* Reverse changes from 5493. Add a stub changelist.
* Add various changes including stub changelist, beginnings of integration test, pass request details to interceptor, obtain partition ID, and stub code for each partition-aware query.
* Spotless. Implement methods and SQLs for both golden and source IDs. Not yet tested. Add default interface methods.
* Fix HQLs that were referring to incorrect columns. Rename parameter. Formatting.
* Fix logic to use single queries by source and golden resource. Filter by partition IDs in Java instead of in SQL. Write a new unit test for MdmLinkExpandSvc.
* Spotless.
* Ensure $everything with mdm expansion works on POST as well as GET. Some cleanup.
* More cleanup.
* Null safety for mdmExpand.
* Spotless.
* Small changes.
* Enhance changelog.
* Delete commented out code.
* First round of code review changes.
* More code review changes.
* 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>
* Rename file to force IT mode
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.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>
* One more fix for #4467
* Enabling massIngestionMode causes incomplete resource deletion (#4476)
* Adding initial test.
* Adding fix and subsequent test.
* Adding changelog.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)
* Adding initial test.
* Adding initial solution implementation.
* Adding change log and code clean up.
* addressing comments from 1st code review.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Change visibility of migration method (#4471)
* change migration visibility
* add empty migration method for 640
---------
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)
* First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests.
* Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog.
* Remove erroneous TODOs and tweak the validation logic.
* Enhance unit tests and fix changelog.
* Reindex batch job fails when processing deleted resources. (#4482)
* adding changelog.
* Providing solution and adding changelog.
* Adding new test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* cleaning up checkstyle files (#4470)
* cleaning up checkstyle files
* One more fix for #4467 (#4469)
* added exlusions for files at base project level so checkstyle doesn't error out
* duplicate error code from merge
* changing lifecycle goal for all module checkstyle check
* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code
* wip
* trying to figure out why pipeline cannot copy files
* removing modules that don't actually need to be built.
* I messed up the version
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Bump core to 5.6.881 (#4496)
* Bump core to 5.6.881-SNAPSHOT
* Work on fixing tests
* Work on fixing tests 2
* Bump to core release
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
* Issue 4486 mdm inconsistent possible match score values (#4487)
* Extract method for readability
* Save always normalized score values in POSSIBLE_MATCH links.
* Avoid setting properties to null values. Adjust test.
* Simplify fix
* Fix test. Add RangeTestHelper.
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Revert "cleaning up checkstyle files (#4470)"
This reverts commit efae3b5d5f.
* core version fix
* Loosen rules for id helper
* License
* fix batch2 reduction step (#4499)
* fix bug where FINALIZE jobs are not cancellable
* moved reduction step to message hander
* moving reduction step to queue
* addingchangelog
* cleaning up
* review fixes
* review fix'
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* Scheduled batch 2 bulk export job and binary delete (#4492)
* First commit: Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.
* Refine solution and add a concrete unit test but still work to do.
* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.
* Unit tests complete. New Msg code for new IJobPersistence.fetchInstances() method. Cleanup TODOs and add others.
* Finish final touches on implementation.
* Add changelog.
* Various cleanup.
* Code review feedback.
* Small tweak to changelog.
* Last code review tweak.
* Address more code review comments.
* Reverse changes to consider work chunks. Add a constant for write-to-binary.
* Change bulk import test for valueUri type (#4503)
* change tests
* suggested test change
* CVE resolutions (#4513)
* Bump Postgres for CVE
* Bump jetty
* Verison bump
* Remove comments
* Revrt bump
* Add check in scanner (#4518)
* 4516 create hapi fhir cli command to clear stale lock entries (#4517)
* Initial implementation
* better tests
* Add changelog and docs
* Forgotten files
* Code review comments
* Fix checkstyle
* Unable to Expunge CodeSystem (#4507)
* changes for GL-3943
* changes for GL-3943
---------
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
* New line::
* Update to documentation regarding narrative generation; (#4521)
Providing changelog;
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* changed what score is set for mdmlinks that created new golden resource (#4514)
* changed what score is set for mdmlinks that created new golden resource
* fix test
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* REVERT: change to operationoutcome.html
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* added change log
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fix build (#4530)
* Making narrative_generation.md reference an html snippet (#4531)
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)
* fix + test
* minor fix
* Addressing suggestion
* Minor changes
* 4441 rel 6 4 bad references creation bug (#4519)
* adding a test
* fail in the case of ref enforce on type and on write and autocreate are all true
* update to code
* removing a line
* cleanup
* removing check on urn
* changing just to trigger a build
* adding a comment to the pom
* updating test for better information
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fixed channel import null pointer exception from null header (#4534)
* retryCount 0 on null header + test + changelog
* suggested changes
* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)
This reverts commit 53252b8d15.
