* added aggregate function to the sort columns, as the sql will not work on other dbs other than H2 that use order by
* rename parameter to make it more meaningful
* extract parameter to a field
Co-authored-by: Steven Li <steven@smilecdr.com>
* Fix ForcedId criteria query
* wip parameterizing tests
* Refactor almost all APIs to use ResourcePersistentId. Convert to fhir resource id when necessary (at search time)
* run tests in ANY id mode
* Test fix
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* Change to a minimal first pre-fetch to avoid latency on the async path.
The "async" path is now synchronous, and was causing latency for first page by loading 500 results.
We avoid pre-fetch on the first page, and only pre-fetch after users fetch the second page.
* Fix a nasty bug continuing a pre-fetched search.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3664-shorten-first-prefetch.yaml
* Patch up tests that assumed 500 pre-fetch first step
* Revert TermConceptProperty indexing to not-nested type to avoid hitting elastic default maximums and
fix regexp issue which was main reason to change indexing way in the first place.
* Add changelog
* Document that terminology reindexing is required.
* Implement revision suggestions. Fix file name typo.
* Adjust and enable test created to reproduce bug
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add r4b stuff
* Work on R4B
* Core version bump
* Revert some changes
* Add R4B
* Docs
* Test fixes
* Work on R4B
* Tests passgin
* Add config
* Work on merging
* Work
* Work
* Work
* Test fix
* Fixes
* Test fixes
* Test fix
* Work
* Work
* Fixes
* Test fixes
* Fixes
* Test fix
* Test fix
* Test fix
* Version bump
* Test fix
* Test fix
* ompile fixes
* Fix
* Resolve build warnings
* Updates
* Test fixes
* Fix docs
* 3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long.
* 3052 Added changelog
* 3052 Bumped version
* 3052 Remove mysterious +1 on maximum binary size causing overflow.
* Bumping version to 6.2.0-PRE16-SNAPSHOT
* Adding + 1L as original implementation.
* Getting all tests to pass dealing with + 1L.
* Getting all tests to pass dealing with + 1L.
* Adding migration definition and removing unnecessary comment.
* Preventing register overflow when setting maxBinaryStorage.
* Mering relevant test.
* Fixing typo in migration script
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* added validation for family name and birthdate
* making changes to tests
* update patient identifer return and validatePatientMember
* update patient identifer type for test
* update method name
* update test comment
* Allow for easier override of DataSource and dialect
* Add debug logging
* Load AskAtOrderEntry and AssociatedObservations properties from loinc.cvs.
Add changelog.
* Add disabled sandbox test used to develop loinc upload modifications
* Add flags to easily select running mode
* Add validation counters and use gziped csv input to save space in repo
* Implement revision suggestions.
As test is a sandbox remove large files and add readme and test notes to locate them before running the test.
* Add new CODING property handler to run after all TermConcepts are created, to have them accessible for extracting display value
* Add small test file to ease setup
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Standardize on one Transactional annotation
* Add changelog
* Disable checkstyle rule
* Fix up transactions
* Test fixes
* Test cleanup
* License headers
* One more dep bump
* Resolve commit issue
* Test fixes
* Test fix
* Dep bump
* Fix
* Fix test
* Version bump
* Test fixes
* Adding initial test reproducing the issue.
* some comments and small refactoring to run pipeline to see the extent of the damage that this can cause.
* Parsing dstu3 expression with FHIRpath parser
* fixed code.
* omitting searchParameter expression(xpath) validation for DSTU2
* Added test for search parameter with many expressions
* changed deprecated method.
* removed and modified custom search parameters tests for DSTU3 and DSTU2.
* fixed code
* Added change log
* Test testIndexFailsIfInvalidSearchParameterExists() is back.
* Update createResourceSearchParameter_withExpressionMetaSecurity_succeeds() test
* Update createResourceSearchParameter_withExpressionMetaSecurity_succeeds() test
* Refactoring if statement and exception message.
* Refactoring tests and rewording changelog.
* Fixing tests.
* Fixing more tests.
* Addressing comments from first code review.
