* Make expunge service extensible
* Work
* Licence headers
* Version bump some dependencies
* Version bumps
* Adapt to new html unit version
* Reintroduce errorprone
* Test fix
* Header
* Work on jakarta
* Test fixes
* Restore errorprone
* More pom tweaks
* Apply spotless
* Errorprone tweak
* errorprone tweak
* Version bump
* License headers
* Version bump
* Postgres bump
* Fixed search for resources for $everything operation with partitions and client id mode = ANY
* fixed formatting
* changelog file renamed for tests
* code review fixes: moved generics mocks to class fields, changed size > 0 to empty check
* removed unused fields
* moved fields back to methods, changed generic anys
* changed imports from javax to jakarta
* code review fixes
* 1. Allow callers to choose uppercase or lowercase column names. Default uppercase.
2. Allow callers to pass custom sorting rules: Default no special sorting.
* Spotless.
* Msg.code.
* Get rid of factory method and fix constructor.
* Maintain old constructor for backward compatibility.
* Fix JDK 11 compile error, spotless, and class header.
* Introduce a mechanism to override default SQL column mappings by column type and driver type.
* Add error message code. Tweak column type algorithm.
* Replace javax.annotation with jakarta.annotation.
* Spotless.
* Fix unit test by restoring FOO_COLUMN assertion.
* Add changelog.
* Code review feedback.
* spotless
* Fix Msg.code().
* Add unit test.
* initial tests and implementation of the feature persistence layer.
* initial tests and implementation pointcut to modify JobInstance before persistence.
* spotless happy.
* Addressing comments from first code review.
* happy spotless
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Servlet migrsation changes
* Apply spotless
* Work on migration
* Start working on JPA migration
* Test fixes
* Test fixes
* Test fixes
* Work
* Work on servlet migration
* Work on migration
* Work on fixes
* Imports fix
* Work on tests
* Test fix
* All tests passing
* Work on migration
* Schema generator
* Refactor ID strategy
* Some test fixes
* Test fixes
* API additions
* Work on websockets
* Test fixe
* Version bump
* Work on migration
* All tests have passed!
* Work on test fixes
* Fixes
* Work on fixes
* CDR fix
* Work on migration
* Fixes
* Spotless
* Disable onetoone ban
* Adjust migratyions
* Transaction service fix
* Add tinyint to migrator
* Work
* Migration
* Compile fix
* Add license
* Test fix
* Test fix
* Cleanup
* Cleanup attempt
* Test fix
* Reslve fixmes
* Remove legacy lastn implementation
* Test cleanup
* Cleanup
* Remove dead import
* Bad import setups
* Review comments
* Review fixes
* Build fix
* Test fix
* Spotless
* Account for CR changes
* Compile fixes
* Rollback one change
* Test tweak
* License header
* Test fix
* Test fix part 2:
* Clean up tx isolation
* Spotless
* Spotless apply
* Drop min SQL Server level
* Attempted test fix
* Test fix
* Test fix
* Test fix
* Bump hibernate
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Test cleanup
* One more test fix
* Test fix
* Try to fix test
* Clean up expunge
* Test fix
* Remove unneeded task
* Spotless
* Bump compiler plugin
* Spotless
* Compile fix
* Add license headers
* License header
* Test fixes
* Bump animal sniffer
* Spotless
* Bump Jetty version
* Test fix and version bump
* Cleanup
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient.
* Add FhirContext to ClientResponseContext.
* Introduce a ModifiedStringApacheHttpResponse. Run spotless.
* Remove TDOOs, add and update javadoc.
* Spotless and copyright header.
* Add changelog.
* Unique error message code.
* Only trigger the interceptor if the expected return type is a Bundle.
* Fix spotless.
* Code review feedback.
* Spotless.
* Bump to 6.11.3-SNAPSHOT
* Pass properties through to Remote Terminology Service on CodeSystem operation
* Propagate list of property names throughout. Introduce a parameter object for the lookupCode method. Mark other lookupCode methods as deprecated. Add unit tests.
* Update remote terminology service tests
* Address code review comments
* Fix unit tests
* Address latest code review comments to update default methods
* Address latest code review comments to update default methods - update fallback condition
* Address latest code review comments to update default methods - update fallback condition
* initial test
* Solution with changelog.
* making spotless hapi
* addressing comments from code reviews
* making the test better.
* addressing code review comment and adding test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* - Changed member-match function param names, and return value
- modified existing tests to accomodate for the change
* removed tests unsuitable for new return value
* resolve code review comments
* version bump
* Create SubscriptionTopic before creating Subscription for MDM loader when on R5
* Remove unused properties
* MdmSubscriptionLoader changes to support R5 in MDM - added SubscriptionTopic queryCriteria (draft)
* MDM not supported for R5 - implementation
* MDM not supported for R5 - implementation
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fix
* MDM not supported for R5 - implementation fixes, changelog
* MDM not supported for R5 - fixes
* MDM not supported for R5 - fixes
* MDM not supported for R5 - fixes
* MDM not supported for R5 - fix
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
* Allow cached search with consent active when safe (#5387)
Allow the search cache when using consent if safe
* Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376)
* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources
* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources
* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.
* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389)
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation
* Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177)
* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* _source search parameter needs to support modifiers (#5095)
_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers
* Fix HFQL docs (#5151)
* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)
* Initial failing test.
