
* Update to faulty error message
* Merge changes
* allow checkstyle pom to deploy
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* [dev] Integration of a Jackson serializer and deserializer - first stage
* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers
* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes
* [clean] Small cleanup
* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created
* [improve] Use the ObjectMapper's `readTree` instead of `readValue`
* [dev] Latest fixes and improvements
* [dev] Use the Jackson serializer
* [clean] Removed the ObjectMapper configuration, for now
* [fix] Use the GsonStructure also for the parsing of a FHIR resource
* [clean] Removed the LinkedList usage
* Work on preparing for merge of #1673
* Resolve build errors
* Work on parser integration
* Tests passing
* Resolve fixme
* CLeanup
* Fix dependency
Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
* Start work on refactoring how PIDs work
* Some test fixes
* Test fixes
* Test fixes
* Restore accidentally deleted line
* One more tweak
* Rework resource link extraction
* Test fix
* Split out transaction processor
* Updates
* Test fix
* Test fixes
* Test fixes
* Clean up LGTM warning
* Fix compile failure
* One more test fix
* Fix LGTM issue
* Add spot for metadata
* Add test logging
* Remove testing code
* More test logging
* Add some test logging
* Attempty to fix intermittent test failure
* Improve exception tracking
* Work on simplifying search param registry
* Fix compile
* Fix compile errors
* Fix two test bugs
* 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
* Reorganizing packages and dependencies to support standalone subscription running within a CDR container where all hapi modules are on the classpath.
Moved Subscription registry out of interceptor and introduced SubscriptionLoader
* Created ActiveSubscription and moved cache bits into it
* Moved ExecutorQueue stuff out into its own class
* Add test and supporting code to validate SubscriptionConstants.EXT_SUBSCRIPTION_RESTHOOK_DELIVER_LATEST_VERSION behaviour
* Added SubscriptionCheckingSubscriber
* Moved a few beans to @ComponentScan
* Replaced use of beanFactory with concrete factory classes
* Switched test to use subscribablechannel
* Added SubscriptionLoaderFhirClientTest
* Confirm that our SubscriptionProviderFhirClient works with a live fhir client
* Register interceptors with DaoConfig instead of RestServer.
Also, Rename @VisibleForTesting methods with ForUnitTest
* Fix triggering service so it uses new subscriptionmatcherinterceptor
* Renamed "Database" classes to "Dao"
* processing -> matching naming change
Squashed commit of the following:
commit 12f89a423a
Author: James <jamesagnew@gmail.com>
Date: Sun Aug 13 14:38:51 2017 -0400
Minimize validation resources
commit f6868cce5c
Merge: 3b80779fd31e158311d8
Author: James <jamesagnew@gmail.com>
Date: Sun Aug 13 14:05:34 2017 -0400
Forward port fix for #710
Merge branch 'master' into hapi3_refactor
commit 3b80779fd3
Merge: 1f534985e8356d9acaf7
Author: James <jamesagnew@gmail.com>
Date: Sun Aug 13 12:31:09 2017 -0400
Forward port #705, #708, and #710
Merge branch 'master' into hapi3_refactor
commit 1f534985e8
Merge: 7c39a47852dedd3d635b
Author: James <jamesagnew@gmail.com>
Date: Sun Aug 13 10:52:59 2017 -0400
Forward port #695
Merge branch 'master' into hapi3_refactor
commit 7c39a47852
Merge: e0ffb84d216efafe62f1
Author: James <jamesagnew@gmail.com>
Date: Sun Aug 13 09:53:17 2017 -0400
Forward port #688
Merge branch 'master' into hapi3_refactor
commit e0ffb84d21
Merge: 52388c11c1d19b00ff09
Author: James <jamesagnew@gmail.com>
Date: Sat Aug 12 14:59:46 2017 -0400
Merge branch 'master' into hapi3_refactor
commit 52388c11c1
Author: James <jamesagnew@gmail.com>
Date: Sat Aug 12 06:21:46 2017 -0400
Cleanup
commit 209752cd63
Author: James <jamesagnew@gmail.com>
Date: Thu Aug 10 11:18:19 2017 -0400
Fix tests
commit 4543408dc8
Author: James <jamesagnew@gmail.com>
Date: Sat Aug 5 06:55:50 2017 -0400
Fix a potential deadlock
commit ee360f5376
Author: James <jamesagnew@gmail.com>
Date: Sat Aug 5 06:22:06 2017 -0400
Add R4 code to CLI
commit 1a95ba3b65
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Aug 3 06:14:01 2017 -0400
More cleanup
commit f0d8802681
Author: James <jamesagnew@gmail.com>
Date: Wed Aug 2 11:27:43 2017 -0400
Tests are working!
