update transform provider #780
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sliver007
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* Fhir Implementations * Fhir Implementations * APHL-303 Updated JPA and Repository logic * Updated logic for JPA code to connect to APHL UI * Updated to cqframework version 1.5.11-SNAPSHOT; added cqf-fhir dependency in cql plugin * APHL-303-Fhir-Implementation-Updates * Added the RepositoryService to the CqlConfig * APHL-303 Updated logic for configuring operation * APHL-303 FHIR implementation updates for operation * APHL-303 FHIR Implementation for operation addition * Changed RepositoryService to use r4 resources * APHL-303 Fhir Implementation code for repository service updated logic * APHL-305 Updated logic for release operation * KnowledgeArtifact infrastructure and newVersion implementation to use it * APHL-303 Updates for backend for release and publish operations * APHL-303 Updates for backend for draft operation and canonical logic * Updates for test classes and java 11 * Added operation and injections to config ... added psuedo code for basic operation pattern ... cleaned up operation definitions * Added logic for release and publish operations and tests * Reinstating evaluator FhirDal factory ... updating measure evaluation ... making repository service and associated beans R4 conditional * Updated draftOperation test * Fixed FhirDal search and draft test * Renamed 'newVersion' method to 'draft' * Removed unused imports in JpaFhirDal * Fhir-Implementation-Duplicate-Fix * Updated $draft operation signature and added some validation * Update RepositoryService.java * Fhir Implementation changes for revise * $revise operation changes * Updated $publish operation * Updated draft and revise operation tests * Fhir-Implemenmtation updates for tests * Fhir_Implementation logic updates for test code * Fixed $draft status constraint exception message * Fhir-Implementations-draft-operation-defect * Updates to $draft operation to strip versions on references and on resource drafts * Updated resources * updated $draft test resource and removed unused imports * Updated the Cql FhirDal to implement Translator FhirDal and introduce JpaCRFhirDal for CR plugin * updated fhirContext used by JpaFhirDal * Updated revise operation * Updates to use evaluator utils * Fixed KnowledgeArtifactTest parameters imports * Removed revise and publish operations from this branch * Remove Publish and Revise operations; Draft now throws if a draft already exists. * updated draft bundle so that resources are different from those of that active test bundle to avoid collisions. * Update KnowledgeArtifactProcessor.java * Restored $revise operation * Fhir-Implementations-Updates * Reverted previous commit's changes to RepositoryServiceTest * Refactor of $release operation * Fhir-Implementation-Updates * KnowledgeArtifactAdapter components and dependencies refactor * Adapter getComponents, getDependencies; reviseOperation test * Fhir-Implementations-Updates * Move BooleanType to boolean conversion up a layer; commented out Release operation test. * Aphl 475 approve operation (#691) * [aphl-475] implementation of $approve operation in KnowledgeArtifactProcessor --------- Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * $release operation updates for version pinning * Removed unused import. * Fhir-Implementations-Updates * Fixed a couple of bugs in version validation * $release updates - param names match spec * Updated text cases for $release name changes * Release operation updates (#698) * Update KnowledgeArtifactProcessor.java * [APHL-546] Implementation of artifactAssessment and updating $approve to create Artifact Comments as ArtifactAssessment resources (#697) * [APHL-546] WIP implementation of artifactAssessment * [APHL-546] updated knowledgeArtifactProcessor to use artifactAssessment * [APHL-546] Approve operation and tests updated, ArtifactAssessment implementation still incomplete * [APHL-546] approve operation working and tests final, ArtifactAssessment still WIP * [APHL-546] NPE * [APHL-546] cleanup style errors and match ArtifactAssessment implementation to StructureDefinition * [APHL-549] updated $approve to create a reference instead of using canonical * [APHL-546] minor changes, update to test method * Fixed date filter test cases in DataOperationProviderIT --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Fix bad $approve tests (#702) tests couldn't fail Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 535 rebase to vsm operations (#704) * [APHL-535][APHL-481] Made $draft transactional and updated to allow multiple drafts * Add null check on version argument of $draft; updated $draft test cases to avoid ValueSet collisions --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * [APHL-546] fix