From 6876f3f4487c68880ee45c6a79818c35ece62bcb Mon Sep 17 00:00:00 2001 From: Michael Lescisin Date: Tue, 24 Oct 2023 16:00:13 -0400 Subject: [PATCH] CARDS-2317: Split CARDS into multiple projects Remove the LFS project from the Core CARDS repository --- lfs-resources/clinical-data/pom.xml | 83 - .../cards/resources/media/lfs/background.jpg | Bin 68531 -> 0 bytes .../libs/cards/resources/media/lfs/logo.png | Bin 10465 -> 0 bytes .../resources/media/lfs/logo_light_bg.png | Bin 10145 -> 0 bytes .../content/Questionnaires/Chemotherapy.xml | 705 ------ .../Questionnaires/Patient information.xml | 1917 ----------------- .../content/Questionnaires/Radiotherapy.xml | 867 -------- .../content/Questionnaires/Tumors.xml | 1739 --------------- .../content/Statistics/AgeOfOnset.xml | 48 - .../content/Statistics/AgeOfOnsetByGender.xml | 53 - .../content/Statistics/TumorLocation.xml | 48 - .../Statistics/TumorLocationByGender.xml | 53 - .../content/libs/cards/conf/AppName.json | 4 - .../content/libs/cards/conf/Media.json | 6 - .../content/libs/cards/conf/ThemeColor.json | 4 - lfs-resources/feature/pom.xml | 32 - .../feature/src/main/features/feature.json | 49 - lfs-resources/pom.xml | 39 - lfs-resources/tissue-metrix/pom.xml | 48 - .../content/Questionnaires/TissueMetrix.xml | 751 ------- pom.xml | 1 - 21 files changed, 6447 deletions(-) delete mode 100644 lfs-resources/clinical-data/pom.xml delete mode 100644 lfs-resources/clinical-data/src/main/media/SLING-INF/content/libs/cards/resources/media/lfs/background.jpg delete mode 100644 lfs-resources/clinical-data/src/main/media/SLING-INF/content/libs/cards/resources/media/lfs/logo.png delete mode 100644 lfs-resources/clinical-data/src/main/media/SLING-INF/content/libs/cards/resources/media/lfs/logo_light_bg.png delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Chemotherapy.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Patient information.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Radiotherapy.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Tumors.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnset.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnsetByGender.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocation.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocationByGender.xml delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/AppName.json delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/Media.json delete mode 100644 lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/ThemeColor.json delete mode 100644 lfs-resources/feature/pom.xml delete mode 100644 lfs-resources/feature/src/main/features/feature.json delete mode 100644 lfs-resources/pom.xml delete mode 100644 lfs-resources/tissue-metrix/pom.xml delete mode 100644 lfs-resources/tissue-metrix/src/main/resources/SLING-INF/content/Questionnaires/TissueMetrix.xml diff --git a/lfs-resources/clinical-data/pom.xml b/lfs-resources/clinical-data/pom.xml deleted file mode 100644 index 5390350a14..0000000000 --- a/lfs-resources/clinical-data/pom.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - - 4.0.0 - - - io.uhndata.cards - lfs-resources - 0.9.22-SNAPSHOT - - - lfs-resources-clinical-data - bundle - LFS Resources - Clinical Data - - - - - - org.apache.felix - maven-bundle-plugin - true - - - {maven-resources},src/main/media - - SLING-INF/content/libs/cards/conf/AppName.json;path:=/libs/cards/conf/AppName;overwrite:=true, - SLING-INF/content/libs/cards/conf/ThemeColor.json;path:=/libs/cards/conf/ThemeColor;overwrite:=true, - SLING-INF/content/libs/cards/resources/media/lfs/;path:=/libs/cards/resources/media/lfs/;overwrite:=true;uninstall:=true, - SLING-INF/content/libs/cards/conf/Media.json;path:=/libs/cards/conf/Media;overwriteProperties:=true, - SLING-INF/content/Questionnaires/;path:=/Questionnaires/;overwriteProperties:=true;uninstall:=true;checkin:=true, - SLING-INF/content/Statistics/;path:=/Statistics/;overwrite:=false;uninstall:=true, - - - - - - - - - - ${project.groupId} - cards-patient-subject-type - ${project.version} - runtime - - - ${project.groupId} - cards-tumor-subject-type - ${project.version} - runtime - - - ${project.groupId} - cards-tumor-region-subject-type - ${project.version} - runtime - - - ${project.groupId} - cards-variants - ${project.version} - runtime - - - diff --git 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zrfQd{JonM-{g@>F;3$cCdRV_-g$I(QpU3eg&a^J5J6zVi)Lva?P}Vv@Y0jDKC6dd> z&{f%itvFobXoB+KzWBDsL!5k0hOoJPp8pK|E)lrxh6QZy*Z-0ZgSf~$o75MY zjzr;wX*J2szv2IxW5vYo;Gt9bJ)@Vpm&DoIem$j^_$eCA>`pHs|B8kZmHn&Nvp9#ff6&WKY7NjxEQ2;hz6i@HQ!>&jyB;V>ynyM`+qS zrAs<*U8l|RZv2(Y*86gzryUH!&mHw<3w`#$(-|kjhGnq+sqphg5xxIK{J*wxG}b@U X#U?b*#U!Q{3DcAm)Z}a5K|=lyhXA@7 diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Chemotherapy.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Chemotherapy.xml deleted file mode 100644 index fb64b636f2..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Chemotherapy.xml +++ /dev/null @@ -1,705 +0,0 @@ - - - - Chemotherapy - cards:Questionnaire - - title - Chemotherapy - String - - - requiredSubjectTypes - - /SubjectTypes/Patient - /SubjectTypes/Patient/Tumor - - Reference - - - chemotherapy_section - cards:Section - - chemotherapy - cards:Question - - text - Chemotherapy - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - True - Boolean - - - - - treatment_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - chemotherapy - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - start_date - cards:Question - - text - Chemotherapy start date - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - enableNotes - True - Boolean - - - - protocol - cards:Question - - text - Treatment Protocol - String - - - minAnswers - 1 - Long - - - maxAnswers - 0 - Long - - - dataType - text - String - - - enableNotes - True - Boolean - - - - agent - cards:Question - - text - Chemotherapy Agent - String - - - minAnswers - 1 - Long - - - maxAnswers - 