* Fixing issue number.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Added Test
* Added Integration Test
* Made changes based on comments
* Implemented solution
* Implemented solution
* Debug
* Changelog
* Changes made based on comments
* Changelog
* Made changes based on comments
* Made changes based on comments
Co-authored-by: Karneet Kaur <karneet.kaur@smilecdr.com>
* added attribute to Operation annotation
* add find operation id
* update readOperationDefinition method
* add example to canonicalUrl
* adding more examples
* Add broken test
* Finished writing test
* Add in parameterized test to show it works with one
* Adding extra test asserting sort results when providing short chain
* Providing fix to search with sorting.4098-sort-missing-parameter
* Adding ChangeLog.
* Improving, cleaning up and commenting tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Add unit tests and supporting classes from gitlab issue.
* Commit with changes thus far to be reviewed. Namely, add savepoint capabilities to HapiTransactionService, inject HapiTransactionService into CascadingDeleteInterceptor, add savepoint capabilities to the TransactionDetails, and catch an Exception in BaseHapiFhirResourceDao.delete() then rollback to the checkpoint.
* Fix compile error.
* hapi transaction service test
* hapi transaction service test
* hapi transaction service test
* First draft of RetryTemplate and flush() logic. Try unit testing with PointcutLatch.
* hapi transaction service test
* Latest changes including moving RetryTemplate, cleaning up unit tests.
* First attempt at correct design. Fix compile errors.
* Add failed rollback savepoint test.
* fix propogation
* interesting test failure in SafeDeleterTest
* Latest code
* move delete
* test passing
* all tests pass
* yay we're done just cleanup
* First round of cleanup: Get rid of all exploratory logging, remove unneeded dependencies, move creation of RetryTemplate to SafeDeleter.
* More cleanup. Add changelog.
* Bump to 6.2.0-PRE13-SNAPSHOT.
* Code review feedback: Refactor SafeDeleter to a service and bean. Add comments.
* Code review feedback: Comments on unit test assertions.
* Code review feedback: Rename SafeDeleterSvc to ThreadSafeResourceDeleterSvc. Add javadoc. Add logger to DelayListener. Remove useless commented out code.
* Fix unit test failure in CascadingDeleteInterceptorTest.
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 3240 Added test case. Currently does not reproduce bug.
* 3552 Fixed test case.
* 3552 Added StrictErrorHandler validation before applying patch.
* 3552 Use logger instead of sysout.
* 3552 Use try blocks.
* 3552 Better test name.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* removed flyway, started coding persistence
* started wiring up new dao service
* replace jpa with sqlbuilder
* down to 16 failed tests
* remove outOfOrder test. We no longer support validating order.
* Removed noFlyway mode. It is no longer a thing.
* merge migrator
* down to 1 failing test
* cleanup
* removed unused noflyway cli arguments
* cleanup
* cleanup
* cleanup
* cleanup
* create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot. This allows us to add a bunch of behaviour to that as a first-order thing
* fix test
* fix test
* improve migration table detection to use the catalogue
* Msg.code()
* cleanup
* save version in same format as flyway
* cleanup
* add migration result to migration result class
* failed migrations stay in the table and don't really affect anything.
* change log
* docs
* ugh Flyway requires lower-case column names
* integration test fixes
* log
* fix oracle issue
* lowercase tablenames for postgres. fussy fussy!
* Revert "lowercase tablenames for postgres. fussy fussy!"
This reverts commit 92c9cb263b.
* revert to capital table names. surround table name by quotes for Postgres.
* added log message before executing find all query
* changed log message from info to debug
* javadoc
* pom cleanup
* review feedback
* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* review feedback
* review feedback. Use prepared statement.
* Change installedOn insert from timestamp to date
* Change installedOn column type from timestamp to date
* bump hapi version
* fix poms
* fix poms and cdr compile
* add exclusions to clean up build
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* add failing test
* Fix history search bug and add tests for two more scenarios
* Fix history search bug and add tests for two more scenarios
* - added failing test condition
* Fix history search bug and add tests for two more scenarios
* Fix build test failures
* Fix build test failures
* Add extra verifications for scenarios of _since
* Refactor dao.history interface to add overload method and shall come back to remove old method once cdr is refactored.
