* Allow code validation against enumerated VS
* Work on validation
* Work on this
* Work on tests
* Work on validation
* Work on tests
* Work on validation
* Test fixes
* Add changelog
* For a change
* Test fixes
* Add tests for validation errors
* Work on validation errors
* Bump core version
* Fix validation errors
* Test fixes
* Add changelog
* Test fix
* Test fix
* Test fix
* Work on junit
* Work on junit 5
* Work on junit 5
* Bump errorprone vcersion
* Work on tests
* Junit 5 tweaks
* Fixes
* Work on tests
* Work on junit5
* Work on tests
* Test fixes
* Work on junit5
* Test work
* Get junit5 working
* Test fix
* Work on tests
* WOrk on tests
* Work on tests
* fixes
* Compile fix
* One more tweak
* Compile fix
* Add changelog
* Fix compile error
* Compile fix
* [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>
* Validation enhancements
* Work on validation api reworking
* Keep working on validation API
* Keep working on new term API
* Work on validation api
* Ongoing work on validation
* Work on integrating validation
* Work on validation API
* Add to validation API
* Work on validation
* Work on API
* Work on validation
* Work on validation API
* Work on validation API
* Work on validation api
* Work on validation API
* Work on validation api
* Validation API changes
* Work on API
* More work on validationo API
* Work on validation API
* FIxes
* WOrk on validation api
* Work on validation API
* Tests passing!
* More cleanup
* More validation API changes
* Fix intermittent test failure
* Package reorg
* Validation API work
* Work on doocumentation
* Work on API
* More work on new validation API
* Fix errorprone-reported error
* Test fixes
* Documentation updates
* Documentation tweaks
* Work on API
* Bean name adjustments
* Build fixes
* Some test fixes
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Start working on converter
* Account for compile errors
* Test fix
* Work no validator
* Work on getting core working
* Add some test coverage
* Many test fixes
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
* Work on upgrading core
* Work on R5 updates
* Work on core updates
* Test fix
* Update model version properties file for R5
* Bump core version
* Test fixes
* Add 4.2.0-SNAPSHOT version to versions page in docs
* Some CI surefire improvements
* Build tweak
* More tweak
* Update azure-pipelines.yml for Azure Pipelines
* Update azure-pipelines.yml for Azure Pipelines
* One more CI attempt
* Update azure-pipelines.yml for Azure Pipelines
* Tweak command line
* Another build test fixc
* More build cleanup
* Don't succeed validation on unknown codesystem
* Test fixes
* Work on error messages
* Work on code validation API
* work on tests
* Work on validation
* Test fix
* Update DSTU3 validation reources
* Upgrade structures
* Test fixes
* 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
* 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
* Resolve XXE issue in validator
* Ensure that we're blocking XXE events into validator XML parser
* A bit of cleanup
* Add an LGTM config
* Add one more fix
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.
* 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
* 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
* 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
* Start work on delta operations
* Add changelog
* Some build fixes
* Move upload terminology command to CodeSystem resource
* Updates
* Some test fixes
* Add changelog
* Some test fixes
* More test fixes
* Test fix
* Add additional tests
* Transaction boundary fixes
* Ongoing work on core structures suport
* Ongoing work on this merge
* Ongoing work to clean up structures
* Credit for #1179
* Address compile issues
* Latest changes
* Work on parallel execution
* Work on getting tests passing
* Add H2 to migrator
* Test fix
* Initial consent svc
* Ongoing consent svc work
* Add docs
* Ongoing consent service work
* Work on consent service
* More work on consent svc
* License header updates
* Ongoing consent svc work
* Some test fixes
* Some test fixes
* More work on consent svc
* Tests working
* Test fix
* Propagate RequestDetails to everything in JPA server
* More interceptor tweaks
* Fix compile error
* One more tweak to captured SQL
* Ongoing interceptor tweaks
* Ongoing interceptor tweaks
* More interceptor tweaks
* Interceptor tweaks
* Tweaks to tests
* Fix tests
* Test fix
* Raise warnings when encoding extensions with missing values
* Consent service work
* More interceptor tweaks
* Consent interceptor tweaks
* Add logging to test
* Starting work on this
* Working on narrative templates
* Work on new narrative system
* Account for some failing tests due to refactoring of narrative mode
* Another test fix
* More test fixes
* One more test fix
* Work on searches
* Address review comments
* 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
* Fix the url of the StructureDefinition extensions
http://hl7.org/fhir/tools/StructureDefinition/ -> http://hl7.org/fhir/StructureDefinition/
That makes the entry for the structuredefinition-expression superfluous.
The url behind IG_DEPENDSON_PACKAGE_EXTENSION does not point is not (yet?) valid too.
* Add ability to configure custom extension domains.
* Testing the extension domains configuration
* Fix obvious bug when determining resource name
The for loop was completely superfluous beforehand.
Either fix it as e.g. in this patch or remove it.
* small improvements and TODO's for possible NPE's
- javadoc see
- use diamond operator for generics
- remove throws clause when exception is not thrown
- add TODO's for some cases a NPE might occur.
My knowledge of the context is not sufficient to suggest the proper
way to solve this.
* Validator fix
* Enhance AuthorizationInterceptor so that it tries to deny access earlier
for compartment searches that are outside the allowable compartment.
* FIx DSTU2 test that wasn't updated
* More test fixes
* Replace phloc with ph
* Enable schematron tests
* Make HAPI-FHIR ph-schematron on OSGI
* Work on getting tests passing
* Another test fix
* Fix up transaction handling for DSTU2
* Add changelog
* Avoid double transaction
* Dont use readonly
* One more test fix
* Update to snapshow build
* Resolve a circular dependency
* Try to fix tests
* Solve recurring NPE in DSTU2 tests
* Fix one more test
* Test fix
* More test threading fixes
* One more attempt to get tests passing
* Refactoring for tests
* Refactoring for tests
'fetcher == null' is ok for a local reference.
Unfortunately, there are now two messages with the same meaning:
- one from the ProfileValidation
- one from the code in this location
Currently an invalid local reference causes an InternalErrorException
caused by: FHIRException: Resource resolution services not provided.
The validation should instead return normally and contain an error
message.
Currently an invalid local reference causes an InternalErrorException
caused by: FHIRException: Resource resolution services not provided.
The validation should instead return normally and contain an error
message.
Without this fix, the 'hasAnswer' element of a questionnaire item is ignored.
This in turn allowes it that one can have both an 'answer' and a 'hasAnswer' item.
A fix is applied for both DSTU3 and R4 and tests are provided.
The tests for R4 are currently ignored, since they require a valid schematron,
e.g. by merging #869
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
jamesagnew
ianmarshall
Diederik Muylwyk
Tadgh
John Poth
Clayton Bodendein
Ken Stevens
Stig Rohde Døssing
Matti Uusitalo
patrick-werner
Eeva Turkka
Ken Stevens
Matti Uusitalo
Okko Kauhanen
hdconradi
Anthony Sute
Heinz-Dieter Conradi
Heinz-Dieter Conradi
David Gileadi