* Better error handling for when channel type is not supported (#4538)
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Avoid logging message payloads that contain sensitive data (#4537)
Don't log payloads - they may contain sensitive data.
* Bulk Export Bug With Many Resources and Low Max File Size (#4506)
* failing test
* fix + changelog
* tweak
* add method to IJobPersistence to use a Stream
* tweak
* tweak
* decrease test time
* clean up
* code review comments
* version bump
* Increase timeout limit to match BulkExportUseCaseTest
* shorten test
* maintenance pass
* add logging
* Revert "add logging"
This reverts commit b0453fd953.
* Revert "maintenance pass"
This reverts commit bbc7418d51.
* test
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* shorten tests
* logging
* move test location
* fixes a regression caused my change in hapi-fhir
* timeout
* Revert "fixes a regression caused my change in hapi-fhir"
This reverts commit 4b58013149.
* testing
* Revert "testing"
This reverts commit aafc95c2f3.
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* bump ver
* License updates'
* Remove checkstyle
* Verison bump
* Move migrations
* semicolon
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Added Solution + test
* Removed old methods
* fixed issues
* Added refactoring
* Deprecated methods on the interfaces
* Remove todo
* Documentation
* Changelog
* Changelog
* Changelog
* Changes made based on comments
* Changes made based on comments
* Clean up
* hapi bumping to version 6.3.6-SNAPSHOT
* hapi bumping to version 6.3.6-SNAPSHOT
* adding version.yaml, updating version in pom.xml
* It is possible to write to a resource in a partition the user is not authorized to. (#3397)
* fixed
* remove sout
* add msg.code
* fix failed tests
* fix equal sign
* update msg code
* extract method
* Fix up code numbers
* Clean changelog
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Revert final artifact version
* add graphql test (#3585)
* added graphql birthdate test
* fix variable name
* typo
* 3506 mdm log enhancement (#3543)
* Providing Fixme's to be reworked at a later time.
* Adding // FIXME Anna to assist our Austrian friend.
* Adding logging test as a first step in addressing issue #2822.
* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
* Update MdmMatchLinkSvc.java
#3506 move "narrowed down" log to different place
* #3506 added scores and tests
#3506 added scores and tests
* #3506 formatting
#3506 formatting
* #3506 create changelog file
#3506 create changelog file
* #3506 fix typo
#3506 fix typo
* #3506 fix part 3, minor formatting
#3506 fix part 3, minor formatting
* #3506 fix tests
#3506 fix tests
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
* mdm matching (#3579)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* begin with failing test
* fixed
* changelog
* add jira tag
* Update to 6 1 (#3582)
* added changelog folder, upped version
* version enum
* add a few more unit tests to assert proper NO_MATCH exclusion
* revert merge master doh! bad reflexes
* revert merge origin master
* unrevert revert. ugh what a pain
* merge recovery. fix poms.
* merge recovery. more reverting
* merge recovery. more reverting
* merge recovery. more reverting
* Revert "merge recovery. fix poms."
This reverts commit ae6e0ddb06.
* more revert revert reversions
* more revert revert reversions
* pre-review cleanup
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)
* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.
* License
* Ks 20220508 log colour (#3592)
* don't use colours when output is redirected to a file
* change log
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* 3584 case sensitive string elasticsearch (#3596)
* Fix for case-sensitive search with newer elasticsearch
* Test and fix ascii normalization too
* more test cases
* comments
* Docs update empi usecase (#3598)
* Update diagram for use case 5
* Add new page for database support
* Licnese
* Mb norm fix (#3604)
* Normalize query since wildcard searches aren't normalized in elastic
* Handle batch2 job cancellation (#3603)
* Handle batch2 job cancellation
* Add CANCELLED status
* Remove unuseful test
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add batch2 interfaces to obtain recent instances (#3601)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* changelog folder
* Documentation change, added warning log and change log for ticket (#3609)
Co-authored-by: Steven Li <steven@smilecdr.com>
* fix ne for lastUpdated search param (#3589)
* init/wip
* add implementation, add tests
* add checks and some refactoring
* refactor and simplify tests
* refactor
* get rid of some of the warnings
* add changelog
* remove my todos
* redo ne logic to account for less precise dates
* add tests
* refactoring
* rename to follow convention
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
* Version bump
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@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>
* Start work on nonunique combo search params
* Work on SQL
* Version bump
* A fix
* Test fixes
* Fixes
* Undo version bump
* Test fixes
* Resolve fixme
* 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
James Agnew
jdar8
TipzCM
Ken Stevens
Luke deGruchy
Tadgh
jmarchionatto
samguntersmilecdr
karneet1212
Johnson Lu
Tadgh
Nick Goupinets
long