* initial roughout of mdm clear batch job
* still roughing out classes
* finished first draft of reader
* most tests passing now
* all tests pass. now FIXMEs
* FIXMEs done. Time for regression.
* fix test
* changelog and docs
* fix test
* pre-review cleanup
* version bump
* move spring autowire deps for cdr
* move spring autowire deps for cdr
* finally got beans working phew
* rearrange method calls so persistence module can perform clear operation on its own
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
* review feedback
* Remove inheritance
* fix beans
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Start work on nonunique combo search params
* Work on SQL
* Version bump
* A fix
* Test fixes
* Fixes
* Undo version bump
* Test fixes
* Resolve fixme
* 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
* Search param service cleanup
* Work on collapsing search param
* Search param cleanup
* Work on build
* Test fix
* Test fixes
* Ongoing work
* Test fix
* Compile fix
* Test fixes
* Test fix
* Test fix
* License header updates
* Remove fixme
* Cleanup
* Cleanup
* Add support for revincludes to CapabilotyStatement generator
* Add changelog
* Fixes
* Test fix
* Test fixes
* Test fix
* Test fix
* More fixes to CS cache
* Test fix
* Test fix
* Test fix
* Start work
* Work on testing
* Version bump
* Test fix
* Compile fix
* Test Fixes
* Test fix
* Test fix
* Compile fix
* Tst fix
* Test fix
* Test fix
* Test fix
* Performance tweaks
* Work on processing speed
* Disable no longer relevant tests
* Work on performance
* Work on tests
* Work on large transaction performance
* Add changelog
* Perf tweaks
* Test fixes
* Resolve FIXME
* Fixes
* Test cleanup
* Fix broken changelog entry
* POC for indexing on contained resource - test case may failed
* Test contained url
* Add a spt to handle contained flag
* Added search option for contained resource
* Impl contained resource search
* fixed typo
* Reworked on creating index based on the review comments
* Added changelog
* Added more test cases
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* Automatic reference versions
* Auto reference versions
* resolve fixmes
* Add changelog
* Test fixes
* Test fixes
* Resolve fixmes
* Work on versioning
* Add support for _includes
* Update headers
* Change visibility
* One more tweak
* One more API tweak
* Fixes
* Account for review comments
* Fix errorprone reported issue
* Test fix
* Test fixes
* Test fixes
* Added UcumServiceUtil
* Removed ucum-essense.xml
* Added ucum service existing test cases passed
* Added more test cases
* Merge branch 'master' into ft-ucum-support
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
* Added back extractReferenceParamsAsQueryTokens
* Added changelog and migration script
* Added length for the string type
* Moved UCUM util to hapi-fhir-jpaserver-model
* Renamed UCUM support to Normalized Quantity Search Support
* Moved setNormalizedQuantitySearchNotSupported to AfterEach
* Changed migrate task to 530
* Removed comments
* Fixed in memory search issue and added more test cases
* Fixed the version order
* License header updates
* Updated based on review comments
* Updated the migration task based on review comments
* Fixed RES_TYPE with type String and length 100
* Changed myParamsQuantityNormalizedPopulated type to Boolean class
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)
* Fix spatial API changes, work on BaseTermReadSvcImpl
* Most of the way through the various filter property conversions
* Finished i think with BaseTermReadSvcImpl
* Compiling, but definitely broken
* Start test compilation failures
* All tests compiling (i think)
* remove suggest keywords operation
* Fix bootstrap errors, still have to deal with transient fields
* Rollback CR
* More refactoring, got IDs baked back into docs
* Fix coord util, fix a few more fields which require projection
* merge fixes
* begin refactor of valuesetexpansion tests
* fix another test
* Update tests
* remove todos, add TestContainers
* Fix descendant in
* Add testcontainers, fix another test
* fix more tests, replace embedded es
* Rip out embedded elastic, replace with TestContainer
* merge conflicts for new analyzers
* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs
* Remove dead deps, update testcontainer
* Remove java-hamcrest
* Pull asserts up, refactor tests to pass in RP tests
* Update V2 check
* Remove suggest keyword tests
* Split line for testing
* Fix perhaps one of the dumbest programming mistakes in my career so far
* Refactor tests which no longer rely on a strict known order
* Fix up test config, disable log test temporarily
* Remove log4j from being transitively pulled in. re-enable test
* Update log4j exclusions with new bridge. Update test to check for core class
* Move dependency to root pom in dep management section
* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment
* update testst, remove todos
* Add hibernate props provider method, add elastic regexp query
* Add todo for high level client builder
* Modify ElasticsearchRestClientFactory to support HTTPS hosts
* Remove protocol extraction from rest url
* do we even need to index this...?