* Update with new hapi interface
* Add depreciate comment
* Add depreciate comment
* Version bump to mvn 6.2.0-PRE11-SNAPSHOT
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Allow for easier override of DataSource and dialect
* Add debug logging
* Load AskAtOrderEntry and AssociatedObservations properties from loinc.cvs.
Add changelog.
* Add disabled sandbox test used to develop loinc upload modifications
* Add flags to easily select running mode
* Add validation counters and use gziped csv input to save space in repo
* Implement revision suggestions.
As test is a sandbox remove large files and add readme and test notes to locate them before running the test.
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* remove spring batch
it compiles
expect test failures
* fix test transaction manager bean name (wow that was quite the hunt the wumpus!)
* fix test and fix build
* fix test and fix build
* fix test
* remove spring batch schema initialization
* bump hapi version
* fix schema migrator
* bump to PRE-10
* merge master
* change logs
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix hashCode() to reflect the equals() contract by passing in getValue() instead of getHashIdentity(). Fix bug with DaoSearchParamSynchronizer setting wrong count on AddRemoveCount.addToCount().
* Add hashIdentity to both equals and hashCode. Rename unit test to be more descriptive.
* Add changelog and fix changelog for previous MR.
* Add newline to changelog file.
* added failing tests
* added include to bulk export processor, added support for different resource types in bulk export fetch id step
* added changelog
* fixed duplication issue, and added null check
Co-authored-by: Steven Li <steven@smilecdr.com>
* Add failing and passing tests with bundle JSONs for each scenario based on pared down versions of the following JSON bundle: https://smilecdr.com/docs/fhir_repository/clinical_quality_language/measure-bundle-example.json.html
* Add experimental code to handle cases of "Library" and "Measure". Add a measure report to measure unit test with new JSON with a MeasureReport to Measure resource (can't make it pass yet).
* Refine case statements for JpaPersistedResourceValidationSupport. MeasureReport test passes if -ea is omitted from run configuration.
* Add changelog. Remove TODOs from validator.
* Remove erroneous whitespace chance.
* Ken feedback: Handle SearchParameters from the default case casting a wider net than just Library and Resource. Assume all CanonicalType inputs to the switch statement have a URL.
* Get rid of TODO since it's not relevant.
* Disable test with only MeasureReport and Measure. Fix case issue with filenames that was only discovered by running the github pipeline.
* Add more context to the Disabled text, including a reference to a new issue: https://github.com/hapifhir/org.hl7.fhir.core/issues/930.
* Add more context to the Disabled text, including a reference to a new issue: https://github.com/hapifhir/org.hl7.fhir.core/issues/930.
* Rework includes processing for reuse
* Optimize include
* Test fixes
* Bump version down
* Fixed
* Update
* Test fixes
* Start to add javadoc
* Test fixes
* Change hsearch to consider unquoted parameter strings as prefix match
* Adjust test according to spec (code fixed before).
* Add :text handling to StringParam
* Adjust StringParam tokenization to spec.
Enable StringParam tests.
Add changelog.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4034-align-text-query-syntax-with-hapi-string-search.yaml
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
* Avoid changing simple query parameters.
Implement suggested tests.
* Consider a few Lucene Simple Query Syntax special cases
* Add search syntax changes to documentation and test to make sure samples are good.
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
* Refactored test helper method to be more generic, added new failing test for feature, and changed BulkDataExportOptions to fix compile error
* added field to all objects needed in the bulk export pipeline for adding patient id, added new operation for the feature
* added changelog
* added support for patient parameter to patient export, changed patient id to a list to match the requirements for the patient parameter, added test for multiple id patient export
* refactored methods, added new changes to changelog
* code review changes
* fix test error
Co-authored-by: Steven Li <steven@smilecdr.com>
* add ability to skip loading package resources that already exists, to avoid reindex when loading IGs
* Add a test for validating no updates or creates are called on anything but binaries
* Add changelog
Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com>
* Adding failing test.
