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IP-3074 - Documentation discrepancies #449
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* Catalog Variable Set created
* TumourPresentation/PrimaryOrMetastatic moved to Tumour
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* Catalog Variable Set created
* TumourPresentation/PrimaryOrMetastatic moved to Tumour
…ies' into IP-3074/documentation-discrepancies # Conflicts: # protocols/catalog_variable_set/v7.3/Referral.catalog_vs.json
kenanM
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Antonior26
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* Changes for NGIS + Exit Questionnaire for CNV and STRs * test fixed * setting indentation right!! * refactor referrals * change diagnostic details to a list * fix typos + rename UID * add consent * added flags for CNVs and participant flags * bringing back old consent status and renaming the new one to GmsConsentStatus * Updated NGIS model to include ClinicalIndication,and updated Organisation. Updated CommonParticipant to have ClinicalIndication * Clinical Indication test and technology refactored in records * Updated TumourSample from clinical discussion with Clare Craig, Alona Sosinsky, Antonio Rueda Martin. Added diseasePenetrance at referralTestlevel from request by Ellen Thomas for NGIS * Update dependency manager for VERSION_72 * Added preparationMethod LI_HEP * updated HPOTermModifiers and preparationMethod * added technology and test clinical indication to test * fixed bug with Technology being used before declared * removed duplication of clinicalindicationtest field * Updates to reflect DDF->CDI Clinical Review Meeting * Updated NGIS models with tumour record, updated cancer model * all records using date with exception of clinicalSampleDate have been normalised using the Date record * updated Date record to use int instead of string * updated typo in TumourTopography * Updated Tumour Sample and Germline Sample comprehensively from meetings with Cancer and RD clinicians * Updated NgisTumourType due to typo * Updated CommonParticipant due to typo * Updated Ngis ReferralTest to be tumourSample instead of somaticSample * Update Storage Medium to include FFPE * * Changed CVA 1.2 to 1.3 as 1.2 exists already in develop * Changed build version to 7.3 * * corrected build.json after merge * case in date's fields corrected * * Added 7.3 to json and added python modules * Add NGIS Germline and Tumour sample variablesets (#439) * fixed typo * Fixed Tumour.tumourType use NgisTumourType enum * Updated Priority Enum to reflect DDF payload * IP-3074 - Documentation Discrepancies (#443) * catalog referral model after changes * * Fixes describe in IP-3074 * Catalog Variable Set created * * typos * * version changed * IP-3074 - Documentation discrepancies (#449) * catalog referral model after changes * * Fixes describe in IP-3074 * Catalog Variable Set created * * typos * * version changed * * IndividualId changed to ParticipantId * TumourPresentation/PrimaryOrMetastatic moved to Tumour * * Fixes describe in IP-3074 * Catalog Variable Set created * * IndividualId changed to ParticipantId * TumourPresentation/PrimaryOrMetastatic moved to Tumour * removed unneeded spaces * Added GMS (testConsent) to the cancer and rd participant models (#450) * Added GMS (testConsent) to the cancer and rd participant models * Added collection to referral payload, Morphology and Topography use now a property like format. * Requested changes * added version for ontology in morphology and topography (#454) * Add three new models for the new summary.csv files to be delivered by illumina as part of NGIS (#453) * IP-3485 - GMS DDF fixes + Cancer Diagnosis addition (#469) * * Fixes for DDF raredisease * Addition of Cancer Diagnosis * consolidating participant ID and individual ID in Cancer Participant * IP-2482: update docker images to match develop branch which works * sets the right java build version * fix cva versioning * Revert "fix cva versioning" This reverts commit 0491b0f. * some refactoring to CVA models * refactor cva models
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