0 - Long - - - dataType - vocabulary - String - - - sourceVocabularies - - CHEBI - - String - - - enableNotes - True - Boolean - - - - weight_at_start - cards:Question - - text - Weight at start of protocol - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - kg - String - - - - height_at_start - cards:Question - - text - Height at start of protocol - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - cm - String - - - - end_date - cards:Question - - text - Chemotherapy end date - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - enableNotes - True - Boolean - - - - - mode_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - chemotherapy - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - mode - cards:Question - - text - Mode - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - Cyclic - cards:AnswerOption - - value - Cyclic - String - - - - Continuous - cards:AnswerOption - - value - Continuous - String - - - - Unknown - cards:AnswerOption - - value - Unknown - String - - - noneOfTheAbove - True - Boolean - - - - - mode_cyclic_details - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - mode - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - Cyclic - - String - - - - - number_of_cycles - cards:Question - - text - Number of cycles - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - enableNotes - True - Boolean - - - - - mode_continuous_details - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - mode - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - Continuous - - String - - - - - total_duration - cards:Question - - text - Total duration - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - months - String - - - - - - dose_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - chemotherapy - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - cumulative_dose - cards:Question - - text - Cumulative dose - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - mg/m² - String - - - enableNotes - True - Boolean - - - - dose_reduction - cards:Question - - text - Dose reduction - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - True - Boolean - - - enableNotes - True - Boolean - - - - - comments_section - cards:Section - - comments - cards:Question - - text - Comments - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Patient information.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Patient information.xml deleted file mode 100644 index 495294b1ce..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Patient information.xml +++ /dev/null @@ -1,1917 +0,0 @@ - - - - Patient information - cards:Questionnaire - - title - Patient information - String - - - requiredSubjectTypes - - /SubjectTypes/Patient - - Reference - - - maxPerSubject - 1 - Long - - - demographics_section - cards:Section - - date_of_birth - cards:Question - - text - Date of birth - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - gender - cards:Question - - text - Gender - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - M - cards:AnswerOption - - label - Male - String - - - value - M - String - - - - F - cards:AnswerOption - - label - Female - String - - - value - F - String - - - - O - cards:AnswerOption - - label - Other - String - - - value - O - String - - - - U - cards:AnswerOption - - label - Unknown - String - - - value - U - String - - - noneOfTheAbove - True - Boolean - - - - - vital_status - cards:Question - - text - Vital status - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - alive and NED - cards:AnswerOption - - value - Alive and NED - String - - - - alive with disease - cards:AnswerOption - - value - Alive with disease - String - - - - dod - cards:AnswerOption - - value - dod - String - - - label - Died of disease - String - - - - U - cards:AnswerOption - - label - Unknown - String - - - value - U - String - - - noneOfTheAbove - True - Boolean - - - - - race_ethnicity - cards:Question - - text - Race/Ethnicity reported - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - list+input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - HANCESTRO - - String - - - vocabularyFilters - cards:VocabularyFilterGroup - - HANCESTRO - - HANCESTRO_0004 - - String - - - - African - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0010 - String - - - label - African - String - - - - Native American - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0013 - String - - - label - Native American - String - - - - Eskimo - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0595 - String - - - label - Eskimo - String - - - - Asian - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0008 - String - - - label - Asian - String - - - - Pacific Islander - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0574 - String - - - label - Pacific Islander - String - - - - Aboriginal Australian - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0552 - String - - - label - Aboriginal Australian - String - - - - Caucasian - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0005 - String - - - label - Caucasian - String - - - description - Also known as European or White - String - - - - Hispanic or Latin American - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0014 - String - - - label - Hispanic or Latin American - String - - - - Indian - cards:AnswerOption - - value - /Vocabularies/HANCESTRO/HANCESTRO_0487 - String - - - label - Indian - String - - - - - - family_section - cards:Section - - family - cards:Question - - text - Family - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - relation_to_proband - cards:Question - - text - Relation to proband - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - list+input - String - - - dataType - text - String - - - Proband - cards:AnswerOption - - value - Proband - String - - - label - This is the proband - String - - - notApplicable - True - Boolean - - - - Mother - cards:AnswerOption - - value - Mother - String - - - - Father - cards:AnswerOption - - value - Father - String - - - - Son - cards:AnswerOption - - value - Son - String - - - - Daughter - cards:AnswerOption - - value - Daughter - String - - - - Brother - cards:AnswerOption - - value - Brother - String - - - - Sister - cards:AnswerOption - - value - Sister - String - - - - Aunt - cards:AnswerOption - - value - Aunt - String - - - - Uncle - cards:AnswerOption - - value - Uncle - String - - - - Niece - cards:AnswerOption - - value - Niece - String - - - - Nephew - cards:AnswerOption - - value - Nephew - String - - - - Cousin - cards:AnswerOption - - value - Cousin - String - - - - Unknown - cards:AnswerOption - - value - Unknown - String - - - noneOfTheAbove - True - Boolean - - - - - pedigree - cards:Question - - text - Pedigree - String - - - dataType - pedigree - String - - - - inherited_from - cards:Question - - text - Inherited from - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - M - cards:AnswerOption - - value - M - String - - - label - Maternal - String - - - - P - cards:AnswerOption - - value - P - String - - - label - Paternal - String - - - - SM - cards:AnswerOption - - value - SM - String - - - label - Suspected Maternal - String - - - - SP - cards:AnswerOption - - value - SP - String - - - label - Suspected Paternal - String - - - - O - cards:AnswerOption - - value - O - String - - - label - Other - String - - - - U - cards:AnswerOption - - value - U - String - - - label - Unknown - String - - - noneOfTheAbove - True - Boolean - - - - - family_history - cards:Question - - text - Family history - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - - diagnosis_section - cards:Section - - reason_for_dx - cards:Question - - text - Reason for Dx - String - - - minAnswers - 1 - Long - - - maxAnswers - 0 - Long - - - displayMode - list - String - - - dataType - text - String - - - enableNotes - True - Boolean - - - NA - cards:AnswerOption - - value - N/A - String - - - notApplicable - True - Boolean - - - - Incidental - cards:AnswerOption - - value - Incidental - String - - - - FHx - cards:AnswerOption - - value - FHx - String - - - - PHx - cards:AnswerOption - - value - PHx - String - - - - Unknown - cards:AnswerOption - - value - Unknown - String - - - noneOfTheAbove - True - Boolean - - - - - date_of_genetic_diagnosis - cards:Question - - text - Date of genetic diagnosis - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - enableNotes - True - Boolean - - - - age_of_genetic_diagnosis - cards:Question - - text - Age of genetic diagnosis - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - years - String - - - - - pathology_section - cards:Section - - age_at_1st_malignant_dx - cards:Question - - text - Age at 1st malignant Dx - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - years - String - - - - total_number_of_lesions - cards:Question - - text - Total number of lesions - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - long - String - - - minValue - 0 - Long - - - - number_of_malignant_tumors - cards:Question - - text - Number of malignant tumors - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - long - String - - - minValue - 0 - Long - - - - comorbidities - cards:Question - - text - Co-morbidities - String - - - description - Non cancerous, including abnormal incidental imaging/labs - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - HP - - String - - - enableNotes - True - Boolean - - - vocabularyFilters - cards:VocabularyFilterGroup - - HP - - HP:0000118 - - String - - - - - - genetics_section - cards:Section - - tp53_variant_cDNA - cards:Question - - text - TP53 variant (cDNA) as stated in file - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - tp53_variant_protein - cards:Question - - text - TP53 variant (protein) as stated in file - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - - c_per_clinvar_2019 - cards:Question - - text - c. per ClinVar 2019 - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - - p_per_ClinVar_2019 - cards:Question - - text - p. per ClinVar 2019 - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - - mutation_pathogenicity - cards:Question - - text - Mutation-Pathogenicity - String - - - minAnswers - 1 - Long - - - maxAnswers - 0 - Long - - - displayMode - list - String - - - dataType - text - String - - - enableNotes - True - Boolean - - - P - cards:AnswerOption - - value - P - String - - - label - Pathogenic - String - - - - LP - cards:AnswerOption - - value - LP - String - - - label - Likely Pathogenic - String - - - - VUS - cards:AnswerOption - - value - VUS - String - - - label - Variant of Unknown Significance - String - - - - VUS_D - cards:AnswerOption - - value - VUS_D - String - - - label - VUS, treated as deleterious - String - - - - LB - cards:AnswerOption - - value - LB - String - - - label - Likely benign - String - - - - B - cards:AnswerOption - - value - B - String - - - label - Benign - String - - - - U - cards:AnswerOption - - value - U - String - - - label - Undetermined - String - - - noneOfTheAbove - True - Boolean - - - - - mutation_function - cards:Question - - text - Mutation-Function - String - - - minAnswers - 1 - Long - - - maxAnswers - 0 - Long - - - displayMode - list - String - - - dataType - text - String - - - enableNotes - True - Boolean - - - fs - cards:AnswerOption - - value - fs - String - - - label - Frameshift - String - - - - fsi - cards:AnswerOption - - value - fsi - String - - - label - Frameshift (small insertion) - String - - - - fsd - cards:AnswerOption - - value - fsd - String - - - label - Frameshift (small deletion) - String - - - - fsid - cards:AnswerOption - - value - fsid - String - - - label - Frameshift (small indel) - String - - - - missense - cards:AnswerOption - - value - Missense - String - - - - missense DN - cards:AnswerOption - - value - Missense DN - String - - - label - Missense, de novo - String - - - - nonsense - cards:AnswerOption - - value - Nonsense - String - - - - splice donor - cards:AnswerOption - - value - Splice donor - String - - - - splice acceptor - cards:AnswerOption - - value - Splice acceptor - String - - - - large insertion - cards:AnswerOption - - value - Large insertion - String - - - - large deletion - cards:AnswerOption - - value - Large deletion - String - - - - synonymous - cards:AnswerOption - - value - Synonymous - String - - - - synonymous splicing - cards:AnswerOption - - value - Synonymous splicing - String - - - - U - cards:AnswerOption - - value - U - String - - - label - Undetermined - String - - - noneOfTheAbove - True - Boolean - - - - - other_positive_genetic_results - cards:Question - - text - Other positive genetic results - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - - testing_section - cards:Section - - test_done_code - cards:Question - - text - Test done (code) - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - list - String - - - dataType - text - String - - - WES - cards:AnswerOption - - value - WES - String - - - - single gene - cards:AnswerOption - - value - Single gene - String - - - - panel - cards:AnswerOption - - value - Panel - String - - - - Kics - cards:AnswerOption - - value - Kics - String - - - - Unknown - cards:AnswerOption - - value - Unknown - String - - - noneOfTheAbove - True - Boolean - - - - - Test_done_per_report - cards:Question - - text - Test done as depicted in the report/file (single gene, fam mutation, gane panel, WES)... - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - - mosaic_consultation - cards:Question - - text - Mosaic consultation - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - - follow_up_section - cards:Section - - date_of_last_fup - cards:Question - - text - Date of last follow-up - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - age_at_last_fup - cards:Question - - text - Age at last follow up - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - years - String - - - - - surveillance_section - cards:Section - - undergoing_surveillance - cards:Question - - text - Undergoing surveillance - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - True - Boolean - - - - surveillance_details - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - undergoing_surveillance - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - surveilled_since - cards:Question - - text - Surveilled since - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - surveilled_until - cards:Question - - text - Surveilled until - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - surveillance_info - cards:Question - - text - Additional information about surveillance - String - - - displayMode - textbox - String - - - dataType - text - String - - - maxAnswers - 0 - Long - - - - - - comments_section - cards:Section - - comments - cards:Question - - text - Comments - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Radiotherapy.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Radiotherapy.xml deleted file mode 100644 index 8388e1be64..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Radiotherapy.xml +++ /dev/null @@ -1,867 +0,0 @@ - - - - Radiotherapy - cards:Questionnaire - - title - Radiotherapy - String - - - requiredSubjectTypes - - /SubjectTypes/Patient - /SubjectTypes/Patient/Tumor - - Reference - - - radiation_section - cards:Section - - radiation - cards:Question - - text - Radiation therapy - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - True - Boolean - - - enableNotes - True - Boolean - - - - - treatment_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - radiation - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - start_date - cards:Question - - text - Radiation start date - String - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - enableNotes - True - Boolean - - - - weight_at_start - cards:Question - - text - Weight at start of radiation therapy - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - kg - String - - - enableNotes - True - Boolean - - - - height_at_start - cards:Question - - text - Height at start of radiation therapy - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - cm - String - - - enableNotes - True - Boolean - - - - end_date - cards:Question - - text - Radiation end date - String - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - enableNotes - True - Boolean - - - - - details_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - radiation - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - radiation_field - cards:Question - - text - Radiation field - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - technique - cards:Question - - text - Radiation technique - String - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - source - cards:Question - - text - Radiation source - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - Xray - cards:AnswerOption - - value - Xray - String - - - - Proton - cards:AnswerOption - - value - Proton - String - - - - - beam_energy - cards:Question - - text - Beam energy - String - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - MV - String - - - - total_dose - cards:Question - - text - Total radiation dose to tumor bed - String - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - cGy - String - - - - fraction_number - cards:Question - - text - Fraction number - String - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - enableNotes - True - Boolean - - - - - boost_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - radiation - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - boost - cards:Question - - text - Boost - String - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - True - Boolean - - - enableNotes - True - Boolean - - - - boost_details - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - boost - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - boost_technique - cards:Question - - text - Boost radiation technique - String - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - boost_beam_energy - cards:Question - - text - Boost beam energy - String - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - MV - String - - - - boost_dose - cards:Question - - text - Boost dose - String - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - cGy - String - - - - - - tbi_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - radiation - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - tbi - cards:Question - - text - Total Body Irradiation (TBI) - transplant conditioning - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - True - Boolean - - - - tbi_details - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - tbi - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - tbi_start_date - cards:Question - - text - TBI start date - String - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - tbi_end_date - cards:Question - - text - TBI end date - String - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - tbi_dose - cards:Question - - text - TBI dose - String - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - minValue - 0 - Long - - - unitOfMeasurement - cGy - String - - - - - - comments_section - cards:Section - - comments - cards:Question - - text - Comments - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Tumors.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Tumors.xml deleted file mode 100644 index b39e1347b7..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Questionnaires/Tumors.xml +++ /dev/null @@ -1,1739 +0,0 @@ - - - - Tumors - cards:Questionnaire - - title - Tumors - String - - - requiredSubjectTypes - - /SubjectTypes/Patient/Tumor - - Reference - - - maxPerSubject - 1 - Long - - - diagnosis_section - cards:Section - - date_of_diagnosis - cards:Question - - text - Date of diagnosis - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - - age_at_diagnosis - cards:Question - - text - Age at diagnosis - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - decimal - String - - - unitOfMeasurement - years - String - - - - short_diagnosis - cards:Question - - text - Short diagnosis - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - diagnosis_code - cards:Question - - text - Diagnosis code - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - ORDO - HP - - String - - - vocabularyFilters - cards:VocabularyFilterGroup - - ORDO - - Orphanet_C001 - - String - - - HP - - HP:0000118 - - String - - - - - diagnosis_from_pathology_report - cards:Question - - text - Diagnosis (Morphology) as on pathology report - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - enableNotes - True - Boolean - - - - ICD_morphology_code - cards:Question - - text - ICD Morphology Code - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - source_of_diagnosis - cards:Question - - text - Source of Tumor Diagnosis - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - list+input - String - - - dataType - text - String - - - Pathology report - cards:AnswerOption - - value - Pathology report - String - - - - Clinic note - cards:AnswerOption - - value - Clinic note - String - - - - Biopsy report - cards:AnswerOption - - value - Biopsy report - String - - - - Autopsy report - cards:AnswerOption - - value - Autopsy report - String - - - - Tissue metrix - cards:AnswerOption - - value - Tissue metrix - String - - - - - symptoms - cards:Question - - text - Symptoms - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - dataType - vocabulary - String - - - sourceVocabularies - - HP - - String - - - enableNotes - True - Boolean - - - - smoking_history - cards:Question - - text - Smoking history (lung tumors) - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - - detection_section - cards:Section - - modality_of_detection - cards:Question - - text - Modality of detection - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - detected_by_imaging - cards:Question - - text - Detected by surveillance imaging - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - - location_section - cards:Section - - location - cards:Question - - text - Location (code) - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - Topography of primary lesion - cards:Question - - text - Topography of primary lesion - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - ICD_topography_code - cards:Question - - text - ICD Topography Code - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - laterality - cards:Question - - text - Laterality - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - 0 - cards:AnswerOption - - value - 0 - String - - - label - N/A - String - - - notApplicable - True - Boolean - - - - 1 - cards:AnswerOption - - value - 1 - String - - - label - Right - String - - - - 2 - cards:AnswerOption - - value - 2 - String - - - label - Left - String - - - - 3 - cards:AnswerOption - - value - 3 - String - - - label - Bilateral - String - - - - - - status_section - cards:Section - - recurrence - cards:Question - - text - Recurrence - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - NA - cards:AnswerOption - - value - NA - String - - - label - N/A - String - - - notApplicable - True - Boolean - - - - P - cards:AnswerOption - - value - P - String - - - label - Progression - String - - - - R - cards:AnswerOption - - value - R - String - - - label - Relapse - String - - - - RC - cards:AnswerOption - - value - RC - String - - - label - Recurrence - String - - - - - malignancy - cards:Question - - text - Malignancy - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - NA - cards:AnswerOption - - value - NA - String - - - label - N/A - String - - - notApplicable - True - Boolean - - - - B - cards:AnswerOption - - value - B - String - - - label - Benign - String - - - - BP - cards:AnswerOption - - value - BP - String - - - label - Benign/premalignant - String - - - - P - cards:AnswerOption - - value - P - String - - - label - Premalignant - String - - - - PM - cards:AnswerOption - - value - PM - String - - - label - Premalignant/malignant - String - - - - M - cards:AnswerOption - - value - M - String - - - label - Malignant - String - - - - U - cards:AnswerOption - - value - U - String - - - label - Unknown - String - - - noneOfTheAbove - True - Boolean - - - - - localized - cards:Question - - text - Localized - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - spread - cards:Question - - text - Spread - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - P - cards:AnswerOption - - value - P - String - - - label - Primary - String - - - - Met - cards:AnswerOption - - value - Met - String - - - label - Metastatic - String - - - - NA - cards:AnswerOption - - value - NA - String - - - label - N/A - String - - - - - grade - cards:Question - - text - Grade - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - list+input - String - - - dataType - text - String - - - enableNotes - True - Boolean - - - NA - cards:AnswerOption - - value - NA - String - - - label - N/A - String - - - notApplicable - True - Boolean - - - - Low - cards:AnswerOption - - value - Low - String - - - - High - cards:AnswerOption - - value - High - String - - - - 1_3 - cards:AnswerOption - - value - 1/3 - String - - - - 2_3 - cards:AnswerOption - - value - 2/3 - String - - - - 3_3 - cards:AnswerOption - - value - 3/3 - String - - - - 1_4 - cards:AnswerOption - - value - 1/4 - String - - - - 2_4 - cards:AnswerOption - - value - 2/4 - String - - - - 3_4 - cards:AnswerOption - - value - 3/4 - String - - - - 4_4 - cards:AnswerOption - - value - 4/4 - String - - - - - group - cards:Question - - text - Group - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - input - String - - - dataType - text - String - - - - stage - cards:Question - - text - Stage - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - list+input - String - - - dataType - text - String - - - I - cards:AnswerOption - - value - I - String - - - - II - cards:AnswerOption - - value - II - String - - - - III - cards:AnswerOption - - value - III - String - - - - IV - cards:AnswerOption - - value - IV - String - - - - - sites_of_metastases - cards:Question - - text - Topography/sites of metastases if present - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - input - String - - - dataType - text - String - - - - specific_features - cards:Question - - text - Specific molecular/cytogenetic/Immunohistochemistry features (ex. HER2+) - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - input - String - - - dataType - text - String - - - - risk_group_assignment - cards:Question - - text - Risk Group Assignment - String - - - minAnswers - 1 - Long - - - maxAnswers - 1 - Long - - - displayMode - list+input - String - - - Low risk - cards:AnswerOption - - value - Low risk - String - - - - Intermediate - cards:AnswerOption - - value - Intermediate - String - - - - High risk - cards:AnswerOption - - value - High risk - String - - - - Very high risk - cards:AnswerOption - - value - Very high risk - String - - - - - classification_schema - cards:Question - - text - Group/Stage/Risk Classification Schema - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - dataType - text - String - - - - - treatment_section - cards:Section - - resected - cards:Question - - text - Resected - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - surgery_extent - cards:Question - - text - Surgery - extent - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - enableNotes - True - Boolean - - - - Chemotherapy - cards:Question - - text - Chemotherapy - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - Radiotherapy - cards:Question - - text - Radiotherapy - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - Immunotherapy - cards:Question - - text - Immunotherapy - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - targeted_therapy - cards:Question - - text - Targeted therapy - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - Bone_Marrow_Transplant - cards:Question - - text - Bone Marrow Transplant - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - boolean - String - - - enableUnknown - true - String - - - - Bone_Marrow_Transplant_Type_Section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - Bone_Marrow_Transplant - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - 1 - - String - - - - - Bone_Marrow_Transplant_Type - cards:Question - - text - Bone Marrow Transplant Type - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - list - String - - - dataType - text - String - - - Autologus - cards:AnswerOption - - label - Autologus (AUTO) - String - - - value - Autologus - String - - - - Allogenic - cards:AnswerOption - - label - Allogenic (ALLO) - String - - - value - Allogenic - String - - - - Other - cards:AnswerOption - - label - Other - String - - - value - Other - String - - - - Unknown - cards:AnswerOption - - label - Unknown - String - - - value - Unknown - String - - - - - - treatment_at_PMH - cards:Question - - text - Describe treatments done at PMH, if any - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - special_AE - cards:Question - - text - Special AE - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - dataType - text - String - - - - preventions - cards:Question - - text - Preventions - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - dataType - text - String - - - - - comments_section - cards:Section - - comments - cards:Question - - text - Comments - String - - - minAnswers - 0 - Long - - - maxAnswers - 1 - Long - - - displayMode - textbox - String - - - dataType - text - String - - - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnset.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnset.xml deleted file mode 100644 index 5f7e74eb1d..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnset.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - - AgeOfOnset - cards:Statistic - - name - Age of onset - String - - - order - 0 - Long - - - type - bar - String - - - xVar - /Questionnaires/Patient information/pathology_section/age_at_1st_malignant_dx - Reference - - - yVar - /SubjectTypes/Patient - Reference - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnsetByGender.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnsetByGender.xml deleted file mode 100644 index ad57d3e1fb..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/AgeOfOnsetByGender.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - AgeOfOnsetByGender - cards:Statistic - - name - Age of onset by gender - String - - - order - 1 - Long - - - type - bar - String - - - xVar - /Questionnaires/Patient information/pathology_section/age_at_1st_malignant_dx - Reference - - - yVar - /SubjectTypes/Patient - Reference - - - splitVar - /Questionnaires/Patient information/demographics_section/gender - Reference - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocation.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocation.xml deleted file mode 100644 index 765285e044..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocation.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - - TumorLocation - cards:Statistic - - name - Tumor location - String - - - order - 2 - Long - - - type - bar - String - - - xVar - /Questionnaires/Tumors/location_section/location - Reference - - - yVar - /SubjectTypes/Patient - Reference - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocationByGender.xml b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocationByGender.xml deleted file mode 100644 index b66ef8f8b9..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/Statistics/TumorLocationByGender.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - TumorLocationByGender - cards:Statistic - - name - Tumor location by gender - String - - - order - 3 - Long - - - type - bar - String - - - xVar - /Questionnaires/Tumors/location_section/location - Reference - - - yVar - /SubjectTypes/Patient - Reference - - - splitVar - /Questionnaires/Patient information/demographics_section/gender - Reference - - diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/AppName.json b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/AppName.json deleted file mode 100644 index 7b623b040b..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/AppName.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "jcr:primaryType": "nt:unstructured", - "AppName": "LFS Data Core" -} diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/Media.json b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/Media.json deleted file mode 100644 index 6f66ba018a..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/Media.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "jcr:primaryType": "nt:unstructured", - "logoDark": "/libs/cards/resources/media/lfs/logo.png", - "logoLight": "/libs/cards/resources/media/lfs/logo_light_bg.png", - "sidebarBackground": "/libs/cards/resources/media/lfs/background.jpg" -} diff --git a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/ThemeColor.json b/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/ThemeColor.json deleted file mode 100644 index 01d2388e5e..0000000000 --- a/lfs-resources/clinical-data/src/main/resources/SLING-INF/content/libs/cards/conf/ThemeColor.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "jcr:primaryType": "nt:unstructured", - "themeColor": "blue" -} diff --git a/lfs-resources/feature/pom.xml b/lfs-resources/feature/pom.xml deleted file mode 100644 index 55c9cdb763..0000000000 --- a/lfs-resources/feature/pom.xml +++ /dev/null @@ -1,32 +0,0 @@ - - - - 4.0.0 - - - io.uhndata.cards - lfs-resources - 0.9.22-SNAPSHOT - - - cards4lfs - slingosgifeature - Cards4LFS - diff --git a/lfs-resources/feature/src/main/features/feature.json b/lfs-resources/feature/src/main/features/feature.json deleted file mode 100644 index 29fbcbfa37..0000000000 --- a/lfs-resources/feature/src/main/features/feature.json +++ /dev/null @@ -1,49 +0,0 @@ -// Licensed to the Apache Software Foundation (ASF) under one -// or more contributor license agreements. See the NOTICE file -// distributed with this work for additional information -// regarding copyright ownership. The ASF licenses this file -// to you under the Apache License, Version 2.0 (the -// "License"); you may not use this file except in compliance -// with the License. You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, -// software distributed under the License is distributed on an -// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY -// KIND, either express or implied. See the License for the -// specific language governing permissions and limitations -// under the License. - -{ - "bundles":[ - { - "id":"${project.groupId}:cards-patient-subject-type:${project.version}", - "start-order":"20" - }, - { - "id":"${project.groupId}:cards-tumor-subject-type:${project.version}", - "start-order":"21" - }, - { - "id":"${project.groupId}:cards-tumor-region-subject-type:${project.version}", - "start-order":"22" - }, - { - "id":"${project.groupId}:cards-statistics:${project.version}", - "start-order":"25" - }, - { - "id":"${project.groupId}:lfs-resources-clinical-data:${project.version}", - "start-order":"26" - }, - { - "id":"${project.groupId}:lfs-resources-tissue-metrix:${project.version}", - "start-order":"26" - }, - { - "id":"${project.groupId}:cards-variants:${project.version}", - "start-order":"26" - } - ] -} diff --git a/lfs-resources/pom.xml b/lfs-resources/pom.xml deleted file mode 100644 index 905091df6e..0000000000 --- a/lfs-resources/pom.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - - 4.0.0 - - - io.uhndata.cards - cards-parent - 0.9.22-SNAPSHOT - - - lfs-resources - pom - LFS Resources - A collection of questionnaires, subject types and other LFS specific code. - - - clinical-data - tissue-metrix - feature - - diff --git a/lfs-resources/tissue-metrix/pom.xml b/lfs-resources/tissue-metrix/pom.xml deleted file mode 100644 index fa05fd9051..0000000000 --- a/lfs-resources/tissue-metrix/pom.