* base batch2 bulk export steps - unimplemented
* added the basic steps
* adding tests
* we have added the tests
* added tests for bulk export stages
* implementing jpa
* 3531 adding the jpabukexportprocessorimplementation
* 3531 first step for mongo bulk export
* jpa stuff updated
* 3531 hapi fhir stuff
* trying to fix up tests
* fixing test
* fixed most tests in batch export
* deprecate
* need some more guidance here
* fixing some tests
* some steps taken
* blah
* stashing
* test
* fixing tests round 1
* many a changes
* updating version
* small updates
* merging in mster again
* fixing up serialization
* added the permission checkers
* cleanup and sonarkube crap
* some more tests
* updating adding tests
* crimes
* blah
* updatingmsg number again
* removal of commented code
* cleanup
* merge confflicts
* fixing msg
* review fixes round 1
* more review fixes
* merging in master
* fixing poms
* review points
* test fix
* test fix
* fix test race condition
* truncate error
* add stack trace to error
* rename to IT
* fix race condition in test
* finally fixed race condition in test. this time I'm optimistic hapi ci will finally pass
* fix mock test. not a fan of mock tests like this.
* any job definition with a reducer step must be gated.
* fixed common batch bean wiring
* fix test
* lazy init ResponseTerminologyTranslationSvc
* change the way we lazy init ResponseTerminologyTranslationSvc
* change the way we lazy init ResponseTerminologyTranslationSvc (for the third time. this is super tricky!)
* disabling testGoldenResourceWithCircularReferenceCanBeCleared for now
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 3770 fixing error handling
* some updates to error handling
* changelog
* blah
* bumping version
* fix test failures
* code review points
* review points
* add retry test
* assert counts in the test
* test fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* added failing test for Map Response Terminology for bulk export
* moved logic for terminology translation out of the interceptor to svc, added translation logic to bulk export file writer, added more tests
* added changelog
* Wip refactor dependency fix
* wip terminology translation code refactor
* terminology translation code refactor
* refactor clean up
* Remove circular dependency
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3719-enable-map-response-terminology-for-bulk-export.yaml
* bump version of hapi to 6.1.0-PRE7-SNAPSHOT
* doc update
* fix issue when search param registry doesn't contain search param for the resource type
* fix beans
* hapi version bump from PRE7 to PRE10
* doc update
* add ResponseTerminologyTranslationSvc as a constructor variable to the interceptor
* fixed ResponseTerminologyInterceptorLoaderTest, added IT for cdr side
* version bump to PRE13
* removed unused import
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* begin with failing test
* begin with failing test
* remove unused Spring Batch classes.
convert service classes
* move provider
* just one test left to fix
* fix test
* msg.code
* change log
* bumping hapi to PRE12
* fix test
* review feedback
* license update
* fix intermittent and status update atomicity
* restore url-level partition selection
* fix tests
Co-authored-by: Ken Stevens <ken@smilecdr.com>
- Added functionality to optionally filter out deleted resources when resolving forced ids to persistent ids
- Bumps version
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* rename field that drives everything includes
* discovered design flaw in completion
* fix intermittent
* ensure batch2 completion handler can't be called twice
* changelog
* changelog
* javadoc
* bump hapi version
* licences
* Batch2 job definitions can now optionally provide an error handler callback that will be called when a job
instance fails, errors or is cancelled.
* Changed error handler and completion handler to take a "read-only" copy of an instance instead of just certain fields.
* comment
* javadoc
* fix test
* change step execution context from taking instance id to instance
* review feedback
* fix test
* replace 20 or so jetbrains annotations
* fixed a few incorrect @NotNull annotations
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* first test passes. onto the next one
* two down two to go
* three down one to go
* licenses
* basic admin-json plumbing confirmed with IT
* FIXME
* FIXME
* FIXME
* FIXME
* changelog
* bump hapi version to 6.1.0-PRE6-SNAPSHOT
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Initial implementation
* Implement job cancellation
* Works for date and token. Cleanup required.
