Add optimistic write lock to $reindex operation to prevent indexing stale data.
Introduce Lockstep Phaser to make testing easier
Add 1 query to every resource reindex :-(
* First commit: Add userSelected and version to ResourceTag and ResourceHistoryTag. Add migration step to migration tasks. For some reason SchemaMigrationTest is failing.
* Fix nullability, update constructors, truncate versions over 30 chars.
* yay we're done just cleanup
* Checkpoint for recent changes.
* Last commit before pausing work.
* Fix bad code to find the version, tweak unit test pid ID to versionless and add TODO about why is update part of the test not passing?
* Fix bad code in extractTagsRi(): Make it leverage the IBaseCoding variable already in the for loop. Fix bad code in populateResourceMetadataRi(). Leverage the existing BaseTag and use it to populate the IBaseCoding tag instance instead. Add more and better assertions in the unit test.
* Merge rel_6_4 in
* Current state for pairing
* Fix CodingDt.getUserSelected method return code in tinder
* Complete migration task and cleanup
* Remove missed fixme
* Bump version temporarily to use it for building core lib
* Use primitive for compatibility with tinder generated CodingDt
* Copyright updates
* Hack to bypass NPE generated by bogus tinder-generated code
* Simplify by removing temporary deprecations as version bump is needed anyway because of TagDefinition entity changes
* Adjust tests
* Fix migration task
* Add test to show problem with tinder generated BooleanDt
* More test adjustments
* Improve BooleanDt NPE avoidance
* Update core dep
* Reverse Juan CVE VersionEnumTest changes.
* Fix unit test.
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Improve performance on bulk export
* Add changelog
* Start working on cleaned up reducer
* Clean up batch calls
* Work on issues
* Build fixes
* Test fixing
* Test fixes
* Work on progress
* Add changelog
* Build tweak
* Fixes
* Fixes
* Fix compile
* Test fixes
* Bump to 6.4.2-SNAPSHOT
* Fix compile
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* First commit: Create new branch from the release branch with changes from James' branch. This probably won't compile as the work is incomplete.
* Second round of changes from integrating James' branch.
* Mark most test failures with TODOs.
* Add whitespace
* Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation.
* Fix CreatePackageCommandTest to assert null instead of empty string. Comments on tests that fail due to the double-quote encoding problem.
* Downgrade to core 5.6.97.
* Fix another test and remove TODOs.
* Fix changelog.
* Clean up some erroneous changes and TODOs.
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* failing test
* fix + changelog
* tweak
* add method to IJobPersistence to use a Stream
* tweak
* tweak
* decrease test time
* clean up
* code review comments
* version bump
* Increase timeout limit to match BulkExportUseCaseTest
* shorten test
* maintenance pass
* add logging
* Revert "add logging"
This reverts commit b0453fd953.
* Revert "maintenance pass"
This reverts commit bbc7418d51.
* test
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* shorten tests
* logging
* move test location
* fixes a regression caused my change in hapi-fhir
* timeout
* Revert "fixes a regression caused my change in hapi-fhir"
This reverts commit 4b58013149.
* testing
* Revert "testing"
This reverts commit aafc95c2f3.
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fix bug where FINALIZE jobs are not cancellable
* moved reduction step to message hander
* moving reduction step to queue
* addingchangelog
* cleaning up
* review fixes
* review fix'
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* cleaning up checkstyle files
* One more fix for #4467 (#4469)
* added exlusions for files at base project level so checkstyle doesn't error out
* duplicate error code from merge
* changing lifecycle goal for all module checkstyle check
* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code
* wip
* trying to figure out why pipeline cannot copy files
* removing modules that don't actually need to be built.
* I messed up the version
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix broken test
* Smile 4892 DocumentReference Attachment url (#4237)
* failing test
* fix
* increase test Attachment url size to new max
* decrease limit to 500
* ci fix
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Overlapping SearchParameter with the same code and base are not allowed (#4253)
* Overlapping SearchParameter with the same code and base are not allowed
* Fix existing tests according to changes
* Cleanup dead code and remove related tests
* Version Bump
* ignore misfires in quartz
* Allowing Failures On Index Drops (#4272)
* Allowing failure on index drops.
* Adding changeLog
* Modification to changelog following code review.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Revert "ignore misfires in quartz"
This reverts commit 15c74a46bc.
* Ignore misfires in quartz (#4273)
* Reindex Behaviour Issues (#4261)
* fixmes for ND
* address FIXME comments
* fix tests
* increase max retries
* fix resource id chunking logic
* fix test
* add modular patient
* change log
* version bump
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Set official Version
* license
* Fix up numbers
* Fix up numbers
* Update numbers
* wip
* fix numbers
* Fix test:
* Fix more tests
* TEMP FIX FOR BUILD
* wip
* Updating version to: 6.2.1 post release.