* What was done:
-Meta source id is not replaced if provided.
-Added change log.
* Fixed code
* More tests for meta source
* Overwriting meta source can be configured.
* Test naming convention uplift and renaming of overwrite flag along with setter/getter
* Fixed when the source did not return if there was no resourceID
* Test naming convention uplift and renaming of overwrite flag along with setter/getter
* WIP in getting search on _source to be returning the correct number of patients.
* Custom requestId now stored on its own column
* Simplified getRequestId method in BaseHapiFhirDao
* Simplified getRequestId method in BaseHapiFhirDao
* An unused variable has been removed
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Tidy versionenum
* Fix import
* Remove files that were repackaged
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* Bump HS version, add support for credential provider
* License files
* Use index settings file instead of injecting a template at boot
* Changelog
* Typo
* fix logs
* Add javadoc
* Add test reproducing bug
* Refactor ValueSet expansion hsearch queries to use scroll.
* Use void method for never used return value.
* Execute action when transaction is active
* Update tests query counts as the CodeSystemVersion.pid is always queried now
* Enable test after reproduced bug fix.
Add changelog.
* Implement suggestions
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* check for valid resource type
* add test and refactor test class
* refactor auto get method name
* introduce parameter object to patient everything methods
* introduce parameter object to patient everything methods
* change record to class
* add hapi error code
* refactor
* refactor
* change code num
* refactor getmethodname to util method
* add docs and rename fields to conform to fhir standard
* typo
* version bump
* resolving merge conflicts.
* Bumping version
* Bumping version to 6.2.0-PRE5-SNAPSHOT
* Encapsulating parameters in a PatientEverythingParameters object.
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Update CLI upload examples for R4.
* Fixes#3734 Add support for ICD-10 (International)
Include all concept properties in ICD-10 loader.
Remove newlines and tabs from ICD Rubrics.
* Bump Msg code and use in Term Loader.
* Added a changelog entry for this addition.
* Update icd10-dummy-test-en.xml
* Added a default impl to the new interface method to avoid breaking upstream projects.
Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: Kevin SmileCDR <kevinsmilecdr@Kevins-MacBook-Pro-2.local>
* consolidated Batch2Helper
check status in assert before running maintenance
ignore illegal job instance state transition
* Fix mock tests
* rename intermittent to IT
* extra logging
* into to debug
* review feedback
* added more logging
* removed fasttracking. replaced with support for triggering a maintenance run
* fixed tests
* fixed tests
* add asserts
* licenses
* snakeyaml cve version bump
* data migration
* merge origin/master
* merge origin/master
* fix test (support triggering jobs when scheduling is disabled)
* add counter to abort potential infinite loop after 100000 calls
* compile error
* move multipartition mdm tests out to a separate IT
update mongo job instance creation with new logic
* fix race condition
* back out infinite loop circuit breaker. it breaks terminology tests that depend on this loop running > 100000 times.
* fix test (triggered job key was missing group)
* revert saveAllDeferred
* Almost finished getting JpaPersistenceR4IT to pass
* testBulkExportDeleteForOnGoingJob still not passing
* testBulkExportDeleteForOnGoingJob still not passing
* Removed method `fetchInstanceAndMarkInProgress`. It was clobbering other state transitions like CANCELLED.
* undo rename of cancelled to cancelRequested. Thymeleaf depends on the old name
* ExpandResourcesStep requires a synchronous search
* Tests are passing but man testBulkExportDeleteForOnGoingJob is a flakey test
* fix test
* fix test
* change log
* allow ERRORED -> FAILED state transition
* add a timeout to saveAllDeferred()
* improve error message on timeout message
* fix tests
* added more logging
* added more logging
* fix semaphore issue
* Msg.code
* fix test
* javadoc
* switch all batch loggers to batch troubleshooting log
* add unit test, improve logging
* move TimeoutManager to its own class. Add tests.