* Solution with changelog.
* fixing format.
* Addressing comment from code review.
* fixing failing test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* documentation update (#5154)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Fix hsql jdbc driver deps (#5168)
Avoid non-included classes in jdbc driver dependencies.
* $delete-expunge over 10k resources will now delete all resources (#5144)
* First commit with very rough fix and unit test.
* Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest.
* Spotless
* Fix checkstyle errors.
* Fix test failures.
* Minor refactoring. New unit test. Finalize changelist.
* Spotless fix.
* Delete now useless code from unit test.
* Delete more useless code.
* Test pre-commit hook
* More spotless fixes.
* Address most code review feedback.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases.
* Deprecate the old method and have it call the new one by default.
* updating documentation (#5170)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* _source search parameter modifiers for Subscription matching (#5159)
* _source search parameter modifiers for Subscription matching - test, implementation and changelog
* first fix
* tests and preliminary fixes
* wip, commit before switching to release branch.
* adding capability to handle _lastUpdated in reverse search (_has)
* adding changelog
* applying spotless.
* addressing code review comments.
---------
Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
* Br 20231019 add cr settings for cds hooks (#5394)
* Add settings used in CR CDS Services. Remove config dependency on Spring Boot.
* Add changelog
* Use String.format rather than concat strings
* spotless apply
* Add javadoc
* Upgrade notes for the forced-id change (#5400)
Add upgrade notes for forced-id
* Clean stale search results more aggressively. (#5396)
Use bulk DMA statements when cleaning the search cache.
The cleaner job now works as long as possible until a deadline based on the scheduling frequency.
* bump version of clinical reasoning (#5406)
* Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408)
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added
* removed unused alias from SQL query of mdm-clear (#5416)
* Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)
* Enable child classes to use Boolean class return type
* spotless
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420)
* If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix
* Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423)
This reverts commit 4e295a59fb.
Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com>
* Use new FHIR_ID column for sorting (#5405)
* Sort `_id` using new FHIR_ID column.
* Fix old tests that put client-assigned ids first.
* Better indexing for sort
* Bump core to 6.1.2.2 (#5425)
* Bump core to 6.1.2.1
Patch release that uses https for primary org.hl7.fhir.core package server
* Bump core to 6.1.2.2
* Make sure to return always a value for Boolean class return type. (#5424)
Implement change in a non-disruptive way for overriders
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428)
Add a non-standard __pid SP.
* Review changes for new _pid SP. (#5430)
Change name to _pid to match our standard and add warning.
* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432)
* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition.
* Fix spotless issue
* CVEs for 6.10.0 (#5433)
* Bump jetty
* Bump okio-jvm
* 8.2.0 mysql connector
* Jena and elastic bumps
* Fix test
* 5412 post bundle on partition incorrect response.link shown (#5413)
* Initial fix and unit test provided
* spottless check
* Made relevant changes to make solution version agnostic
* relevant logic changes made
* spotless changes made
* New logic added to fix failing test cases
* formatting
* New logic to make the function more robust
* spotless checks
* Left a trailing slash in the tests
* Made relevant test changes and changed logic
* spotless changes
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml
changing changelog
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
* Formatting requirements
---------
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
* Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414)
* first fix
* - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber
- refactored code to reduce repeated code
- cleaned unnecessary comments and reformatted files
* Changed myResourceModifiedMessagePersistenceSvc to be autowired
* removed unused import
* added error handling when inflating the message to email and message subscriber
* reformatted code
* Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc
* Changes by gary
* Reformatted file
* fixed failed tests
* implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File.
* - implemented IT
- fixed logical error
- added changelog
* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor
* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor
* resolve code review comments
* reformatted files
* fixed tests
* Fix for failing IT test in jpaserver-starter (#5435)
Co-authored-by: dotasek <dotasek.dev@gmail.com>
* wip
* Bump jackson databind
* Pin Version
* Ignored duplicate classes
* Updating version to: 6.10.1 post release.
* Fix pom
* Skip remorte nexus
* make release faster
* Updating version to: 6.10.1 post release.
* remove skiptests
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Small changes after code review. Doing some variable/method renaming and correcting changelog Jira issue number.
* There is a programmatic filter enabled which skips installation for certain resources based on their status
in PackageInstallerSvcImpl. The filter can now be controlled via StorageSettings.
* Fix typo in variable name from recent pull request 5461.
* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies
* Rev to CR 3.0.0-PRE10
* version bump, pom changes for jakarta conflicts
* undo exclusions from other modules
* Rework exclusions
* Fix type in dependency
* new cr version, exclude conflicts in cr and cds-hooks
* remove exclusions
* pom update
* Redo the exclusions
* add retrieveSettings config
* new CR retrieve settings and config
* update config to new enums and parameters
* update unit tests and config for new cql and terminology properties
* bump CR to 3.0.0-PRE12
* spotless edits, update class path for CR config
* missing dependencies
* swap for jakarta
* moving conflicting dependencies
* Fix a couple code review items
---------
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Small changes after code review. Doing some variable/method renaming and correcting changelog Jira issue number.
James Agnew
TynerGjs
volodymyr-korzh
Luke deGruchy
Chris0296
kateryna-mironova
Tadgh
Etienne Poirier
Michael Buckley
Ken Stevens
TipzCM
Martha Mitran
Taha
dotasek
jmarchionatto
Justin McKelvy