* 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
* improved DateQuery and removed 'OR' in the SQL
* improved DateQuery and removed 'OR' in the SQL
* Date handling cleanup (#2316)
* Date handling cleanup
* Fix codecov
* One more fix
* Fix tests
Co-authored-by: James Agnew <jamesagnew@gmail.com>
+ relative URL resolution in RDFParser
+ test non-DomainResources in RDFParserTest
~ factor/organize RDFParserTest
~ avoid EXTERNAL shapes (for now) in shex-java
- disable the bundle-response.json example as it is apparently malformed
+ added urn:-guard to PreResourceStateHl7Org.wereBack ID update
* 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* replace all out of date properties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>
* 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
* 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>
* 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
* [(release_3_7_SSE)] cache timezone since timezone.gettimezone is static synchronized and performs poorly
* [(fixgettimezoneperformanceissue)] fiximport
* 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
* add rule version
* add rule version
* Rough in model for Golden Record.
* Test Link Rule Version
* add eid match boolean
* added new fields to EmpiLink to provide more information about how the link was created
* add logging to check an edge case
* all tests pass
* wip with failing tests
* tests pass
* FIXME
* optimize imports
* test score in provider output
* FIXME
* FIXME
* Fix jpa test app context
* fix migration string length
* review feedback param name
* review feedback javadoc
* review feedback javadoc
* bean config reorganization for cdr
* add more tests
* 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
* Allow code validation against enumerated VS
* Work on validation
* Work on this
* Work on tests
* Work on validation
* Work on tests
* Work on validation
* Test fixes
* Add changelog
* For a change
* Test fixes
* Add auto retry of transactions
* Experiment in Maven build
* Transaction autoretry
* Work on transaction retries
* Work on transaction retry
* Work on transaction retry
* Fix tests
* Avoid version conflicts
* Add changelog
* Resolve LGTM issue
* FIx transaction scope error
* Test fixes
* Test fix
* Test fixes
* Test fix
* Test fixes
* 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
The description for SERVER_INCOMING_REQUEST_PRE_HANDLED referred to itself rather than to SERVER_INCOMING_REQUEST_PRE_PROCESSED. Along with this corrected begin into begun.
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Add columns
* Work on multitenancy
* Work on muiltitenancy
* Work on multitenancy
* Work on uniques
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* More work on multitenancy
* Work on multitenancy
* Multitenancy work
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Work on docs
* Work on multitenancy
* Work on docs
* DOcs work
* Tenancy docs
* Work on docs
* Finish docs
* Add changelog
* Rename config
* Add migration tasks
* Fix typo
* Migration fix
* One more migration fix
* A couple more migration fixes
* Docs cleanup
* Work on docs
* Bump boot version
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Work on review comments
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Compile fx
* Test fixes
* One more bugfix
* Update operation name
* Add one more constant
* Roll back a change that was causing test failures
* Test fixes
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* add debug log
* add debug log to value iteration
* fix _filter issue on /$graphql, fix dash and underscore issue on /$graphql, and give helpful error message on wrong argument.
* remove debug logging
* implement JpaStorageServicesTest
* 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
* 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
* [dev] Integration of a Jackson serializer and deserializer - first stage
* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers
* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes
* [clean] Small cleanup
* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created
* [improve] Use the ObjectMapper's `readTree` instead of `readValue`
* [dev] Latest fixes and improvements
* [dev] Use the Jackson serializer
* [clean] Removed the ObjectMapper configuration, for now
* [fix] Use the GsonStructure also for the parsing of a FHIR resource
* [clean] Removed the LinkedList usage
* Work on preparing for merge of #1673
* Resolve build errors
* Work on parser integration
* Tests passing
* Resolve fixme
* CLeanup
* Fix dependency
Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
* 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>
I ran into an issue trying to use the old .class style property. The validation message was useful, but I spotted some unreachable code investigating which I've removed. I also enhanced the configuration exception to indicate what was wrong with a supplied key and expected extension types.
* 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
* Don't succeed validation on unknown codesystem
* Test fixes
* Work on error messages
* Work on code validation API
* work on tests
* Work on validation
* Test fix
* Update DSTU3 validation reources
* Upgrade structures
* 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
* 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
* 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
* Resolve XXE issue in validator
* Ensure that we're blocking XXE events into validator XML parser
* A bit of cleanup
* Add an LGTM config
* Add one more fix
* Terminology Delta Uploading
* Add delta operations
* Fix up tests
* Improve test coverage a bit
* Improve test coverage reporting
* fix yaml
* A couple of test enhancements
* FIx intermittent test failure
* 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
* Handle cascading deletes correctly with circular references
* A bit of cleanup
* Address review comments
* FIx some javadocs
* Fix an incorrect message
* Initial commit of _filter keyword implementation.
* - Completed all search parameter types for _filter.
- Implemented handling for _has, _id, _security, language, _profile, _security, and _tag.
* - Changes to support "ne" matching on resource ID for _filter
* Implemented language
* Commit/push before creation of pull request
* Ongoing merge work
* Ongoing merge work
* Merge master in
* 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 work on changing over
* Update tests
* More test fixes
* Work on generalizing binary access provider a bit
* Add expunge capability to binary storage, and also support actual binary
resources
* Work on binary provider
* Get the DB bound binary storage service working
* Test fixes
* Compile fix
* Fix compile error
* Test fix
* Test tweak
* Trying to figure out an intermittent failure
* Work on tests
* More work on tests
* Another test fix
* Ongoing work on core structures suport
* Ongoing work on this merge
* Ongoing work to clean up structures
* Credit for #1179
* Address compile issues
* Latest changes
* Work on parallel execution
* Work on getting tests passing
* Add H2 to migrator
* Test fix
* Start working on this
* Ongoing fixes to H2 branch
* Work on fixing tests
* Updated fixes
* Some test fixes
* More work on H2 migration
* Fixes to try and get the H2 migration building
* Test seem to be passing!
* Tweaks to locale randomization
* Add changelog
* Added experimental implementation for storing expanded ValueSets in terminology tables.
* Minor tweak to log message for consistency.
* Another minor tweak to log message for consistency.
* Renamed test.
* Addressing review comments.
* Added migration tasks.
* 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
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