* fix tests
* comment cleanup
* test race condition
* review feedback
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
Co-authored-by: Steven Li <steven@smilecdr.com>
* 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
* Add skip of checkstyle to upload
* Typo
* upping version enum, upping version number, 6.0.1
* Group Bulk Export rules exiting too early. (#3643)
* Implementation, test, changelog
* Add jira link
* adding backport in yaml for 3642
* adding folder for 6.0.1 release
* pom changes to publish checkstyle to sonatype
* bad version in pom file
* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider
* AUtomcplete error code
* updating comment indicating final erorr code
* Bump error code
* fixing version enum so release docs generate correctly, adding additional changelog for 3650
* 3684 subscription for delivering delete events formatted wrong (#3685)
* Fixed issue with delivering delete events Subscriptions
* Extracted deliverer class name to a constant, now shared across tests and interceptor class
* Added change log and doc changes
* moved the constant to a more appropriate place
Co-authored-by: Steven Li <steven@smilecdr.com>
* Version bump
* Add version enum
* Version enum and folder
* adding release pipeline yml file fo azure
* Adding autoclose for sonatype publishing (#3797)
* Add impl test and changelog (#3713)
* fix up changelog, new version
* Version bump
* Updating version to: 6.0.4 post release.
* reverting 6.0.4 commit
* Updating version to: 6.0.4 post release.
* removing double entry from preious release
* Add support for DSTU3 delete subscrion events, add test
* Add changelogP
* Add version enum
* Remove notnull
* Add test for DSTU2
* Updating version to: 6.0.5 post release.
* Fix up
* wip
* Adding solution and changeLog file.
* Adding failing test.
* fix up
* 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>
* Add license headers
* Move partition interceptor
* More cleanup
* One more tweak
* Headers
* Add changelog
* Test logging enhancement
* Test fix
* Test fixes
* Add test method
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Bump Version for non-breaking purposes
* Fix broken test
* bump error code
* revert internal logic
* Revert offset mode change
* wip
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fixing response message when deleting non-existing or deleted resource.
* Changed names of properties.
* The full ID shown in message, not just IdPart
* Fallback direct resource HSearch to JPA when resources are not found in index
* Use specific exception instead of identifying it by the message
* Add Message code to exception
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Make sure that direct resource load path is only executed for synchronous searches
* Remove unneeded mockito extension
* Only allow for resource loading from fulltext index when advanced search (indexed parameters) is also enabled
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Start direct HSearch path
* Support no HSearch
* Spike out the direct resource query
* Implement hsearch fast load
* Fix last master merge in issues
* Implement revision requests
* Test direct resources (no IDs query) sorting
* Use mock to count freetext searches to avoid implementing interface in test
* Remove fixme
* Make listener optional as it is used only for tests
* Provide new dependency
* Widen fast path test scope and fix previously untested configurations
* Make method transactional as it can be called from outside a TX (at least testObservationLastNAllParamsPopulated does)
* Update test validation
* Allow hsearch sorted offset searches
* Add changelog
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* 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
* added support for OO.issue.details from Java RI Validator
* remove duplicated Msg.code
* 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
* removed duplicated dependency with wrong version
* fixed test file(added a Base64 string)
* fixed tests
* fixed test:
history?_since is an instant
* removing time from date-strings in examples
* fixed more instant strings
* changed filtering of messages to messageId
* fixed messageId filter on missing profiles
* changed messageID system string to Grahames preferred String
* updated MsgIds of unsupported methods
* removed fixed commons-codec version as fhir.core uses commons-codec:1.15
This will introduce issues with the android built.
* fixed GraphQL Test
* fixing test issue caused by different message string, switch to details code assertion
* fixing test issue caused by different message string, switch to details code assertion
* updated Msg.codes
* updated Msg.codes
* fixed duplicated Msg.codes
* setErrorOnInvalidValue set to false in test
* reverted date precision test changes
* updated r5 resources to latest build version
* updated to latest snapshot, https://github.com/hapifhir/org.hl7.fhir.core/issues/884 causes test failures.
* Try to fix message codes
* Test fixes
* Checkstyle fix
* Test fix
* Try to avoid CME
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.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: James Agnew <jamesagnew@gmail.com>
* Fix range calculation for number or quantity search parameters
* Unify clause building for prefixed numeric parameters.