* Works for string and quantity.Cleanup pending.
* Works for reference and perform cleanup.
* Cleanup configuration and add missing tests
* Eliminate sort property registry (no go for a cluster) for a static property map.
* Missed in previous commit
* Implement HSearch number parameter
* Implement HSearch number sorting
* Unify different hibernate search names (HibernateSearch, Freetext and Lucene) to HSearch
* Move analysis configures for lucene and elastic to same file to enforce the need to keep them in synch
* Use new defined constant
* Rename package too
* Rename additional elastic references
* bump version to 6.1.0-PRE5-SNAPSHOT
* Restore Hap prefix to hapi configurers
* fixing hapi version of new maven module
* fix pom
* fix pom
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* begin with failing test
* continue building out
* continue building out
* reworking chunk api
* replace ChunkId zippers with proper iterator
* progressing test
* yay test passes!
* switch to idchunk interface
* fixmes
* compiles
* fixme
* fixme
* rename classes
* rename json classes with json suffix
* work towards homogeneous chunks
* fixme
* fixme
* unit test
* fixme
* fixme
* pull out builder
* moar tests
* moar tests
* preserve order
* moar test
* moar test
* fixme
* fixme -> wip to start ci
* msg code
* msg code fix test
* fixme
* change provider implementation
* final WIPs
* IT failing
* IT passes
* java 11
* fix test
* fix test
* fix test
* changelog
* use batch size if provided
* last WIP
* fix test
* fix test
* fix test
* whitespace change to trigger new build
* fix test
* bumping hapi version
* bumping hapi version
* fix test
* review feedback
Co-authored-by: Ken Stevens <ken@Kens-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* adding a bunch of stuff
* most of the steps are working now
* writing more tests
* adding more tests
* updated the batch2 coordinators
* updating version
* some minor test tweaks
* added a new test
* adding more tests
* blah
* blah
* review fixes 1
* fixing tests and refactoring
* review points
* updated for code review
* review fixes
* updated
* step 1 on review step 5
* final touches
* blah
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* fix config settings for system-level expunge
* clean up expunge everything interface
* extract common system provider
* changelog
* version bump
* touch changelog to force a fresh pipeline
* re-enable publishing of checkstyle
* back out Gary's Sonatype change entirely
* committed changes discussed at tasking
* Changed the subscription message to store the request partition
* modified mdm subscription loader to create a cross partition subscription in the default partition if multitenancy is enabled
* Fix errors when running Multitenant IT for mdm
* Added partition id to mdm golden resource search and creating/updating golden resource
* added partition id column to the mdm link table
* Added partition id of the source resource to partition id column of the mdm link table
* broken build
* working -links, missing hapi tests
* Fixed the mdm link db table due to feedback
* added IT for create link mdm operation, also added changes to pass the IT
* Fixed test for create mdm links, added test for update mdm link on partitioned server
* changed mdmLink search from searchbyExample to criteriaBuilder, added partitionHelperSvc to determine partition
* added test for merge golden resource and search golden resource on partitioned server
* added unit test for not duplicate on partitioned and non-partitioned server
* added criteriabuilder search and tests
* code cleanup
* added partition support to -merge-golden-resources operation
* test cleanup
* fixed operations with multitenancy
* added test for mdm clear operation
* added waiting for batch job to finish in mdm clear operation test
* added query to dao to support partitioned server for mdm clear operation
* resolve mistake from merge conflict
* added mdm-submit operations, also fixed paging for -query
* added partitionIds constant
* fixed build issue where there was no Code.msg in mdm partition exceptions
* code review fixes
* fix broken test, also fix a bug where query link could not query by linkSource properly
* fix test stubbing
* bump hapi version to 6.0.0-PRE10-SNAPSHOT
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Long Ma <long@smilecdr.com>
* 2991 - WIP, starting to implement test to reproduce the issue.