* Add a whack of logging
* wip
* add implementation
* wip and test
* wip
* last-second-fetch
* expose useful method
* remove 10000 limit
* Strip some logging
* Fix up logging
* Unpublicize method
* Fix version
* Make minor changes
* once again on 6.2.1
* re-add version enum
* add folder
* fix test
* DIsable busted test
* Disable more broken tests
* Only submit queued chunks
* Quiet log
* Fix wrong pinned version
* Updating version to: 6.2.2 post release.
* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)
* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276
* Credit for #4291
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* backport and changelog for 6.2.2
* Updating version to: 6.2.3 post release.
* fix https://simpaticois.atlassian.net/browse/SMILE-5781
* Version bump to 6.2.3-SNAPSHOT
* Auto retry on MDM Clear conflicts (#4398)
* Auto-retry mdm-clear on conflict
* Add changelog
* Build fix
* Disable failing test
* Update to 6.2.3 again
* Update license dates
* Dont fail on batch2 double delivery (#4400)
* Don't fail on Batch2 double delivery
* Add changelog
* Update docker for release ppipeline
* Updating version to: 6.2.4 post release.
* Add test and implementation to fix potential NPE in pre-show resources (#4388)
* Add test and implementation to fix potential NPE in pre-show resources
* add test
* WIP getting identical test scenario
* More robust solution
* Finalize Code
* Add changelog, move a bunch of changelogs
* Remove not needed test
* Minor refactor and reporting
* Fix up megeback
* update backport info
* update backport info
* Updating version to: 6.2.5 post release.
* Prevent chunk from returning to in-progress unless it is errorred, in-progress, or queued
* changelog
* Update logger
* Indicate backport
* Add version and upgrade info. add backport
* hapi-fhir side done
* cdr side
* add assert
* add test
* Fix import
* prevent multiple reduction step runs in maintenance run (#4423)
* setting job to inprog to prevent multiple maintenance passes from running reduction steps
* added a new status
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* Add backport info
* Fix up tests
* Fix discrepancies
* Fix test
* Version bump
* bump ips
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* breaking up package installer and package config
* breaking out parsing of resources
* wrong nullable
* added an integration test
* adding a changelog
* added a few minor tests
* review fixes
* unit test fixes
* fixing code checkstyle
* moving fetching local package data to package loader svc
* updating the method name
* splitting the fhirversion parsing
* updating table creation task for pretty printing and use in RTE
* adding foreign keys
* Adding mroe info
* minor prettiness changes
* fixing fk generation
* minor changes
* update version
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Add new Clinical Reasoning module
* Add config to get test up and running
* Removed FhirClient from tests
* First passing test
* Remove unused utilities
* Build updates
* exclude xxp3 and substitute with unbundled version
* Refactor to use provider factory and loader pattern
* First passing dstu3 test
* CR r4 test config and immunization tests
* Add base test classes
* Exclude transitive dependency xmlpull
* More dependency cleanup
* Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr
* Fixes for duplicate xpp3 classes
* Remove more references to jpa
* Add mock FHIR server for terminology endpoint tests
* fix cql file for making providerr4 tests pass
* fix pom
* fix generic
* Adding r4 test cases for measure operations.
* Fix endpoint tests
* javadoc comment, temporarily comment out test results for practitioner sync
* javadoc typo fix
* adding java docs for cr module WIP
* Updates to clinical reasoning documentation
* More documentation updates
* docs now compile
* fix test
* DqmR4IT now successfully starts up, but the test does not pass
* Fix additionalData test
* Make measure service bean overridable
* adding clinical reasoning javadoc information
* Rename interfaces to start with I
* More styleguide updates
* Reformat all code in the storage-cr module
* More coding convention updates
* Remove bunches of unused code, reogranize so that fhir version in package name is consistent
* Clean up some static array initializations
* add practitioner patient list
* refactor product-line constant
* test dependency update
* add change log for cr module
* Add hapi-validation to the pom
* Exclude dependencies that are causing duplicates
* More dependencies and exclusions
* Make some base MeasureService components protected
* Update to latest cql compiler release
* fix measure service for null subject & practitioner and open up practitioner test
* Rev to release versions
* Add remaining Dstu3 tests
* update hedis bundle from policyHolder to beneficiary
* update snapshot
* Delete old CQL module
* Post-master-merge recovery
* Fix Java 17 feature usage issue
* update changelog with more information about new functionality
* Remove support chain wrapper usage
* Add javadocs to IResourceLoader
* added the property versioning for antlr jar.