bad target canonical handling in $approve (#710) Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Fixed release operation validation messages - made parameter names consistent with actual param names * Update RepositoryServiceTest.java * Updated $release operation parameter names to camelCase * [APHL-584] update backend to remove endorser (#714) * [APHL-584] update backend to remove endorser * [APHL-584] remove $release tests until we update the operation --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * $approve fixed and new test added to ensure it won't block $release (#716) Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 305 release operation (#720) * [APHL-305] release operation with limited tests * [APHL-305] release operation tests * [APHL-305] added dependency and component test * [APHL-305] $release tests completed --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 608 is owned and effective period (#727) * [APHL-305] release operation tests * [APHL-305] added dependency and component test * [APHL-608] isOwned checking and effectivePeriod propagation * [APHL-608] added some notOwned relatedArtifact Components for testing and updated draft to use isOwned * [APHL-608] updated tests and handling of relatedArtifacts * [APHL-608] remove deprecated methods --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * simplify version update logic in $release (#732) * [APHL-608] style edit * [APHL-608] simplified version checking logic for relatedArtifacts * removed unused method --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * [APHL-630] update to ci cd (#731) * [APHL-630] Additional CI job to generate and publish Docker image based on vsm-operations branch --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 630 ci cd update - version fix (#733) * [APHL-630] update to ci cd * [APHL-630] different jobs for master and vsm-operations branches --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 630 ci cd update (#734) * [APHL-630] update to ci cd * [APHL-630] different jobs for master and vsm ops * [APHL-630] names * [APHL-630] remove wildcards * [APHL-630] more changes --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 630 ci cd update (#735) * [APHL-630] update to ci cd * [APHL-630] different jobs for master and vsm ops * [APHL-630] names * [APHL-630] remove wildcards * [APHL-630] more changes * [APHL-630] add maven install --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 469 transactional package operation (#737) * MVP Implementation of the $crmi.package operation --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Aphl 655 clear approval date, releaseLabel, releaseDescription (#738) * [APHL-469] minimal package (just search and add to bundle) * [APHL-469] check if entry exists before adding * [APHL-469] get components and dependencies * [APHL-469] added capability support * [APHL-469] move to own function * [APHL-469] everything except packageOnly is in a WIP state * [APHL-469] basic testable implementation * [APHL-469] added test and nicer error messages for Capability * [APHL-469] canonicalVersion, checkCanonicalVersion, forceCanonicalVersion tests complete * [APHL-469] test for `include` * [APHL-469] tests for count, offset * [APHL-469] transactional package tests * [APHL-469] better wording * [APHL-469] pending TODO * [APHL-469] simplified error types * [APHL-655] clear approvalDate * [APHL-655] removed releaseLabel and releaseDescription * Merge branch 'vsm_operations' into aphl-655-clear-approval-date --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * (manual) merge of master * updated submodule reference * Dockerfile ruler-server version update * Update hapi-fhir-jpaserver-starter * Updated the backend CRMI operation names with "crmi." prefix * Aphl 656 propogate new version to artifact assessment (#742) * [APHL-656] WIP update the derived-from relatedArtifact link in ArtifactAssessment * [APHL-659] updated the backend names * [APHL-656] copying extensions instead of casting Basic to ArtifactAssessment * [APHL-656] test complete --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * [Aphl 647] new semver and releaseLabel (#743) * [APHL-647] release label and new versioning scheme Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Release operation experimentalBehavior parameter and handling (#744) added experimentalBehavior parameter to $release operation --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Aphl 731 release operation priority indication (#745) * preserve priority extensions when releasing --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 732 package priority (#746) * Release operation preserves priorities indicated via extension in the root artifact --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Update package