* remove purge of non-indexed resources
* Add longer timeout to testcontainers
* Add task to add docker CLI to azure pipeline via task, for testcontainers
* WIP remove this
* Dont update version
* Add test for duplicate termconcepts
* Use real hibernate ORM methods
* merge issues
* Add partitionsettigns bean to match master
* Trying to debug testcontainers on azure...
* Trying to debug testcontainers on azure...
* Run even on previous failure
* Fix testcontainer port binds
* Add full text logs attaching, and test reporting
* I love yaml
* Remove comment
* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue
* Modify TX beheaviour
* wip
* Rework to use config and mocked beans for partition-aware lastN
* rework to not use beans and just inject vars i need for test, keps test envs cleaner
* update azure pipeline to only copy test results
* Remove erroneous publish
* Always get test logs
* Make it so indexing works,
* Add todos
* revert deleteByPid
* Work on test fixes
* Test fixes
* Test fixes
* Another test fix
* Test fix
* Work on tests
* Test fixes
* All tests passing locally
* Fix test failure
* FIx build error
* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider
* Update ngram of token filters
* Tidying
* subvert the purpose of hibernate elastic props builder to inject template
* dead space
* Rename changed class
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* init rev
* fix build
* Tweaked the POM config settings and also added some dependency exclusions (commented out for now).
* More re-factoring of the CQL Unit Tests.
* Removed a LogMessages.html file and a minor Unit Test change.
* Unit Tests.
* added debug logging to troubleshoot the dao that has no name
* added debug logging to troubleshoot the dao that has no name
* workaround to get past null dao resourceName issue
* fix jsons to get test to pass. Test still fails with library id problem
* gitignore
* gitignore
* test passes! Woohoo!
* undo troubleshooting logging
* added timer and logging.
* added asserts and time multiple evaluations and measure the average
* readme
* adding explanations
* added more explanatory notes
* measure 2 patients
* move pom to use cqf snapshot
* roughed out cache
* roughed out cache
* Added code to VersionChangeCache class.
* added tests
* added polling test
* wrote init version
* wrote init version
* optimized versioncache
* worked on getting tests to pass
* redesigned interfaces
* all tests pass
* fixmes
* fixmes
* rename param
* Added Unit Tests.
* javadoc
* Fixed the 2-Patient Unit Test.
* More Unit Test work.
* make ResourceVersionMap immutable
* Fixed a Unit Test that was failing intermittently by adding a new way to refresh the cache.
* Use a new method called doRefreshAllCaches(0) to force a refresh and have all Listeners called immediately.
* Cleaned up IVersionChangeListenerRegistry interface to make methods more clear and resolved all Unit Tests.
* disabled tests
* disabled tests
* removed unused test method
* fixed refresh logic and added asserts
* moved cache so it can be used by searchparamregistry
* Updated the Cql Unit Tests to be properly configured for Dstu3 or R4.
* started rewriting SearchParamRegistryImpl to use new cache
added init method to listener interface
* added fixmes
* adding tests
* tests pass
* added tests
* Fixed the way CqlProviderFactory Autowires Beans so it can work with both Dstu3 and R4 contexts.
* moar tests
* fix test
* work tests
* reverting unneccessary refactors
* undo unneccessary import changes to reduce MR size
* undo unneccessary import changes to reduce MR size
* Unit Test fixes...more to come...
* add unregister
* fix tests
* Changed ResourceVersionCache to use a Map of Maps.
* searchparam test
* test passes
* resolved fixme
* fixmies
* strengthen test asserts
* More Unit Test changes and added some FIMXME items.
* changed from long to changeresult
* renamed VersionChange -> ResourceChange
* fixed delete bug
* organize imports
* fix test
* add update test
* add test reset function
* fix stack overflow
* fix startup race condition (might still be intermittent)
* found the problem. delete doesn't work because we can't look up the deleted resource to find out what its name is
* fixed regression
* abandoned idea of incrementally updating searchparam registry. Rebuilding every time--it doesn't change that often.
* fix test
* begin with failing test
* test passes
* fixmes and javadoc
* fix test
* fixme
* fix test
* whack-a-mole. Either subs pass or cql passes. Something's fishy with the FhirContext
* fix subscription test initialization
* fix method name
* Re-factored the CqlProvider Unit Tests.
* changed ResourceChange API
* add interface
* add interface
* fix test
* add schedule test
* add doc
* init rev
* FIXME
* modify FhirContext change
* change fhirContext.getResourceTypes to lazy load
* converted subscriptions
* converted subscriptions
* begin with failing test
* test passes
* fix test
* test coverage
* test coverage
* test coverage
* test coverage
* good coverage now
* pre-review cleanup. I think I found a bug.