* Adding capability to extract url & version from the valueSet.include.url
* parsing codeSystem canonical URL to extra version if required.
* WIP
* Cleaning up the test.
* Replacing hard code value with variable.
* Removing non required test.
* Modifications following first code review.
* Further modifications following first code review.
* Refining the test for better code coverage.
* Prefixing the change log file name with the hapi-fhir issue number.
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
* moved classes
* Bump version
* licensing
* Repackage, fix messages
* reject empty streams
* Remove dead import
* Version bump
* Fix up test to actually return a data stream
* Move null binary svc to storage
* Start working on reindex job
* Updates
* Ongoing work
* Ongoing work
* Work on reindex
* Reindex work
* Add logging
* Fix typo
* Test fix
* Test fix
* Address fixme
* Liocense header
* Resolve fixme
* Add logging
* Update logs
* Address review comments
* License header
* Test fixes
* Test fix
* Test fixes
* Test fix
* Version bump
* Version bump
* Enable search narrowing on large ValueSets
* ValueSet improvements
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Add test
* Work on narrowing interceptor
* Work on narrowing
* License headers
* Refactor code narrowing
* Add docs
* Version bump
* Test fix
* Test fixes
* Build fix
* Fixes
* Version bump
* Test fix
* License header updates
* Build fix
* Test fixes
* Test fix
* Test fix
* Docs fix
* Test fix
* Test fix
* Resolve fixme
* Bump
* Force a CI build
* Make CI happen again
* Work on new batch framework
* Work on new batch framework
* Work on new batch framework
* Work on batch
* Compile working
* Work on bulk import
* Adjust import
* Work
* Work on batch
* Bump version
* WOrk on new batch processes
* Work on bath
* Bump to PRE4
* Build fixes
* CLeanup
* Small tweak
* Add exception code
* Test fixes
* Test fixes
* Test fix
* Additional synchronization
* Add license headers
* Test fixes
* Test fixes
* Add changelogs
* Address PG
* Test fix
* Test fix
* Test fixes
* Review notes
* Work on tests
* Test fixes
* Test fix
* Work on tests
* Tets fix
* Test fixes
* Test fixes
* Add missing exception codes
* Test fix
* Test fixes
* More test fixing
* License headers
* Test fix
* Add new test logging
* Work on tests
* Test fixes
* Test fix
* Resolve fixme
* Try to avoid test failure
* Add import command
* Work on storage
* Fix error codes
* Fixes
* License header
* Build fix
* Build fixes
* Fix dep
* 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>
* 3156 fix race condition that results in multiple tags being created
* 3156 added changelog
* cleanup
* added smile jira ticket
* 3156 review fixes
* review fixes
* 3156 added an additional integratoin test
* cleanup
* review fix and master merge
* threadsafe stuff
* small change
* upping min threads for tests to pass
* changing test
* test check
* fix
* test testing
* one more update
* using threadpoolutil
* temporary measure
* git push
* all builds
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Bump a number of versions
* Fixes
* Work on version bump
* Bump
* Test fix
* More version bumps
* Build fixes
* Test fixes
* Fixes
* Fixes
* Test fix
* Bump jacoco
* Test fix
* Test fix
* Test fix
* Build fix
* Build fix
* Remove versioned H2
* Build fix
* Avoid memory issue in validation tests
* JDK bump
* Restore compile with errorprone
* Force coloured output
* Force jansi
* Try again to force jansi
* Fix for hardcoded date that just passed
* Fixes to JPA
* Improve changelog
* Work on failing test
* Test fix
* Compile fix
* One more version bump
* Test fixes
* some fixmes to start
* Added some FIXMEs
* added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage
* ResourceDeliveryMessage and ResourceModifiedMessage tests
* fixed issue with test missing partitionHelperSvc mocked bean
* Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription
* modified implementation of partitionId in CanonicalSubscription
* Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)
* Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)"
This reverts commit fe40fb9733.
* Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work
* added SubscriptionTriggering test, also added partition support to subscriptionLoader
* Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation
* added all subscription systemRequestDetails with all partition to subscription reader
* refactored a generic system request details with default all partition request
* Added test for dao subscriptions, fixes to get the test working
* added partition support for latest version delivery
* added doc changes and changelog for multitenancy subscription
* cleanup and added partitioned subscription manually trigger test
* fixed mocked subscriptionDao
* added package-info for subscription module
* some code review changes
* removed AllPartitionSystemRequestDetail, added new text for multitenant subscription
* renamed method for code review
* version bump to 5.7.0PRE7
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* try xml -> json
* Change from xml serialization to json serialization. Also fix a deadlock in how the validation cache is used.
* changelog
* back out logback
change
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* move mail config to mail service constructor
* update subscription email sender
* added license text
* [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT
* add changelog
* First cut at multithreading bundle validation
* javadoc
* change test to a red-green test
* add daoconfig
* move bundle concurrency config from validationsupport to request validator
* Moved concurrent details from ValidationOptions to FhirValidator
* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)
* validate threadpool prefixes
* FIXME cleanup
* reassign FIXMEs to JB
* only create the threadpool if it will be used
* Add the MdcTaskDectorator to all threadpools
* Add bundle path to concurrently validated bundle resource validation messages.
* Add test to check bundle entry path being added to validation messages
* Threaded validation of contained resources initial checkin
* FHIR validator refactored to maintain correct bundle path and async validation task
* Refactored to use validation complete invoke callback to support raw string resource or resource object
* switch from XML to JSON
* # Conflicts:
# hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
# hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
* Updated to use new HAPI-FHIR version
* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation
* Updated to use new HAPI-FHIR version
* Revert "Updated to use new HAPI-FHIR version"
This reverts commit 910b7f676b.
* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"
This reverts commit c7d60fc3e6.
* Revert "Updated to use new HAPI-FHIR version"
This reverts commit aa8a7af455.
# Conflicts:
# hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
* Fix Test dependencies after reverting changes.
* merge 'validate_contains_change' to 2564-contained-resource-validation-flag
* Disable threadpool prefix name validate check.
* merge master
* fix thread regexp
* pre-review cleanup
* change log
* fix test
* revert to XML as default validation serialization
* fix test
* fix test
Co-authored-by: Jaison B <jaisonb@gmail.com>
* wip
* The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version.
* pointing to stable core version
* review feedback
* Add changelog
Co-authored-by: markiantorno <miantorno@pop-os.localdomain>
* 3136 - Send validate-code requests to an Instance of IValidationSupport instead of directly to the DAO.
* 3136 - Added support for R4 validate-code calls to a Remote Terminology Server.
* Added more Unit Tests.
* Added NULL checks based on code analysis.
* Adding some cleanup code to the Unit Tests since some other unrelated Unit Tests were failing when running in an Azure Pipeline.
* Adding @Ignore to both of my Unit Test classes to try and see if this is the cause of other unrelated Unit Test failures in the Azure Pipeline.
* Commented out ALL CODE in my Unit Tests to see if this fixes the other Unit Tests.
* Added 1 Unit Tester called RemoteTerminologyServiceResourceProviderR4Test to see if it causes other Unit Test failures.
* Added a Unit Tester called ResourceProviderR4RemoteTerminologyTest with the code that creates a RemoteTerminologyServiceValidationSupport instance commented out for now, just to see if this allows all other Unit Tests to pass.
* Added a Unit test back in to verify how the RemoteTerminologyServiceValidationSupport works when inserted into the front of the IValidation chain. Lets see if this will mess up any other Unit Tests in the Azure Pipeline...
* Added an @AfterEach method to remove the RemoteTerminologyServiceValidationSupport instance from the ValidationSupportChain to see if it allows all the other Unit Tests to work as before.