commit a4cbda357e
Author: James Agnew <jamesagnew@gmail.com>
Date: Wed Aug 2 10:42:04 2017 -0400
Connection handling cleanup for new tests
commit 0e2cecfbd0
Author: James Agnew <jamesagnew@gmail.com>
Date: Wed Aug 2 10:16:28 2017 -0400
Clean up R4 JPA tests
commit 40317a650d
Author: James <jamesagnew@gmail.com>
Date: Wed Aug 2 09:12:38 2017 -0400
Work on R4 for JPA server
commit e7f8f8c30d
Author: James <jamesagnew@gmail.com>
Date: Tue Aug 1 20:43:47 2017 -0400
More work on porting tests
commit 43c9003258
Author: James <jamesagnew@gmail.com>
Date: Tue Aug 1 07:09:29 2017 -0400
Work on porting DSTU1 tests
commit 602857f1e2
Author: James Agnew <jamesagnew@gmail.com>
Date: Mon Jul 31 22:34:08 2017 -0400
More work on bring unit tests up to date
commit e326a7b0cd
Author: James Agnew <jamesagnew@gmail.com>
Date: Mon Jul 31 17:36:38 2017 -0400
Credit for #686 and forward port the fix to R4 validator
commit 96543c3992
Merge: 3fb75aa61a9901b802c4
Author: James Agnew <jamesagnew@gmail.com>
Date: Mon Jul 31 17:12:33 2017 -0400
Merge branch 'master' into hapi3_refactor
commit 3fb75aa61a
Author: James <jamesagnew@gmail.com>
Date: Mon Jul 31 15:21:30 2017 -0400
More work on cleanup
commit b02fbb6804
Author: James Agnew <jamesagnew@gmail.com>
Date: Sun Jul 30 22:11:07 2017 -0400
Work on porting STU1 tests
commit 1ae37b0db3
Author: James Agnew <jamesagnew@gmail.com>
Date: Sun Jul 30 20:56:10 2017 -0400
Try to get coverage report working
commit 72b88849b3
Author: James Agnew <jamesagnew@gmail.com>
Date: Sun Jul 30 20:27:02 2017 -0400
Fix android tests
commit e5f6c35aea
Author: James <jamesagnew@gmail.com>
Date: Sun Jul 30 19:31:18 2017 -0400
More work on getting legacy code cleaned up
commit 0b513b0845
Author: James <jamesagnew@gmail.com>
Date: Sun Jul 30 18:41:13 2017 -0400
Continue work on removing deprecated API
commit defea69aa3
Author: James Agnew <jamesagnew@gmail.com>
Date: Sun Jul 30 17:10:01 2017 -0400
More cleanup of legacy code
commit 9ae7295705
Author: James <jamesagnew@gmail.com>
Date: Sun Jul 30 07:11:45 2017 -0400
More cleanup of legacy code
commit ebd3eeb5ee
Author: James Agnew <jamesagnew@gmail.com>
Date: Sun Jul 30 06:43:25 2017 -0400
More work on removing legacy code
commit 92224c2532
Author: James <jamesagnew@gmail.com>
Date: Sat Jul 29 18:44:06 2017 -0400
Remove DSTU1 Bundle
commit c52cacf71b
Author: James <jamesagnew@gmail.com>
Date: Sat Jul 29 14:27:42 2017 -0400
Now compiling
commit b405e51773
Merge: c3ddf04e25cb2cea54d7
Author: James Agnew <jamesagnew@gmail.com>
Date: Fri Jul 28 06:21:02 2017 -0400
Merge branch 'master' into hapi3_refactor
commit c3ddf04e25
Author: James <jamesagnew@gmail.com>
Date: Thu Jul 27 11:06:06 2017 -0400
Sync R4 releases in
commit b13333c3c0
Author: James <jamesagnew@gmail.com>
Date: Fri Jul 14 05:52:33 2017 -0400
JPA server is now able to handle placeholder IDs (e.g. urn:uuid:00....000) being used in Bundle.entry.request.url as a part of the conditional URL within transactions.