* moved cache into listener entry
tests pass with fixmes
* fix test
* fix test
* fix test
* fixme
* FIXMEs
* merge cache and registry
* method reorg
* javadoc
* javadoc done. all FIXMEs resolved.
* change log
* changes needed by cdr
* spring config cleanup
* james feedback
* james feedback
* might not work. Try moving resourcechangeconfig into searchparam config
* merge ResourceChangeListenerRegistryConfig.java into SearchParamConfig
* fix test
* fix SubscriptionLoader
* fix SubscriptionLoader
* create ResourceVersionMap from resources
* added cache handle interface
* fix test
* javadoc
* fix test
* fix test
* James feedback: clone searchparametermap
* fix startup
* fix test
* fix test
* fix intermittent
* pre-review cleanup
* FIXME
* final FIXME yay!
* Address a couple of my own reviw comments
Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* switched to adding annotations. Just did a test with Token, but the sql looks clean.
* switched to adding annotations. Just did a test with Token, but the sql looks clean.
* added the other six index links
* trying different annotations
* Start testing
* Update resources on package install
* Add changelog
* Join rework
* CLean up SQL builder
* Add docs
* SP rework
* Join work
* Work on params
* Work on refactor
* Work on chains
* Work on joins
* Rework queries
* Work on queries
* Many more tests passing
* Refs test
* Work on sorting
* Work on tests
* More joins work
* Work on tests
* Work on queries
* Tests passing
* More test fixes
* Test fixes
* Work on SQL
* Tests passing
* Add some tests
* Add some tests
* License headers
* Use entity manager to get datasourcd
* One more fix
* Model cleanup
* Ongoing work
* Fixes
* Fixes
* Work on joins
* Ongoing fixes
* Merge conflict
* Cleanup
* clean up unused fields
* Work on join
* COmpile fix
* Rework querying
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Resolve fixmes
* Test fix
* Test fixes
* Test fix
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Improve synchronous searching by providing offset & limit support
Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)
* Review and test fixes
Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)
* Remove temporary count querying fix for synchronous loads
* Fix offsetting of everything operations, do not drop zero offset
* Fix jpa test default and maximum page size, add some fixmes to tests before resolved
* Ignore one failing test, fix others
* Fix Dereferenced variable may be null
* Fix everything paging in R4 by adding DISTINCT if synchronous load is used
Also fix assertion of size when hitting fetchSizeDefaultMaximum
* Add documentation about offset annotation and paging
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Add test
* Fix
* Add changelog
* Test fixes
* Test fix
* Test fixes
* Resolve fixme
* Test fixes
* Remove debug logs
* Try to get CI tests passing again
* Work on junit
* Work on junit 5
* Work on junit 5
* Bump errorprone vcersion
* Work on tests
* Junit 5 tweaks
* Fixes
* Work on tests
* Work on junit5
* Work on tests
* Test fixes
* Work on junit5
* Test work
* Get junit5 working
* Test fix
* Work on tests
* WOrk on tests
* Work on tests
* fixes
* Compile fix
* One more tweak
* Compile fix
* Add changelog
* Fix compile error
* Compile fix
* start with failing test
* test passes with fixmes
* javadoc and config
* pre-review cleanup
* generalize encoding
* test passes, but indexing needs to be optimized
* test passes, but indexing needs to be optimized
* step 1 of optimization. big refactor of all predicates
* step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation
* integrated new phonetic encoders into empi
* phonetic search implemented
* IT passes
* pre-review cleanup
* final pre-review cleanup
* final pre-review cleanup
* Fix compile error
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Terser should create correct Enumeration on create
* Start work
* Work on subscriptions
* Work on seed bundles
* Bundle transmission
* Add changelog
* Test fix
* Fix LGTM warning
* Begin rework of package management
* Work on NPM
* Work on package management
* Work on NPM
* NPM rework
* Work on NPM
* NPM package rework
* Updates
* Updates
* Add license
* Work on package server
* Work on package importing
* Work on package management
* Package rework
* Work on packages
* Work on package manager
* Work on pkgs
* NPM work
* NPM rework
* Work on package cache
* Work on NPM
* Work on NPM
* Package fixes
* Add tests
* Tweaks
* Test fixes
* Add changelog
* Avoid snapshot dep
* Start working on FHIRPatch
* More work on fhirpatch
* Work on FHIR Patch
* Add patch
* Test fixes
* Test fixes
* Get tests fixed
* Chnage to trigger a build
* Compile fix
* Dependency version fixes
* Test fix
* COmpile fix
* Try to fix build
* Test fix attempt
* Another build attempt
* Another build tweak
* Cleanup
* Work on search params on contained
* Add workaround for stored decimals with leading decimal point
* Add changelog
* Cleanup
* Test fix
* Test fix
* One more test fix
* Validation enhancements
* Work on validation api reworking
* Keep working on validation API
* Keep working on new term API
* Work on validation api
* Ongoing work on validation
* Work on integrating validation
* Work on validation API
* Add to validation API
* Work on validation
* Work on API
* Work on validation
* Work on validation API
* Work on validation API
* Work on validation api
* Work on validation API
* Work on validation api
* Validation API changes
* Work on API
* More work on validationo API
* Work on validation API
* FIxes
* WOrk on validation api
* Work on validation API
* Tests passing!