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - - 4.0.0 - - - io.uhndata.cards - lfs-resources - 0.9.22-SNAPSHOT - - - lfs-resources-tissue-metrix - bundle - LFS Resources - Tissue Metrix Data - - - - - - org.apache.felix - maven-bundle-plugin - true - - - SLING-INF/content/Questionnaires/;path:=/Questionnaires/;overwriteProperties:=true;uninstall:=true;checkin:=true - - - - - - diff --git a/lfs-resources/tissue-metrix/src/main/resources/SLING-INF/content/Questionnaires/TissueMetrix.xml b/lfs-resources/tissue-metrix/src/main/resources/SLING-INF/content/Questionnaires/TissueMetrix.xml deleted file mode 100644 index f3e121638d..0000000000 --- a/lfs-resources/tissue-metrix/src/main/resources/SLING-INF/content/Questionnaires/TissueMetrix.xml +++ /dev/null @@ -1,751 +0,0 @@ - - - - TissueMetrix - cards:Questionnaire - - title - Tissue Metrix - String - - - requiredSubjectTypes - - /SubjectTypes/Patient - - Reference - - - subject_information_section - cards:Section - - donor_number - cards:Question - - text - Donor number - String - - - mandatory - True - Boolean - - - maxAnswers - 1 - Long - - - - species - cards:Question - - text - Species - String - - - displayMode - list+input - String - - - maxAnswers - 1 - Long - - - human - cards:AnswerOption - - label - Human - String - - - value - human - String - - - - canide - cards:AnswerOption - - label - Canide - String - - - value - canide - String - - - - murine - cards:AnswerOption - - label - Murine - String - - - value - murine - String - - - - - sex - cards:Question - - text - Sex - String - - - description - Sex must be recorded as biological sex rather than gender. - String - - - displayMode - list+input - String - - - maxAnswers - 1 - Long - - - M - cards:AnswerOption - - label - Male - String - - - value - M - String - - - - F - cards:AnswerOption - - label - Female - String - - - value - F - String - - - - O - cards:AnswerOption - - label - Other - String - - - value - O - String - - - - U - cards:AnswerOption - - label - Unknown - String - - - value - U - String - - - - - vital_status - cards:Question - - text - Life status - String - - - displayMode - list - String - - - maxAnswers - 1 - Long - - - alive - cards:AnswerOption - - label - Alive - String - - - value - alive - String - - - - deceased - cards:AnswerOption - - label - Deceased - String - - - value - deceased - String - - - - - date_of_birth - cards:Question - - text - Date of birth - String - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - maxAnswers - 1 - Long - - - - dod_section - cards:Section - - condition - cards:Conditional - - comparator - = - String - - - operandA - cards:ConditionalValue - - value - - vital_status - - String - - - isReference - True - Boolean - - - - operandB - cards:ConditionalValue - - value - - deceased - - String - - - - - date_of_death - cards:Question - - text - Date of death - String - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - maxAnswers - 1 - Long - - - - - maternal_ethnicity - cards:Question - - text - Maternal ethnicity - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - HANCESTRO - - String - - - vocabularyFilters - cards:VocabularyFilterGroup - - HANCESTRO - - HANCESTRO_0004 - - String - - - - - paternal_ethnicity - cards:Question - - text - Paternal ethnicity - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - HANCESTRO - - String - - - vocabularyFilters - cards:VocabularyFilterGroup - - HANCESTRO - - HANCESTRO_0004 - - String - - - - - date_registered - cards:Question - - text - Date registered - String - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - maxAnswers - 1 - Long - - - - last_fup - cards:Question - - text - Last follow-up - String - - - dataType - date - String - - - dateFormat - yyyy-MM-dd - String - - - maxAnswers - 1 - Long - - - - perinatal_history - cards:Question - - text - Perinatal history - String - - - maxAnswers - 1 - Long - - - displayMode - textbox - String - - - - reason_for_referral - cards:Question - - text - Reason for referral - String - - - maxAnswers - 1 - Long - - - displayMode - textbox - String - - - - - diagnostics_section - cards:Section - - disease - cards:Question - - text - Disease - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - list+input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - MONDO - - String - - - vocabularyFilters - cards:VocabularyFilterGroup - - MONDO - - MONDO:0000001 - - String - - - - - disease_site - cards:Question - - text - Disease site - String - - - minAnswers - 0 - Long - - - maxAnswers - 0 - Long - - - displayMode - input - String - - - dataType - vocabulary - String - - - sourceVocabularies - - UBERON - - String - - - vocabularyFilters - cards:VocabularyFilterGroup - - UBERON - - BFO_0000002 - - String - - - - - tumor - cards:Question - - text - Tumor type - String - - - maxAnswers - 0 - Long - - - - mutation_status - cards:Question - - text - Mutation status - String - - - maxAnswers - 0 - Long - - - - - data_section - cards:Section - - file1 - cards:Question - - text - File1 - String - - - maxAnswers - 1 - Long - - - - file2 - cards:Question - - text - File2 - String - - - maxAnswers - 1 - Long - - - - file3 - cards:Question - - text - File3 - String - - - maxAnswers - 1 - Long - - - - source1 - cards:Question - - text - Source1 - String - - - maxAnswers - 1 - Long - - - - source2 - cards:Question - - text - Source2 - String - - - maxAnswers - 1 - Long - - - - source3 - cards:Question - - text - Source3 - String - - - maxAnswers - 1 - Long - - - - - comments_section - cards:Section - - comments - cards:Question - - text - Comments - String - - - displayMode - textbox - String - - - maxAnswers - 0 - Long - - - - diff --git a/pom.xml b/pom.xml index fa269f2fd3..4a0a60956b 100644 --- a/pom.xml +++ b/pom.xml @@ -2046,7 +2046,6 @@ modules aggregated-frontend - lfs-resources test-resources distribution Utilities