operation output to distinguish collection and transaction (#749) * [APHL-778] update package output to distinguish collection and transaction * [APHL-778] Updated tests * [APHL-778] no total for transactions --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Whitespace and convention/style updates * Whitespace and convention updates --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * $validate Operation implementation * [APHL-752] getting NoSuchMethod * Fixing HAPI dependencies; added test for validate operation * [APHL-752] basic validate implementation * [APHL-752] added common codesystems to validation chain * [APHL-752] make validation failures more obvious * [APHL-752] update external dep to use the correct version of r5 * [APHL-752] validate simple implementation * [APHL-752] throw NotImplemented for mode and profile * [APHL-752] add fullUrls to bundles * [APHL-752] update active transaction bundle to pass validation * [APHL-752] update tests * $validate test case for unsatisfied PlanDef slice * [APHL-752] updated test for plandefslice * [APHL-752] validate each entry alone * [APHL-752] add resource fetcher * [APHL-778] update package output to distinguish collection and transaction * [APHL-778] Updated tests * [APHL-752] validate whole bundle * [APHL-778] no total for transactions * [APHL-752] expect extension validation error --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: c-schuler <hoofschu@gmail.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * v2 -> v1 plugin (#748) Added new eCR module with eRSD V2 to V1 conversion operation --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * targetversion parameter for ersd v1 transform * [APHL-788] add targetversion parameter * rename transform module to ecr --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * [APHL-798][APHL-799] Condition useContext management (#752) * [APHL-300] valueset interceptor initial implementation * [APHL-300] preserve useContext extensions when releasing * [APHL-300] package is aware of useContext * [APHL-300] updated to use vsm-specific extension * [APHL-300] fix test * [APHL-300][APHL-798][APHL-799] updates to package and release * [APHL-799] update package validation test for depends-on relatedArtifact * remove interceptor * [APHL-799] update package test data * [APHL-798] preserve all RelatedArtifact extensions to keep it generic * [APHL-799] replace existing useContexts for condition and priority * comments * cleanup * fix bad assignment * simplify * cleanup * [APHL-300] forgot to update reference --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * update jpa * update external * Remove "crmi" operation code prefix (#755) Removed "crmi" operation code prefix; fixed transform provider test case data * updating to latest hapi * compiled ruler with updates, wip * operation migration table in readMe * RepositoryService $draft operation not clears out effectiveperiod (#758) * [APHL-784] update test * [APHL-784] remove effective period as part of draft operation * [APHL-784] update test to account for all owned resources * update version --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * [APHL-780] initial implementation (#751) * [APHL-750] initial implementation * [APHL-750] draft implementation with Parameters tree * [APHL-750] cache and remove duplicates * [APHL-750] fix draft bug where dependencies pointing at owned resources were not updated * [APHL-750] fix draft issues * [APHL-780] fix tests * [APHL-780] updated test and test data, now handling gaps in reference lists * [APHL-780] updated addition deletion logic * [APHL-780] temporarily expand ValueSets as part of diff * [APHL-780] refactoring * [APHL-780] fix array indices on output * [APHL-780] update test data and tests * [APHL-780] fix tests and test cases * [APHL-780] remove extra file * [APHL-780] cleanup * [APHL-780] cleanup * [APHL-780] implement cloneable * [APHL-780] remove namespace * [APHL-780] remove crmi namespace * Updated test case to use new forEachMetadataResource method introduced by previous merge. --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * [APHL-798][APHL-799] release and package should throw an error if a ValueSet doesn't have a condition (#756) * [APHL-798][APHL-799] updated tests * [APHL-798][APHL-799] updating tests * [APHL-798][APHL-799] updating tests * [APHL-798][APHL-799] updating tests * [APHL-798][APHL-799] update test data * update test data versions --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Aphl 796 update package parameters (#759) * [APHL-796] match package operation to specification * [APHL-796] update names --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Aphl 582 move to hapifhirrepository (#760) * [APHL-582] initial implementation * [APHL-582] fix tests * [APHL-582] Cleanup * [APHL-582] cleanup * [APHL-582] cleanup * merge conflicts * [APHL-582] Cleanup * Address spotbugs error * Fixed a few issues related to the update of the $package operation parameters * [APHL-582] fix NPE --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Aphl 830 test data (#761) * [APHL-830] update test data * [APHL-830] active program needs active groupers * [APHL-830] add condition text * Updated versions in test bundles (#765) --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <adam.stevenson@smiledigitalhealth.com> * [APHL-551] update cqf-ruler to use clinical-reasoning * [APHL-551] update tests to get rid of weird concurrency issue * [APHL-551] cleanup * [APHL-551] undo changes to ifNoneExist * [APHL-551] update pom * Add common getExpansion() function (#763) * Add common getExpansion() function * Mock out server calls * Specify charset * Add TerminologyServerClient Bean to config * Refactor - make client non VSAC specific & add statuc variables * getExpansion changes * Refactor - take credentials from properties, cleanup, add IT * Fix issue with authoritative source url and system-version parameter Update test file to reflect actual value set * Remove addition of ValueSet level system-version param & update test to reflect. Privatise getters/setters. --------- Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * [APHL-551] update pom * Aphl 300 valueset interceptor (#757) * ValueSet update interceptor for updating code synonyms --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> * Update dependency versions * Delete unused code * Update to br-cs-merged code * More dependency cleanup * Update to use MR cache * Whoops, didn't mean to override * More dependency fixes * Update github actions * jacoco * Fix integration tests * Fixing tests * Various test fixes and updates * WIP, fixing tests * Disable extract provider and fix extract tests * Fixing tests * Update to latest jpaserver-starter branch * Remove extract provider * wip ra * Update the Readme with migration status of operations * Fix cds hooks test * Update eCR plugin * removing RA plugin due to spec changes that are not implemented * removing failing tests, re-adding RA module * Fix up ecr poms * Remove unused transform provider * Merge ecr plugin into case reporting * remove broken submodule * Update to latest br-cs-merged branch * Move RepositoryService and KnowledgeArtifactProcessor to case-reporting plugin (#775) * move knowledge artifact processor * - use clinical reasoning utilities - WIP changelog updates * add terminology client * update pom * Move Repository Service and Test * update tests * initial getChangelog test * update changelog to make operations match groupers better * [APHL-309] update changelog tests and fix relatedArtifact extensions diff --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Aphl 300 move valueset interceptor to plugin (#777) * [APHL-300] move the interceptor to case-reporting * cleanup --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * Replace RepositoryService with CaseReportingOperationProvider * update transform provider (#780) Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * [APHL-551] fix test failures (#781) Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * APHL-913-add_grouper_type_use_context (#782) * add group type to groupers that do not have them while importing --------- Co-authored-by: Ivan Baisi <ivan.baisi@smiledigitalhealth.com> * Fix ExampleServerDstu3IT * Update to latest br-cs-merged branch * Update Launch_Server__Live_Reload_.xml * Test disabling batch jobs and indexing on the DSTU3 tests * Add @DirtiesContext annotation * Throwing more at the wall * Huh, threading be tough * Use the maven wrapper * update to clinical-reasoning snapshot and fix approve variable names * flaky async test is fixed downstream * remove case-reporting now that it's migrated to aphl-vsm * Adding test ordering to prevent singleton list error stemming from repository including patient from bundle and server --------- Co-authored-by: Hayes Murdock <hayesmurdock@Hayess-MacBook-Pro-Alphora.local> Co-authored-by: Hayes Murdock <hayes@alphora.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com> Co-authored-by: c-schuler <hoofschu@gmail.com> Co-authored-by: Hayes Murdock <hayes.murdock@smilecdr.com> Co-authored-by: Taha <TahaAttari@users.noreply.github.com> Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <adam.stevenson@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: Adam Stevenson <adam.stevenson@smiledigitalhealth.com> Co-authored-by: Chris0296 <38321098+Chris0296@users.noreply.github.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Ivan Baisi <i.baisi@gmail.com> Co-authored-by: Ivan Baisi <ivan.baisi@smiledigitalhealth.com>
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