* 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
* fixed an issue with matching compartments to lists of ids
* change log
* Added extra guards against false rule matches.
* changelog
* fix inCompartment
* cleanup
* 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
* Work on changes
* Work on perf
* Work on testing
* Work on perf
* Work on perf
* Work on fix
* Work on perf
* Ongoing work
* Add changelog
* Additional docs
* Test fixes
* Address review comments
* Test fix
* Use pageSize variable to hold page size as previously used variable has other function, so not always hols intended value required for previous link
* Adjust test to standards and use RestfulServerExtension instead of own server
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix new searchbuilder limit similar to legacy searchbuilder
* Fix returning includes when using offset query
* Add unit tests for offset query with include
* Only use count param if offset is given (sometimes we want to search synchronously more if DAO is used directly)
* Throw if offset is tried to use with everything operations
* Do not offer offset paging for everything operations and fix tests to assert that
* 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
* 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
* reduce _count to the maximum page size rather than throwing an error.
Also when setting the paging provider on a restful server, automatically set the default page size and max page sized of the restful server from the paging provider.
* reword log message
* fixing this paging issue has uncovered all sorts of interesting things, including this long hidden bug!
* fix tests in sub-optimal way
* fix NPE
* fix test
* fixed a couple of bugs in SearchCoordinatorSvcImpl that surfaced when i added a default page size to RestfulServer
* Start work on validation rules interceptor
* Work on interceptor
* Add tests
* Work on validation interceptor
* Work on interceptor
* Test fix
* Documentation tweaks
* Partitioning rework
* Work on partition improvements
* Partition updates
* Work on partitiong
* Test fixes
* Add docs
* Add changelog
* Resolve FIXME
* Test fixes
* Test fixes
* Test fixes
* Compile fix
* Fix compile error
* Test fix
* Test fixes
* 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 simple CorsInterceptorTest
* add relevant exposedHeaders to custom CorsConfiguration
* use SLF4J Logger.info() instead of System.err.println(), and run the test assertions first
* Add logback-classic dependency to test scope, to enable SLF4J logging within unit tests. (SLF4J defaults to NOP binding if no binding found on classpath, see also http://www.slf4j.org/codes.html#StaticLoggerBinder)
* RDF Support in HAPI FHIR
* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser
* Add null checks to appease LGTM
* Correct null check logic
* consent bug test
* Fix#2012 - Always filter total from search results when consent
interceptor in use
* Add changelog
* Address coverage issues
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
Co-authored-by: jvi <jvi@trifork.com>
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation
* GraphQLQueryBodyParameter to recognize application/graphql
* fix 500 error on method without @GraphQLQueryBody
* refactor to processGraphQlGetRequest and processGraphQlPostRequest
* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest
* fix imports
* 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
* 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
* Add cascading delete to client
* Add changelog
* Client delete should return MethodOutcome
* Rerturn more appropriate type for delete operations
* Refactor cascade detection to be reusable
* Work on search method binding priority
* Work on method priority
* Work on binding priority
* Test fixes
* Add changelog
* Test fixes
* compile fix
* One more comple fix
* Test cleanup
* 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
* 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
* Work on accepting codesystem reources for delta operations
* Ongoing work on term uploader
* Restore the ability to use CodeSystem resources for the delta
* Add tests
* Fix NPE
* Test fixes
* 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
* Test fixes
* ElasticSearch work
* Add ElasticSearch properties builder
* Clean up POM
* Remove redundant project
* Try to troubleshoot embedded elasticsearch
* Another test attempt
* Add credentials to elasticsearch config
* Work on lastn
* Address review comments
* A couple of test fixes
* 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
* Work on indexing source
* Work on tests
* Refactor query count tests
* Unit test fixes
* Add some tests
* DAO fix
* Fix compile error
* Unit test fix
* Cleanup
* Test fix
* Fix compile error
* One more test fix
* This should be working now - need to check tests
* Add a changelog and some docs
* One more test fix
* Tests should be passing
* Fix compile
* Test fixes
* Ignore outdated DSTU2 validation test
* Start work on delta operations
* Add changelog
* Some build fixes
* Move upload terminology command to CodeSystem resource
* Updates
* Some test fixes
* Add changelog
* Some test fixes
* More test fixes
* Test fix
* Add additional tests
* Transaction boundary fixes
* Start working on cascading deleets
* WOrk on cascading deletes
* Work on cascading deletes
* Enable cascading deletes
* Cascade deletes almost working
* FIx test
* Test fix
* Initial consent svc
* Ongoing consent svc work
* Add docs
* Ongoing consent service work
* Work on consent service
* More work on consent svc
* License header updates
* Ongoing consent svc work
* Some test fixes
* Some test fixes
* More work on consent svc
* Tests working
* Test fix
* Propagate RequestDetails to everything in JPA server
* More interceptor tweaks
* Fix compile error
* One more tweak to captured SQL
* Ongoing interceptor tweaks
* Ongoing interceptor tweaks
* More interceptor tweaks
* Interceptor tweaks
* Tweaks to tests
* Fix tests
* Test fix
* Raise warnings when encoding extensions with missing values
* Consent service work
* More interceptor tweaks
* Consent interceptor tweaks
* Add logging to test
* Make IBundle list interface more flexible
* Make matchResourceLinks visible
* Make matchResourceLinks visible
* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module
* Added more accessors to version independent resource classes
* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)
* add AnyComposition
* cleanup of Any classes
* create searchparam config so people can use that module without using subscriptions
* create searchparam config so people can use that module without using subscriptions
* fix broken test
* added derivedFrom
* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types
* TokenParam.equals
* add error check to searchable hashmap resource provider
* added support for R4
* add successor to measure
* delete conflict hook
start with failing test
* test passes.
hook is called.
* added delete conflict hook
all delete conflict tests pass
* added javadoc
* Performance test
* test bad interceptor case
* typo
* rename criteria matcher
* added support for multiple topics
* fix method name
* add effective period
* Temporarily excluding StressTest from build to try to get Travis under time limit
* change log
* review feedback
* review feedback
* review feedback
* reported issue with proposed fix that breaks tests
* Fix spelling
* Merge my changes into this
* Correctly check referential integrity on deletes
* Add one more test
Squashed merge: Add elements exclude mode
* Start working on elements enhancement
* Work on elements projection
* Work on elements filter
* Feature is now working
* Just some cleanup
* Address compile issues
Ken Stevens
Tadgh
markiantorno
Vadim Karantayer
VK-SMILECDR
jamesagnew
Nick Goupinets
jmarchionatto
Michael Buckley
ianmarshall
Tuomo Ala-Vannesluoma
Tadgh
Jari Maijenburg
Diederik Muylwyk
Nick Goupinets
Kevin Dougan SmileCDR
Bill Denton
Joel Schneider (NMDP)
Josh Collins
Ibrohim Kholilul Islam
gematik FuE
Thomas Papke
Jafer Khan
ttn
Jennifer Chan
Stig Rohde Døssing
Anthony Sute
jvi
bdenton
Petro Mykhaylyshyn
Tuomo Ala-Vannesluoma
Stig Rohde Døssing
Ken Stevens
Ken Stevens
Drew Mitchell