* 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>
* Refactor to restore LGTM functionality
* Compile fix
* Work on cleanup
* Attempt to restore LGTM
* Work on tests
* Fixes
* Build fixes
* Build fix
* Test fix
* Test fixes
* Work on build
* License header updates
* Test fixes
* Test fixes
* License header
* Test fix
* Test fix
* Test fixes
* Restore LGTM
* Fix azure
* Disable test
* Test fixes
* Test cleanup
* Build fix
* Build fix
* Test fix
* Test fix
* Test fixes
* markers for new quantity hibernate search support
* Add quantity search
* Add normalized (canonical) quantity search
* Add comment
* Use double values instead of BigDecimal to avoid scaling
* Remove multiple case labels which are not supported until source version 14
* Remove switch rules which are not supported until source version 14
* Use constant for error message used in tests
* A failing test for multiple indexed quantity paths
* Disallow dirtying context for nested classes
* failing test for normalized units
* Make sp.value-quantity.quantity a nested structure to handle correlated queries for code and value.
Save units for canonical case and consider them when querying.
Collapse normalized sub-structure under *.quantity.
* Nest sp.value-quantity instead of sp.value-quantity.quantity for compatibility with other nested types (IE. token)
* Comment out debug statements
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneClauseBuilder.java
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
* Add test for nested correlated quantity query
* Address MR comments
* Add proper handling of or query predicates
* Use positive conditions for better readability
* Add tests to validate behavior of combined and and or clauses, including some making no sense but still syntactically correct.
* Only consider normalized quantity searching if ModelConfig search level is NORMALIZED_QUANTITY_SEARCH_SUPPORTED
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
* Start working on reindex job
* Updates
* Ongoing work
* Ongoing work
* Work on reindex
* Reindex work
* Add logging
* Fix typo
* Test fix
* Test fix
* Address fixme
* Liocense header
* Resolve fixme
* Add logging
* Update logs
* Address review comments
* License header
* Test fixes
* Test fix
* Test fixes
* Test fix
* Version bump
* Version bump
* New Add Index forced-INCLUDE columns, and Online option
* Remove forced-include. Simpler just to add all columns to index.
* New date index definitions.
* Oops. Remove test for deleted feature.
* Cleanup
* Drop IDX_SP_DATE_UPDATED
* Add online option to drop index
* Update annotations to match and redefine FK
* Push sp->resource FK down to control name
* remove dead end
* Cleanup date tests
* New token query test cases for sql extraction
* New token search param indexing.
* Continue to allow the legacy hibernate names while we update the indexing.
* Fix jpa annotations with overloaded field
* Decide on token sorting - we do it.
* review comments
* fixme
* disable dead data migration too
* review fixups
* Test cases for numeric search
* add ne and ap
* Test for Numeric SP
* start
* finish number
* new indexing for quantity
* Move config
* cleanup
* Enable search narrowing on large ValueSets
* ValueSet improvements
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Add test
* Work on narrowing interceptor
* Work on narrowing
* License headers
* Refactor code narrowing
* Add docs
* Version bump
* Test fix
* Test fixes
* Build fix
* Fixes
* Version bump
* Test fix
* License header updates
* Build fix
* Test fixes
* Test fix
* Test fix
* Docs fix
* Test fix
* Test fix
* Resolve fixme
* Bump
* Force a CI build
* Make CI happen again
* Work on new batch framework
* Work on new batch framework
* Work on new batch framework
* Work on batch
* Compile working
* Work on bulk import
* Adjust import
* Work
* Work on batch
* Bump version
* WOrk on new batch processes
* Work on bath
* Bump to PRE4
* Build fixes
* CLeanup
* Small tweak
* Add exception code
* Test fixes
* Test fixes
* Test fix
* Additional synchronization
* Add license headers
* Test fixes
* Test fixes
* Add changelogs
* Address PG
* Test fix
* Test fix
* Test fixes
* Review notes
* Work on tests
* Test fixes
* Test fix
* Work on tests
* Tets fix
* Test fixes
* Test fixes
* Add missing exception codes
* Test fix
* Test fixes
* More test fixing
* License headers
* Test fix
* Add new test logging
* Work on tests
* Test fixes
* Test fix
* Resolve fixme
* Try to avoid test failure
* Add import command
* Work on storage
* Fix error codes
* Fixes
* License header
* Build fix
* Build fixes
* Fix dep
* Change token and reference search params to 'keyword' field type
* remove normalizer for keyword field
* WIP - refactor lastN operation to use hibernate search generated ES index.
* Add ES native aggregation builder for lastN
* added date search param support for searching resourcetable ES index
* * Added DateSearch parameterized tests to ElasticSearch test suite
* Added more tests cases for Date searches
* WIP refactor LastN test data to central generator class and use it for both hibernate-search and elastic search implementations.
* WIP fix lastNDataGenerator to avoid assertion errors.
* Fixed tests to run test suite on both existing lastN search implementation and newer extended lucene index based search.