commit 2e60ff7521
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 13 20:02:46 2017 -0400
Fix imports
commit a92ace2e0d
Merge: 3196db96d11a6b3ea867
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 13 12:02:27 2017 -0400
Merge branch 'master' into hapi3_refactor
commit 3196db96d1
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 13 11:48:10 2017 -0400
Don't add false paging link to request
commit bd4e1d3388
Author: James <jamesagnew@gmail.com>
Date: Sun Jul 9 21:32:16 2017 -0400
Finally building correctly!
commit 6464ce9304
Author: James <jamesagnew@gmail.com>
Date: Sun Jul 9 16:38:28 2017 -0400
Work on refactor
commit 0059f2e48e
Author: James <jamesagnew@gmail.com>
Date: Sat Jul 8 07:16:20 2017 -0400
Keep working on refactor
commit 6c2e87e8cc
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 6 22:35:13 2017 -0400
Lots of work on refactor
commit 11cab97504
Merge: 34ec6b88076c47bd4c51
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 6 21:43:57 2017 -0400
Merge branch 'master' into hapi3_refactor
commit 34ec6b8807
Merge: f8e647511bc520e60ac1
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 6 21:43:49 2017 -0400
Merge branch 'hapi3_refactor' of github.com:jamesagnew/hapi-fhir into hapi3_refactor
commit f8e647511b
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Jul 6 18:46:55 2017 -0400
Work on hapi3 changes
commit c520e60ac1
Author: James <jamesagnew@gmail.com>
Date: Wed Jul 5 08:08:40 2017 -0400
Keep working on refactor
commit f1d2ee9092
Author: James Agnew <jamesagnew@gmail.com>
Date: Mon Jul 3 22:10:59 2017 -0400
Continue refactor for HAPI 3
commit 9281ccafc3
Merge: ea1264cd8e294d080bd3
Author: James Agnew <jamesagnew@gmail.com>
Date: Mon Jul 3 20:34:16 2017 -0400
Merge branch 'master' into hapi3_refactor
commit ea1264cd8e
Author: James <jamesagnew@gmail.com>
Date: Wed Jun 28 10:26:01 2017 -0400
Continue work on refactor
commit fbe2f98a02
Merge: b2bef471000a4dcc32ec
Author: James <jamesagnew@gmail.com>
Date: Wed Jun 28 06:21:22 2017 -0400
Merge branch 'master' into hapi3_refactor
commit b2bef47100
Author: James <jamesagnew@gmail.com>
Date: Tue Jun 27 21:13:23 2017 -0400
Work on refactor
commit 8f76e4e463
Author: James Agnew <jamesagnew@gmail.com>
Date: Sun Jun 25 21:55:35 2017 -0400
Lots of work on refactoring
Tadgh
Ken Stevens
Johnson Lu
James Agnew
Tuomo Ala-Vannesluoma
Alejandro Medina
Tadgh
jiaola
Jafer Khan
Ken Stevens
David Conlan