* Added more Unit tests.
* Added more Unit Tests to increase code coverage.
* Added some NULL checks.
* Added a changelog for this feature add.
* Removed the decision logic in the REST APIs and also the isRemoteTerminologyServiceConfigured() method, and letting the ValidationSupportChain figure out how to perform the validate-code Operation.
* Removed a NULL check that was not needed.
* Reverting the previous change where I tried using the IValidationSupportChain for each and every incoming Operation request. Splitting the implementation between local and remote seems to be required at this time.
* 3170 language portion of language code is case insensitive
* 3170 adding changelog
* 3170 house keeping
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* issue-1134 initial work on adding retry handler
* issue-1134 subdscription creation fixes
* issue-1134 update the test
* issue-1134 retry policy off canonicalsubscription
* issue 1134 base subscription changes
* add failing test
* issue 1134 retry configs on base parameters
* issue 1134 passing forward params
* issue-1134 added more tests for making sure subscriptions create their channels correctly
* issue-1134 updates to get the retry to channels
* issue-1134 updating channel factory
* issue-1134 remove the dlq since it's not defineable
* issue-3120 changelog added
* issue-3120 cleaning up
* issue-3120 test fix
* issue-3120 review fixes
* issue-3120 fixed bad master merge
* issue-3120 updates for new release
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* issue-1134 initial work on adding retry handler
* issue-1134 subdscription creation fixes
* issue-1134 update the test
* issue-1134 retry policy off canonicalsubscription
* issue 1134 base subscription changes
* add failing test
* issue 1134 retry configs on base parameters
* issue 1134 passing forward params
* issue-1134 added more tests for making sure subscriptions create their channels correctly
* issue-1134 updates to get the retry to channels
* issue-1134 updating channel factory
* issue-1134 remove the dlq since it's not defineable
* issue-3120 changelog added
* issue-3120 cleaning up
* issue-3120 test fix
* issue-3120 review fixes
* issue-3120 fixed bad master merge
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet work when code system is present, even when theOptions.isInferSystem() is true
* Add test for specific use case added
* Consider ValueSets with multiple component includes
* Fix typo
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add tests. Add implementation in R4. Add changelog
* Wip partial fixup of other STU versions
* Updated usages of new patient type everything api
* Partial commit of incomplete documentation
* Remove docs
* Cut to token instead of string
* Bump hapi version due to breaking api changes
* Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet work when code system is present, even when theOptions.isInferSystem() is true
* Add test for specific use case added
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Migration finished
* Work on LOBS
* Add to ClobMigrated annotation
* Deal with lobs
* Work on new approach
* HAPI FHIR version bump
* Add changelog
* Add license header
* Fix intermittent
* CLeanup
* Cleanup
* Add test
* Test fixes
* Work on expansion errors
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Work on fix
* Test fixes
* Test fixes
* Test fix
* Cleanup
* Test fixes
* Remove accidental commit
* Test fixes
* Version bump
* Add changelog
* Fixes
* Test fix
* Fix conflicts
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens
* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
* first pass moving core storage classes to storage-api
* move term service apis
* nearly done
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* create new SearchConstants class to store platform independent search constants
* move a couple of subscription services
* move transaction processor adapter to storage
* version bump
* move searchparam
* fix test
* fix compile includes
* fix text
* fix docs
* failed attempt to get it to work
* Use simplified FhirContext.forCached methods
* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Avoid dead SearchParameter links in CapabilityStatement
* Resolve fixmes
* Build fix
* Test fix
* Test fix
* Test fix
* Work on metadata
* Fixes
* Test fixes
* Test fix
* Test fix
* Test fixes
* Test fix
* Work on test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fix params
* Resolve fixme
* Adjust changelogs
* Version bump to 5.6.0-PRE7
* Add license header
* Bump version to 5.6.0-PRE5-SNAPSHOT
* initial roughout of mdm clear batch job
* still roughing out classes
* finished first draft of reader
* most tests passing now
* all tests pass. now FIXMEs
* FIXMEs done. Time for regression.