Fix range tests for quantity.
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* added a paging api to ijobcoordinator
* adding changelog
* moved location
* added a comment
* Added Sort parameter to JobInstanceFetchRequest
* Bump HAPI-FHIR version
* Updated JPA api to include sort
* Add changelog
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: David Chen <david.chen@smilecdr.com>
* small refactor
* refactored MDM module to use iterface IMDMLink, refactored MDMLink to use ResourcePersistenceId wrapper rather than pid as long
* removing IJpaIdHelperService and refactor IIdHelperService
* fixed bugs for GoldenResourceMergerSvcImpl and FindCandidateByExampleSvc
* changes to IIdHelperService
* move MdmSearchParamSvc and MdmSubmitSvcImpl out of jpaserver-mdm
* moved JpaResourceLoader to hapi-fhir-storage, renamed to ResourceLoaderImpl
* added error Msg code, removed Fixme
* fixed error code, update last used code in Msg.java to 2083
* fixed accidentally throwing unprocessableentityException
* added MdmLinkExpandSvc interface
* build adding license to files
* MdmLinkdao refactor
* fix build
* mdm config refactoring
* MdmStorageInterceptor and IExpungeEverythingService changes
* fix bug where a pid is converted to ResourcePersistenceId twice
* minor refactor to IMdmLink, change id from long to ResourcePersistenceId
* changed PageImpl to Page interface
* refactor MdmSearchExpandingInterceptor to use interface
* fixed missed refactor where the resourcePersistenceId is still assumed to be long
* resolve test failures resulting from merging master
* changed conflicting exception code
* fixed issue with bulk export wrapping resourcePid inside resourcePersistenceId
* added IMdmLinkImpl to MdmSettings
* fixed missing import in IdHelperService from merging master
* fixed MdmLinkDaoSvcTest importing wrong MdmLinkTuple
* restored JpaIdHelperService and added changelog
* modified msg.code to non-duplicate
* code review changes
* refactored some bulk export batch 2 files to accomodate change in beans being exported
* fixed jpa bulk export failing tests
* removed duplicate bean declaration of MdmLinkImplFactory in BaseMdmR4Test
* merged master and bump version to pre25
* extracted expungeEverythingByType to IExpungeEverythingService
* fixed wiring issue
* messed up merging pom with master
* fixed broken changelog
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Samuel Lee <samuel.lee@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Add logback definition to project to stop debugging all output
* Fix limit definition to include _offset=0 case
* Move test required resources from previous test module
* Add changelog
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* step one
* blah
* no working test
* updated existing tests
* delete code system version and code system jobs
* trying to get terminology fixed
* updating tests
* need to have some movement
* added completion handler
* added clearing code for failsafe
* review points
* fixing tests
* fixing tests
* more test fixes
* fixing more tests
* review fixes
* todo
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* added a paging api to ijobcoordinator
* adding changelog
* moved location
* added a comment
* blah
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Creating an exception to be raised when searching for _tag/_provide/_security where the associated tokenParam is not properly formatted.
* Adding changelogs.
* Adding integration test.
* Rewording ChangeLog.
* Rewording exception message.
* Addressing code review comments.
* Addressing code review comments.
* Bumping hapi-fhir version to 6.1.0-PRE20-SNAPSHOT
* Modifications to pass checkstyle.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* broke some tests
* invoke batch 2 reindex
* changelog
* fix compile error after merge
* fix failing test
* hook up partition support
* fix some failing tests
* deprecate the old reindex service
* fix more failing tests
* fix broken test
* Not the final version
* Support PATCH operation
* minor modifications
* minor modifications
* Final version
* Final version
* Version Bump
* bump version again
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 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>
* Start direct HSearch path
* Support no HSearch
* Spike out the direct resource query
* Implement hsearch fast load
* Fix last master merge in issues
* Implement revision requests
* Test direct resources (no IDs query) sorting
* Use mock to count freetext searches to avoid implementing interface in test
* Remove fixme
* Make listener optional as it is used only for tests
* Provide new dependency
* Widen fast path test scope and fix previously untested configurations
* Make method transactional as it can be called from outside a TX (at least testObservationLastNAllParamsPopulated does)
* Update test validation
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* fix handling of common search parameters
* Revert "fix handling of common search parameters"
This reverts commit 89c45eebdc.