* addressing code review comments.
* addressing code review comments.
* Fix typos in changelog
* Remove azure pipeline for cql module, add it for cr module
* Address exception comments, add Msg.code calls to exceptions
* Fix self-assignment bug
* Add storage-cr module to bom
* addressing coding comments.
* Addressed the variable naming convention to camelCase.
* Snapshot version bump
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* fix handling of Windows line ends
* some tests need to wait a little longer for things to get done
* Windows path separator fix
* simpler lineend fix
* more timeouts and another path separator issue
* redo some timeout issues
* Issue in Windows: URI is not hierarchical
* another timeout issue
* Add test and implementation to fix potential NPE in pre-show resources
* add test
* WIP getting identical test scenario
* More robust solution
* Finalize Code
* Add changelog, move a bunch of changelogs
* Remove not needed test
* Minor refactor and reporting
* Added Solution + test
* Removed old methods
* fixed issues
* Added refactoring
* Deprecated methods on the interfaces
* Remove todo
* Documentation
* Changelog
* Changelog
* Changelog
* Changes made based on comments
* Changes made based on comments
* Clean up
* hapi bumping to version 6.3.6-SNAPSHOT
* hapi bumping to version 6.3.6-SNAPSHOT
* Start work on sharded DB
* Work on migrating
* Work
* Ongoing work
* Ongoing work
* Work
* Work
* Ongoing work
* Work
* Work
* Test fix
* Test fix
* Work
* Compile fix
* Test cleanup
* Test fix
* Resolve fixmes
* Resolve fixme
* Resolve compile errors
* Compile fix
* Fixes
* Work
* Add note for later
* Test fix
* Test fixes
* Build fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fixes
* Fixes
* Remove dead code in pom
* More test cleanup
* Docs fix
* Changes
* Fix
* Fixes
* Resolve merge conflicts
* Build update
* Merge build fixes
* Version bump
* Address review comments
* Review comments
* Review comments
* Test fixes
* Test fix
* Cleanup
* init rev
* id to jpa and mongo id
* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods
* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods
* fixed conflicts, pulled from master
* fixed code for passing tests successfully
* changed PersistentId to Jpa in MdmSearchInterceptor
* added the todo comments with questions
* added one more question
* renamed TODO questions
* first pass at converting to generic ResourcePersistentId
* fix test
* fix test
* fix test
* make ResourcePersistentId abstract
* Generic type MdmLink
* Final TODOs
* Final TODOs
* cleanup
* fix test
* fix id to string
* fix cyclic package dep
* add <?> to Base so we can extract interface
* Revert "add <?> to Base so we can extract interface"
This reverts commit a806f3d2bc.
* switch to interface
* javadoc
* replace base with interface
* fix test
* add generic template to mdmdao
* remove unneccessary JpaPid casts
* remove unneccessary JpaPid casts
* remove unneccessary JpaPid casts
* remove unneccessary MongoPid casts
* fix test
* fix regression
* fix compile issues arising from merging master
* fix beans
* bump version to 6.3.3-SNAPSHOT
* change logs
* review feedback
* review feedback
* fixme
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Improve JPA response messages
* FIxes
* Test fixes
* Test fixes
* Ongoing testing
* Work on messages
* Work on messages
* Add valueset
* Add response code enum
* Version bump
* Undo bump
* Improve changelog
* Test fixes
* Add javadocs
* Version bump HAPI
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Account for review changes
* Test fix
* Docs fix
* Work on API
* Improve SqlQuery api
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix broken test
* Smile 4892 DocumentReference Attachment url (#4237)
* failing test
* fix
* increase test Attachment url size to new max
* decrease limit to 500
* ci fix
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Overlapping SearchParameter with the same code and base are not allowed (#4253)
* Overlapping SearchParameter with the same code and base are not allowed
* Fix existing tests according to changes
* Cleanup dead code and remove related tests
* Version Bump
* ignore misfires in quartz
* Allowing Failures On Index Drops (#4272)
* Allowing failure on index drops.
* Adding changeLog
* Modification to changelog following code review.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Revert "ignore misfires in quartz"
This reverts commit 15c74a46bc.
* Ignore misfires in quartz (#4273)
* Reindex Behaviour Issues (#4261)
* fixmes for ND
* address FIXME comments
* fix tests
* increase max retries
* fix resource id chunking logic
* fix test
* add modular patient
* change log
* version bump
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Set official Version
* license
* Fix up numbers
* Fix up numbers
* Update numbers
* wip
* fix numbers
* Fix test:
* Fix more tests
* TEMP FIX FOR BUILD
* wip
* Updating version to: 6.2.1 post release.
