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* Resolve merge * Rename rule validation helper * Estimands analysis population cross reference * Fix failing tests * Revert the changes to the study data json V5 * estimand.interventions cross references * StudyDesignDto.studyInterventionIds * study design entity interventions refactor * ref integrity validation * Revert organization scope studyDataV5 changes * Reference integrity for StudyDesign.StudyInterventionIds * Add Organizations to StudyVersion * Identifier Scope cross reference Dto * AssignedPerson.OrganizationId cross ref * Assigned person organization cross ref * ProductOrganizationRole OrganizationID cross ref * StudyRole ORganization ID cross ref * Revert change to studyData json * Add studydesign.documentVersion cross reference * Reverse changes to StudyDataV5.json * Update DTOs * Update study design entity * StudyVersion.NarrativeContentItems master copy * Add missing master copies of collections * Estimand cross refs * administration cross ref * analysis population cross ref * Move conditions list (dto) * move bcSurrogates (dto) * Move BcCategories (dto) * Move dictionaries (dto) * Move conditions (entity) * Move bcSurrogates (entity) * Move bcCategories (entity) * Move dictionaries (entity) * Another cross ref * CriterionIdemId cross ref * IndicationIds cross ref * subject enrollment cross ref * Update IdentifierEntity to use scope cross ref * Fix circular loop in Substance validator * Fix nullable HttpContext in ApiBehaviourOptionsHelper * Remove accidentally added line in test class * Update develop,yml to use GHCR * Fix broken Constants file * Fix build and unit tests * Develop.yml - combine jobs * Develop.yml - correct Docker build * Develop.yml - better step names * Integrate CDISC Rules Engine for Rules Validation * Better name for container image * Re-add step to add keyvault details * Fix appsettings.json ConnectionString naming * Address PR comments * Address PR comments * Fix study design elements V5 constants * Fix whitespace * Fix study design elements V5 constants * Add unit tests for Binary Runner * Add validate usdm conformance failure unit tests * Re-use GetPopulationsForAnalysesFromStudyDesign * whitespace * Fix validate usdm conformance json result * Clean up StudyServiceV5 * Revert "Merge branch 'model-cross-refs-scopes' into 1181-CDISC-Rules-Engine" This reverts commit f4854ab, reversing changes made to 0fade59. * Update error response * Add cdisc rules engine to dockerfile * Update target framework to dotnet 8 * Update runtime image to work with rules engine expected python version * Fix non-ascii escape handling * Fix incorrect logging and variable name * Add ValidateUsdmConformance to Post and Put study methods * Add cdisc rules engine relative cache * Remove App Insights and usage reports * Remove routes * Remove token routes * Remove Azure Service Bus * Clean up remaining Azure dependencies * Clean up * Remove Azure AD packages * Fix non-root user missing home dir * Remove non-root user * Fix CDISC Rules Engine paths env vars * Fix common repo mongodb errors * Pass cdisc rules engine latest release url as env This will allow us to use our temporary forked binary before cdisc release updated binary with performance enhancements * Update build args * Update vars context * Fix env var name * Move change audit data filter from v2 to common * Remove V2 api endpoints and code * Add process change audit * Add process change audit to study service v3, v4, and v5 * Remove Azure Function project * Fix logging method names * Avoid nested .First() calls in mongo LINQ projection * mike's fixed cdisc pliot usdm 4 data * Fix Range model to use Quantity entities/dtos * Remove unused data * Fix USDM Version to v4 * Code cleanup * Fix merge branch 'model-cross-refs-scopes' * md changes * Fix method names * md update * Add back missing function * fix method name * fix method names * Revert "Merge pull request #534 from transcelerate/1024-InterventionalStudyDesign-CPT-mapping" This reverts commit 4bd828a, reversing changes made to add25cc. * Progress made on fixing tests * Fix last test * Rename build API container image to include 'ddf' * Remove unused GitHub Actions * Allow warnings (partially executable rules) for post/put study * Fix studyIdentifiers map to commonStudyIdentifiers for search * Fix unit tests * Update ignore casing for executability value * Add default USDM Version mapping string to API image * Search title fix * Update quantity range abstract class * Add