* Cleanup json string to avoid carriage return noise
* Fix checkstyle issues
* Fix checkstyle Msg code issues
* Fix checkstyle Msg code issues
* Add more test case for GT, SA precision modifier
* Fix date precision test cases
* Fix Msg Code conflicts
* Add more logging
* Add way more loggging
* even more logging
* fix msg code conflicts
Co-authored-by: Tadgh <garygrantgraham@gmail.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>
* Make RestfulClientFactory.myValidatedServerBaseUrls usage thread safe so capability validation request is sent only once per client-endpoint
* Can't use @GuardedBy for fields which are not always locked by annotation object
* Use same variable when checking and setting
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Allow Subscription to be configured to send delete messages
* Add tests and implement MR suggestions
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add indexes to foreign keys
* Add new version enum
* Add TermCodeSystem and TermCodeSystemVersion deletion job artifacts
* Add Propagation.NOT_SUPPORTED to allow starting jobs from transactional code
* New jobs artifacts
* Improve comments
* Restructure job configurations to avoid bean name collisions
* Restructure job configurations to avoid bean name collisions
* Use new offline deletion by job
* Test using multiple versions
* Retrieve only Pids
* Revert to master
* Maintain deferred functions synchronization as similar as possible to the way it was
* Bypass validations to allow calling an index same as a foreign key to make SchemaMigrationTest happy as H2 adds FK indexes automatically
* Adjust tests
* Add copyrights
* Add test
* Revert to delete CodeSystemVersions using deferred ITermDeferredStorageSvc
* Allow to wait for jobs tentatively
* Organize imports
* Fix tests
* Increase timeout to cover for possible additional heavy DB activity
* Add indexes to two remaining non-indexed foreign key fields to avoid much longer transactions which produce locks on heavy DB load
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3108-terminology-large-code-system-deletion-performance.yaml
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Remove opening stars from logging messages
* Relax index name checking logic to allow for indexes on FK columns to be called same as the FKs, to make SchemaMigrationTest happy even when H2 adds indexes to FKs automatically.
* Use static array to enumerate platforms which doesn't add indexes to foreign keys automatically.
* Cleanup also job executions when performing test artifact cleanup
* Adjust to property name change
* Add ABANDONED status to the list of waited job statuses to avoid test failures due to wait timeouts
* Add also UNKNOWN status to the list of waited job statuses to avoid test failures due to wait timeouts
* Filter job executions to be stopped
* Set trace to debug test problem
* Add STOPPED status to the list of waited job statuses to avoid test failures due to wait timeouts
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* publish test-jar from hapi-fhir-storage
* Extract BaseDateSearchDaoTests up to hapi-fhir-storage.
Share a date search tests between JPA and Mongo.
* Use ITestDataBuilder for setup
* Move Mongo date cases into common set
* cleanup
* More cleanup
* naming
* issue-1134 initial work on adding retry handler
* issue-1134 subdscription creation fixes
* issue-1134 update the test
* issue-1134 retry policy off canonicalsubscription
* issue 1134 base subscription changes
* add failing test
* issue 1134 retry configs on base parameters
* issue 1134 passing forward params
* issue-1134 added more tests for making sure subscriptions create their channels correctly
* issue-1134 updates to get the retry to channels
* issue-1134 updating channel factory
* issue-1134 remove the dlq since it's not defineable
* issue-3120 changelog added
* issue-3120 cleaning up
* issue-3120 test fix
* issue-3120 review fixes
* issue-3120 fixed bad master merge
* issue-3120 updates for new release
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* issue-1134 initial work on adding retry handler
* issue-1134 subdscription creation fixes
* issue-1134 update the test
* issue-1134 retry policy off canonicalsubscription
* issue 1134 base subscription changes
* add failing test
* issue 1134 retry configs on base parameters
* issue 1134 passing forward params
* issue-1134 added more tests for making sure subscriptions create their channels correctly
* issue-1134 updates to get the retry to channels
* issue-1134 updating channel factory
* issue-1134 remove the dlq since it's not defineable
* issue-3120 changelog added
* issue-3120 cleaning up
* issue-3120 test fix
* issue-3120 review fixes
* issue-3120 fixed bad master merge
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
* Start work on OpenAPI
* Fixes
* Work on OpenAPI
* Cleanup
* Cleanup
* More swagger work
* Build fix
* More work
* More work
* Add documentation
* Docs fixes
* Add changelog
* License updates
* Add API
* Cleanup
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Work on scripts
* Add docs
* Compile fix
* Work on fixes
* Fix tests
* Test fix
* Test fix
* Build fix
* Tests
* Build fix
* Work on pipeline
* Version bump
* Test fix
* Version bump
* Test fix attempts
* Test fix
* Test fix
* Remove accidentally committed files
* Fixes
* Tets fixes
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Test fixes
* License header updates
* test fix
* Test fixes
* Test fix
* Test fixes
* Test fix
* Checkstyle bump
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Start work on bul;k import
* Work on bulk import
* Have batch working
* Working
* Working
* More work
* More work on bulk export
* Address fixmes
* License header updates
* Test fixes
* License header updates
* Test fix
* Test fix
* Version bumps
* Work on config
* Test cleanup
* One more version bump
* Version bump
* CLeanup
* A few additions
* Test fixes
* Test fix
* Test fix
* Migration fix
* Test fix
* Test fix
* Add support for revincludes to CapabilotyStatement generator
* Add changelog
* Fixes
* Test fix
* Test fixes
* Test fix
* Test fix
* More fixes to CS cache
* Test fix
* Test fix
* Test fix
* Start work
* Work on testing
* Version bump
* Test fix
* Compile fix
* Test Fixes
* Test fix
* Test fix
* Compile fix
* Tst fix
* Test fix
* Test fix
* Test fix
Tadgh
Ken Stevens
James Agnew
michaelabuckley
Jaison B
Johnson Lu
jmarchionatto
Tadgh
michaelabuckley
TipzCM
juan.marchionatto
Diederik Muylwyk