* Add a whack of logging
* wip
* add implementation
* wip and test
* wip
* last-second-fetch
* expose useful method
* remove 10000 limit
* Strip some logging
* Fix up logging
* Unpublicize method
* Fix version
* Make minor changes
* once again on 6.2.1
* re-add version enum
* add folder
* fix test
* DIsable busted test
* Disable more broken tests
* Only submit queued chunks
* Quiet log
* Fix up checkstyle
* log to console
* Remove double import
* Version bump
* licenses
* Fix up version
* fix build
* wip
* wip
* Fix up search expansion to use new behaviour of idhelper service
* Fix up MDM Search Expansion
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* started converting System.setProperty to HapiSystem
* added a couple more. renamed class
* all the setProperty calls done
* finished System.getProperty()
* Split HapiSystemProperties into HapiSystemProperties and HapiTestSystemProperties
* Javadoc
* Javadoc
* review feedback
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Extracting a Cache interface and building service loaders for Caffeine and Guava
* Fix estimated size interface
* Use LoadingCache when needed.
* Removing Caffeine from dependency lists.
* Adding hapi-fhir-cache-caffeine as a test dependency
* Putting caching solutions in a single module.
* Fixing the spacing
* Standardizing the use of TimeUnits
* Making a new module to simplify the switch of the cache library in tests.
* Making sure the Guava design matches the behavior of Caffeine.
* Making sure the Cache structure also does not throw InvalidCacheLoading exception to match the LoadingCache.
* Renaming module names for the caching group.
* Better error handing that informs devs what to do.
* Improving documentation
* Typo
* Matching error message design with Caffeine.
* Matching the behavior of Caffeine with Guava
* Final adjustments for the test dependencies on the cache modules.
* Fixing relative pom path.
* Adding caffeine as a testing requirement for the new modules.
* Add changelog and set JPA server to use caffeine cache
* POM fixes
* Build fix
* Buid fix
* Fixes
* Address review comment
* One more cache
* Move changelog to next release
* Update pom versions
* Build fix
* Build fixes
* Build fix
* Try to get build working
* Experiment with failing build
* Rever change
* Fix POM version
* Build fix
* Build fix
* Add Msg.code to new exceptions
Co-authored-by: Vitor Pamplona <vitor@vitorpamplona.com>
* POST release deferred cleanup
* Fixes
* One more test fix
* Test fixes
* Test fixes
* Test cleanup
* Test fixes
* Fixes
* ValueSet cleanup
* Test fix
* Test fixes
* Fixes
* Test fixes
* Fixed
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixc
* Build fix
* Fix merge artifact
* Build fix
* Work on tests
* Test fixes
* Work
* Fixes
* Changelog fix
* Add changelog
* Test fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Tests
* Bumps
* Fixes
* Add errorprone
* Drop bz2 bins
* POM fix
* Build fix
* Update
* Test fix
* Fix tests
* Add changelog
* Test fix
* Avoid intermittent
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* POST release deferred cleanup
* Fixes
* One more test fix
* Test fixes
* Test fixes
* Test cleanup
* Test fixes
* Fixes
* ValueSet cleanup
* Test fix
* Test fixes
* Fixes
* Test fixes
* Fixed
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixc
* Build fix
* Fix merge artifact
* Build fix
* Work on tests
* Test fixes
* Work
* Fixes
* Changelog fix
* Add changelog
* Test fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Tests
* Bumps
* Fixes
* Add errorprone
* Drop bz2 bins
* POM fix
* Build fix
* Update
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix
* Bump HAPI version
* Remove jetbrains
* Fix broken test
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add loinc upload handler to process MAP_TO properties.
* Move test to test folder
* Fix mapto file location property name
* Allow override as full loinc upload tests take (much) longer than defined timeout
* Move handler later to make sure all concepts were added to map
* Update test to check all project enhancements
* Restore project unrelated changes
* Rename base test class properly and move to right package
* Condition MapTo.csv file processing to file presence for backwards as file is optional
* Document and annotate test-only usage for disabling deferred tasks timeout
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* added aggregate function to the sort columns, as the sql will not work on other dbs other than H2 that use order by
* rename parameter to make it more meaningful
* extract parameter to a field
Co-authored-by: Steven Li <steven@smilecdr.com>
michaelabuckley
Tadgh
Luke deGruchy
James Agnew
markiantorno
Nathan Doef
Isaac Wen
TipzCM
Ken Stevens
Qingyixia
Justin McKelvy
William Denton
karneet1212
Kevin Dougan SmileCDR
kateryna-mironova
jmarchionatto
samuelwlee2
StevenXLi