* fix test
* changelog and docs
* fix test
* pre-review cleanup
* version bump
* move spring autowire deps for cdr
* move spring autowire deps for cdr
* finally got beans working phew
* rearrange method calls so persistence module can perform clear operation on its own
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
* review feedback
* Remove inheritance
* fix beans
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Impl displayLanguage for $lookup - first cut
* Added original lookupCode method
* Added original lookupCode method to IFhirResourceDaoCodeSystem
* Added more test cases and changelog
* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
* 2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.9.
* 2540 - Updated the Unit Test messages due to the upgraded dependencies.
* 2540 - Fixed some additional Unit Test message checks.
* 2540 - Updated the POM to refer to fhir_core_version 5.3.10-SNAPSHOT so a FULL Pipeline Build can run to verify that everything is fixed now.
* 2540 - Added some DEBUG Sysout logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Added some more logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Updated a Unit Test to account for a newly returned search param.
* 2540 - Updated a Unit Test to account for a newly returned search param and removed some debug output.
* Start work on OpenAPI
* Fixes
* Work on OpenAPI
* Cleanup
* Cleanup
* More swagger work
* Build fix
* More work
* More work
* Add documentation
* Docs fixes
* Add changelog
* License updates
* Add API
* Cleanup
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Work on scripts
* Add docs
* Compile fix
* Work on fixes
* Fix tests
* Test fix
* Test fix
* Build fix
* Tests
* Build fix
* Work on pipeline
* Version bump
* Test fix
* Version bump
* Test fix attempts
* Test fix
* Test fix
* Remove accidentally committed files
* Fixes
* Tets fixes
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Test fixes
* License header updates
* test fix
* Test fixes
* Test fix
* Test fixes
* Test fix
* Checkstyle bump
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Start work on bul;k import
* Work on bulk import
* Have batch working
* Working
* Working
* More work
* More work on bulk export
* Address fixmes
* License header updates
* Test fixes
* License header updates
* Test fix
* Test fix
* Version bumps
* Work on config
* Test cleanup
* One more version bump
* Version bump
* CLeanup
* A few additions
* Test fixes
* Test fix
* Test fix
* Migration fix
* Test fix
* Test fix
* Search param service cleanup
* Work on collapsing search param
* Search param cleanup
* Work on build
* Test fix
* Test fixes
* Ongoing work
* Test fix
* Compile fix
* Test fixes
* Test fix
* Test fix
* License header updates
* Remove fixme
* Cleanup
* Cleanup
* Add support for revincludes to CapabilotyStatement generator
* Add changelog
* Fixes
* Test fix
* Test fixes
* Test fix
* Test fix
* More fixes to CS cache
* Test fix
* Test fix
* Test fix
* Start work
* Work on testing
* Version bump
* Test fix
* Compile fix
* Test Fixes
* Test fix
* Test fix
* Compile fix
* Tst fix
* Test fix
* Test fix
* Test fix
* Bump jaxb-runtime from 2.3.1 to 3.0.0
Bumps jaxb-runtime from 2.3.1 to 3.0.0.
Signed-off-by: dependabot[bot] <support@github.com>
* Bump jaxb-runtime from 2.3.1 to 3.0.0
Bumps jaxb-runtime from 2.3.1 to 3.0.0.
Signed-off-by: dependabot[bot] <support@github.com>
* Add jakarta bindings
* Dependency cleanup
* More depndency cleanup
* Work on deps
* Replace transaction annotation
* Cleanup
* Another fix
* Build fix
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* Start work on validation rules interceptor
* Work on interceptor
* Add tests
* Work on validation interceptor
* Work on interceptor
* Test fix
* Documentation tweaks
* 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
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