administrations attribute for study intervention * Update documentation * Change BlindingSchema data type * Update study design abstract class * Update identifier abstract class * Update syntax template abstract class * Update abstract classes * Fix PrimaryPurpose and InterventionModel on V5 studies ecpt * Fix numberOfParticipants by handling Quantity entities * ecpt recognises SPONSOR as a sponsor ID * Use IsSponsorDecode helper * Use IsSponsorDecode helper * Fix search with sponsor Id query bug * Add null check for sponsor Id * Include Interventional study design in search response * Revert "Use IsSponsorDecode helper" This reverts commit ca521c2. * Updated the V5 methods of datafiltercommon * Revert "Updated the V5 methods of datafiltercommon" This reverts commit 8608a1f. * Use valid mongo C# driver query * Ignore extra fields * Update sponsor decode * Get value from min and max * Fix V5 intervention model filtering * Remove observationalStudyDesign from filter * Update API docs * Update readme * Update readme * Fix quotes * SDR v5 Release (#537) * Move biomedical concepts to study design * Move organization data into studyIdentifiers data directly * Move analysisPopulation to Estimands * Set default rule level cascade mode to reduce verbosity of code * Rule helper methods to reduce code duplication and verbosity * Refactor common study definitions entity v5 * Update helper unit tests * re-enabled commented out test * Updated some usdm version numbers * Corrected studyElements version numbers * enabled disabled tests * Address comments on study service unit tests * Refactor and add abbreviation validator * Add cascade mode stop for abbreviation errors * Separate errors and warnings * Update study elements and design elements constants * Move to helpers folder * Use severity and error codes for rule validation * Resolve merge * Rename rule validation helper * Estimands analysis population cross reference * Fix failing tests * Revert the changes to the study data json V5 * estimand.interventions cross references * StudyDesignDto.studyInterventionIds * study design entity interventions refactor * ref integrity validation * Revert organization scope studyDataV5 changes * Reference integrity for StudyDesign.StudyInterventionIds * Add Organizations to StudyVersion * Identifier Scope cross reference Dto * AssignedPerson.OrganizationId cross ref * Assigned person organization cross ref * ProductOrganizationRole OrganizationID cross ref * StudyRole ORganization ID cross ref * Revert change to studyData json * Add studydesign.documentVersion cross reference * Reverse changes to StudyDataV5.json * Update DTOs * Update study design entity * StudyVersion.NarrativeContentItems master copy * Add missing master copies of collections * Estimand cross refs * administration cross ref * analysis population cross ref * Move conditions list (dto) * move bcSurrogates (dto) * Move BcCategories (dto) * Move dictionaries (dto) * Move conditions (entity) * Move bcSurrogates (entity) * Move bcCategories (entity) * Move dictionaries (entity) * Another cross ref * CriterionIdemId cross ref * IndicationIds cross ref * subject enrollment cross ref * Update IdentifierEntity to use scope cross ref * Fix circular loop in Substance validator * Fix nullable HttpContext in ApiBehaviourOptionsHelper * Remove accidentally added line in test class * Update develop,yml to use GHCR * Fix broken Constants file * Fix build and unit tests * Develop.yml - combine jobs * Develop.yml - correct Docker build * Develop.yml - better step names * Integrate CDISC Rules Engine for Rules Validation * Better name for container image * Re-add step to add keyvault details * Fix appsettings.json ConnectionString naming * Address PR comments * Address PR comments * Fix study design elements V5 constants * Fix whitespace * Fix study design elements V5 constants * Add unit tests for Binary Runner * Add validate usdm conformance failure unit tests * Re-use GetPopulationsForAnalysesFromStudyDesign * whitespace * Fix validate usdm conformance json result * Clean up StudyServiceV5 * Revert "Merge branch 'model-cross-refs-scopes' into 1181-CDISC-Rules-Engine" This reverts commit f4854ab, reversing changes made to 0fade59. * Update error response * Add cdisc rules engine to dockerfile * Update target framework to dotnet 8 * Update runtime image to work with rules engine expected python version * Fix non-ascii escape handling * Fix incorrect logging and variable name * Add ValidateUsdmConformance to Post and Put study methods * Add cdisc rules engine relative cache * Remove App Insights and usage reports * Remove routes * Remove token routes * Remove Azure Service Bus * Clean up remaining Azure dependencies * Clean up * Remove Azure AD packages * Fix non-root user missing home dir * Remove non-root user * Fix CDISC Rules Engine paths env vars * Fix common repo mongodb errors * Pass cdisc rules engine latest release url as env This will allow us to use our temporary forked binary before cdisc release updated binary with performance enhancements * Update build args * Update vars context * Fix env var name * Move change audit data filter from v2 to common * Remove V2 api endpoints and code * Add process change audit * Add process change audit to study service v3, v4, and v5 * Remove Azure Function project * Fix logging method names * Avoid nested .First() calls in mongo LINQ projection * mike's fixed cdisc pliot usdm 4 data * Fix Range model to use Quantity entities/dtos * Remove unused data * Fix USDM Version to v4 * Code cleanup * Fix merge branch 'model-cross-refs-scopes' * md changes * Fix method names * md update * Add back missing function * fix method name * fix method names * Revert "Merge pull request #534 from transcelerate/1024-InterventionalStudyDesign-CPT-mapping" This reverts commit 4bd828a, reversing changes made to add25cc. * Progress made on fixing tests * Fix last test * Rename build API container image to include 'ddf' * Remove unused GitHub Actions * Allow warnings (partially executable rules) for post/put study * Fix studyIdentifiers map to commonStudyIdentifiers for search * Fix unit tests * Update ignore casing for executability value * Add default USDM Version mapping string to API image * Search title fix * Update quantity range abstract class * Add administrations attribute for study intervention * Update documentation * Change BlindingSchema data type * Update study design abstract class * Update identifier abstract class * Update syntax template abstract class * Update abstract classes * Fix PrimaryPurpose and InterventionModel on V5 studies ecpt * Fix numberOfParticipants by handling Quantity entities * ecpt recognises SPONSOR as a sponsor ID * Use IsSponsorDecode helper * Use IsSponsorDecode helper * Fix search with sponsor Id query bug * Add null check for sponsor Id * Include Interventional study design in search response * Revert "Use IsSponsorDecode helper" This reverts commit ca521c2. * Updated the V5 methods of datafiltercommon * Revert "Updated the V5 methods of datafiltercommon" This reverts commit 8608a1f. * Use valid mongo C# driver query * Ignore extra fields * Update sponsor decode * Get value from min and max * Fix V5 intervention model filtering * Remove observationalStudyDesign from filter * Update API docs * Update readme * Update readme * Fix quotes --------- Co-authored-by: Jon Masson <jonathan.masson@capgemini.com> Co-authored-by: jonmassoncap <118985141+jonmassoncap@users.noreply.github.com> Co-authored-by: Matt Kendall <mattk91@gmail.com> Co-authored-by: Matt Kendall <matthew.kendall@tessella.com> * Change medical device notes cardinality * Add files via upload Errata update. * Update SMG to v2.1 * Remove old SMG * Update and rename ddf-sdr-api-study-cdisc-pilot-sample-json-v5.0.json to ddf-sdr-api-study-cdisc-pilot-sample-usdm-v4json Updated with latest USDM 4.0 conformance. * Rename ddf-sdr-api-study-cdisc-pilot-sample-usdm-v4json to ddf-sdr-api-study-cdisc-pilot-sample-usdm-v4.json * Update and rename ddf-sdr-api-study-observational-sample-json-v3.0.json to ddf-sdr-api-study-observational-sample-usdm-v4.json * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Update README.md * Update README.md * Add files via upload * Update README.md * Add files via upload * Update README.md * Fix #1226 Handle Study Identifiers null Scope Id * Fix #1227 Study Search Sort By Study Title Error * Update SMG to v2.2 (#588) * Move timelineExit and timeline properties to ScheduledActivityInstance class (#593) * Set AdministrableProduct identifiers property to an empty array when missing in json data (#594) --------- Co-authored-by: Jon Masson <jonathan.masson@capgemini.com> Co-authored-by: Matt Kendall <mattk91@gmail.com> Co-authored-by: Matt Kendall <matthew.kendall@tessella.com> Co-authored-by: jonmassoncap <118985141+jonmassoncap@users.noreply.github.com> Co-authored-by: mikerippin <106111791+mikerippin@users.noreply.github.com>
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Fixes https://github.com/transcelerate/ddf-sdr-backlog/issues/1229