* Fix implementation, add test (#3378)
* Fix implementation, add test
* Tighten test
* Rip out dead modules
* Add changelog
* Jr 20220210 handle common search params in contained searches (#3377)
* fix handling of common search parameters
* add support for reference search parameters with multiple paths
* Issue 3357
* Version bump
* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests
* added changelogs for this fix
* Fix broken changelog file
* Can't specify specific resource type permissions for bulk export (#3376)
* deny user from exporting without perms
* add unit tests
* add changelog
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
* Make migration donothing as it was added in error
* Remove ehcache
* Add version.yaml:
* Add to sources/javadocs for dist
* Fix typo
* fix up pom
* wip test removing checkstyle plugin from deployable pom
* remove test pom changes, instead just dont deploy to sonatype
* typo
* Version bump
* Add implementation, testing, and changelog
* Add backport info, make aware of 6_0_0
* add jira ref
* Fix test
* Add versionenum
* Bump dep for spring, add changelog, add versionenum, add changelog folder
* Actually do the version bump
* 3654 postgres lobs (#3656)
* Implementation, test, changelog
* Modify changelog
* Fix changelog
* Add upgrade.md file
* Modify to yaml changes
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_3/3654-lob-problems.yaml
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* tidy
* more work
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Fix bad yaml indent
* Version bump
* Back out the reindex changes introduced in 5.7.3
* update changelog
* version bump
* added fix for subscription in default partition when default partition's id is null
* added changelog
* Add version info and changelog folder
* adding release pipeline yml file fo azure
* Fix parameter count limitation on MSSQL/Oracle large transactions (#3075)
* Fix parameter count limitation on MSSQL/Oracle large transactions
* Changelog fix
* Move changelog
* Force a change to trigger CI
* Test refactoring
* Backport oracle fix
* Fix backport
* upping version to 5.7.5 for release
* add versionenum
* Updating version to: 5.7.6 post release.
* Add query-chunk-aware code
* Add new folder
* Fix up versionenum
* Remove imports
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.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>
* Start direct HSearch path
* Support no HSearch
* Spike out the direct resource query
* Implement hsearch fast load
* Fix last master merge in issues
* Implement revision requests
* Test direct resources (no IDs query) sorting
* Use mock to count freetext searches to avoid implementing interface in test
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* add system SPs to resource
* populate include list
* wip
* wip
* Tighten test
* Chaneglog
* Use old-style collectors
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* 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
* Add skip of checkstyle to upload
* Typo
* upping version enum, upping version number, 6.0.1
* Group Bulk Export rules exiting too early. (#3643)
* Implementation, test, changelog
* Add jira link
* adding backport in yaml for 3642
* adding folder for 6.0.1 release
* pom changes to publish checkstyle to sonatype
* bad version in pom file
* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider
* AUtomcplete error code
* updating comment indicating final erorr code
* Bump error code
* fixing version enum so release docs generate correctly, adding additional changelog for 3650
* 3684 subscription for delivering delete events formatted wrong (#3685)
* Fixed issue with delivering delete events Subscriptions
* Extracted deliverer class name to a constant, now shared across tests and interceptor class
* Added change log and doc changes
* moved the constant to a more appropriate place
Co-authored-by: Steven Li <steven@smilecdr.com>
* Version bump
* Add version enum
* Version enum and folder
* duplicate import
* duplicate import
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>
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James Agnew
StevenXLi
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Tadgh
Ken Stevens
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michaelabuckley
Etienne Poirier
KGJ-software
MykolaMedynskyiSCDR
Luke deGruchy
weiping202209
Luke deGruchy
michaelabuckley
TipzCM
jdar8
Kai Kewley
Patrick Werner
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JasonRoberts-smile
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