* More cleanup
* More validation API changes
* Fix intermittent test failure
* Package reorg
* Validation API work
* Work on doocumentation
* Work on API
* More work on new validation API
* Fix errorprone-reported error
* Test fixes
* Documentation updates
* Documentation tweaks
* Work on API
* Bean name adjustments
* Build fixes
* Some test fixes
* Add forced ID caching
* Work on id optimization
* Test fixes
* More optimization work
* Add some docs
* Work on docs
* Test fixes
* Test fixes
* Test fixes
* Address review comments
* Compile fix
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Start working on converter
* Account for compile errors
* Test fix
* Work no validator
* Work on getting core working
* Add some test coverage
* Many test fixes
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
* Copy identifiers to placeholder resources
* Add tests
* Maven cleanup
* Still messing around with azure
* Adding to logging
* More azure work
* One more attempt
* More messing around with azure
* Test fix
* Another caching attempt
* More work on azure pipeline
* Fix pipeline file
* Keep working on pipeline
* More work on azure
* More azure
* More azure work
* More azure
* Work on upgrading core
* Work on R5 updates
* Work on core updates
* Test fix
* Update model version properties file for R5
* Bump core version
* Test fixes
* Add 4.2.0-SNAPSHOT version to versions page in docs
* Some CI surefire improvements
* Build tweak
* More tweak
* Update azure-pipelines.yml for Azure Pipelines
* Update azure-pipelines.yml for Azure Pipelines
* One more CI attempt
* Update azure-pipelines.yml for Azure Pipelines
* Tweak command line
* Another build test fixc
* More build cleanup
* Start work on refactoring how PIDs work
* Some test fixes
* Test fixes
* Test fixes
* Restore accidentally deleted line
* One more tweak
* Rework resource link extraction
* Test fix
* Split out transaction processor
* Updates
* Test fix
* Test fixes
* Test fixes
* Clean up LGTM warning
* Fix compile failure
* One more test fix
* Fix LGTM issue
* Add spot for metadata
* Add test logging
* Remove testing code
* More test logging
* Add some test logging
* Attempty to fix intermittent test failure
* Improve exception tracking
* Work on simplifying search param registry
* Fix compile
* Fix compile errors
* Fix two test bugs
* Start refactoring terminology delta operations
* Work on delta operations
* Work on concept saving
* Split term services into smaller services
* Work on term delta operations
* Work on term svcs
* Work on term operations
* More work on delta uploader
* Add a test
* Wrk on term service
* Fix compile error
* Some refactoring
* Test fix
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Work on delta
* Work on tests#
* Test fixes
* Improve resequencing logic
* Build test
* More testing
* More build testing
* More work on tests
* CHange test logging
* Fix term service PID issue
* Update src/changes/changes.xml
Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>
* Address review comment
* Some cleanup
* Test fix
* Fix some tests
* Work on upload command
* Test fixes
* Work on validation fixes
* Work on validation against pre-expansion
* Work on direct validation
* A bit of cleanup
* Add some javadoc
* Force another build
* Test fixes
* Fix tests
* Fix tests
* Add some logging
* Add more test logging
* Work on some test logging
* Fix compile error
* Work on codecov
* Work on codecov
* Remove test debug messages
* Start working on subscription processor
* Work on new scheduler
* Test fixes
* Scheduler refactoring
* Fix test failure
* One more test fix
* Updates to scheduler
* More scheduler work
* Tests now all passing
* Ongoing work on export
* Ongoing scheduler work
* Ongoing testing
* Work on export task
* Sync master
* Ongoing work
* Bump xml patch version
* Work on provider
* Work on bulk
* Work on export scheduler
* More test fies
* More test fixes
* Compile fix
* Reduce logging
* Improve logging
* Reuse bulk export jobs
* Export provider
* Improve logging in bulk export
* Work on bulk export service
* One more bugfix
* Ongoing work on Bulk Data
* Add changelog
Ken Stevens
Tadgh
jamesagnew
Nick Goupinets
Diederik Muylwyk
Frank Tao
Kevin Hartmann
Patrick Werner
Jari Maijenburg
Mike G
Tadgh
Tuomo Ala-Vannesluoma
ianmarshall
Gary Graham
Tuomo Ala-Vannesluoma