From 7c17d7f42dc1b6a1e86bb5a4d893b6f98f32926b Mon Sep 17 00:00:00 2001 From: evans-g-crsj Date: Fri, 7 Jun 2024 15:57:05 -0400 Subject: [PATCH] :wrench: Remove fields from mock studies --- admin/confInclude.json | 2 +- admin/confKfNext.json | 2 +- admin/mockStudies.mjs | 213 ----------------------------------------- 3 files changed, 2 insertions(+), 215 deletions(-) diff --git a/admin/confInclude.json b/admin/confInclude.json index ee52b0e..bc6d8ee 100644 --- a/admin/confInclude.json +++ b/admin/confInclude.json @@ -176,7 +176,7 @@ } }, { - "field": "data_source", + "field": "data_sources", "graphqlField": "study", "extendedFieldMappingInput": { "isArray": true diff --git a/admin/confKfNext.json b/admin/confKfNext.json index 513dd16..b4e3f28 100644 --- a/admin/confKfNext.json +++ b/admin/confKfNext.json @@ -201,7 +201,7 @@ } }, { - "field": "data_source", + "field": "data_sources", "graphqlField": "study", "extendedFieldMappingInput": { "isArray": true diff --git a/admin/mockStudies.mjs b/admin/mockStudies.mjs index 79c773f..3d692ee 100644 --- a/admin/mockStudies.mjs +++ b/admin/mockStudies.mjs @@ -2,9 +2,6 @@ import Ajv from 'ajv'; export const mockStudies = [ { - biobank_contact: 'dsresearch@cuanschutz.edu', - biobank_request_link: 'https://redcap.link/HTPVBRrequest', - biospecimen_count: 39430, controlled_access: ['Registered', 'Controlled'], data_category: [ 'Genomics', @@ -17,7 +14,6 @@ export const mockStudies = [ 'Imaging', 'Clinical', ], - data_source: ['Investigator Assessment', 'Medical Record', 'Patient or Caregiver Report'], data_types: [ { file_count: 2865, @@ -89,7 +85,6 @@ export const mockStudies = [ date_collection_end_year: '2020', data_category: 'Transcriptomics', data_types: ['Normalized relative expression (FPKM)'], - expected_data_categories: ['Transcriptomics'], expected_number_participants: 400, experimental_strategy: 'Bulk polyA+ RNAseq', experimental_platform: 'Illumina Novaseq', @@ -112,7 +107,6 @@ export const mockStudies = [ date_collection_end_year: '2020', data_category: 'Metabolomics', data_types: ['Preprocessed metabolite relative abundance'], - expected_data_categories: ['Metabolomics'], expected_number_participants: 418, experimental_strategy: 'LCMS Metabolomics', experimental_platform: 'Ultra high-performance liquid chromatography-mass spectrometry (UHPLC-MS)', @@ -136,7 +130,6 @@ export const mockStudies = [ date_collection_end_year: '', data_category: 'Unharmonized Demographic/Clinical Data', data_types: [], - expected_data_categories: ['Clinical'], expected_number_participants: 1055, experimental_strategy: '', experimental_platform: '', @@ -159,7 +152,6 @@ export const mockStudies = [ date_collection_end_year: '2020', data_category: 'Proteomics', data_types: ['Protein abundance (absolute protein concentration)'], - expected_data_categories: ['Proteomics'], expected_number_participants: 477, experimental_strategy: 'Multiplex immunoassay', experimental_platform: 'Meso Scale Discovery Assays (MSD)', @@ -177,18 +169,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '2016', - expected_data_categories: [ - 'Genomics', - 'Demographic', - 'Transcriptomics', - 'Proteomics', - 'Metabolomics', - 'Immune maps', - 'Microbiome', - 'Imaging', - 'Clinical', - ], - expected_number_participants: 2500, experimental_strategies: [ { file_count: 3200, @@ -208,25 +188,14 @@ export const mockStudies = [ }, ], external_ids: ['phs002330', 'phs002981'], - file_count: 4975, - guid: 'NDAR', institutions: ['Linda Crnic Institute for Down Syndrome'], investigator_names: ['Joaquin M. Espinosa'], is_harmonized: true, - part_lifespan_stages: ['Pediatric', 'Adult'], - participant_count: 1062, - program: 'INCLUDE', study_code: 'HTP', - study_name: 'The Human Trisome Project', - website: 'https://www.trisome.org', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 834, controlled_access: ['Registered', 'Controlled'], data_category: ['Genomics', 'Clinical'], - data_source: ['Unknown'], data_types: [ { file_count: 0, @@ -339,8 +308,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Genomics', 'Clinical', 'Unharmonized Demographic/Clinical'], - expected_number_participants: 530, experimental_strategies: [ { file_count: 0, @@ -360,26 +327,14 @@ export const mockStudies = [ }, ], external_ids: ['phs002330'], - file_count: 7211, - guid: 'No GUID', institutions: ['Baylor College Of Medicine'], investigator_names: ['Phillip J. Lupo'], is_harmonized: true, - part_lifespan_stages: ['Pediatric'], - participant_count: 530, - program: 'INCLUDE/KF', study_code: 'DS-COG-ALL', - study_name: - 'INCLUDE: (Lupo) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 1344, controlled_access: ['Controlled'], data_category: ['Genomics', 'Clinical'], - data_source: ['Unknown'], data_types: [ { file_count: 0, @@ -492,8 +447,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Genomics', 'Clinical', 'Unharmonized Demographic/Clinical'], - expected_number_participants: 1327, experimental_strategies: [ { file_count: 0, @@ -513,26 +466,14 @@ export const mockStudies = [ }, ], external_ids: ['phs002330'], - file_count: 4922, - guid: 'No GUID', institutions: ['Emory University School of Medicine'], investigator_names: ['Stephanie Sherman'], is_harmonized: true, - part_lifespan_stages: ['Pediatric'], - participant_count: 1327, - program: 'INCLUDE/KF', study_code: 'DS360-CHD', - study_name: - 'INCLUDE: (Sherman) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 1344, controlled_access: ['Controlled'], data_category: ['Genomics', 'Clinical'], - data_source: ['Medical Record', 'Participant or Caregiver Report'], data_types: [ { file_count: 0, @@ -645,8 +586,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Genomics', 'Clinical', 'Unharmonized Demographic/Clinical'], - expected_number_participants: 369, experimental_strategies: [ { file_count: 0, @@ -666,26 +605,14 @@ export const mockStudies = [ }, ], external_ids: ['phs001138', 'phs002330'], - file_count: 818, - guid: 'No GUID', institutions: ["Cincinnati Children's Hospital Medical Center"], investigator_names: ['Eileen C. King'], is_harmonized: true, - part_lifespan_stages: ['Pediatric'], - participant_count: 369, - program: 'INCLUDE/KF', study_code: 'DS-PCGC', - study_name: - 'INCLUDE: (PCGC) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome', - website: '', }, { - biobank_contact: 'hakonarson@chop.edu', - biobank_request_link: '', - biospecimen_count: 1908, controlled_access: ['Registered'], data_category: ['Genomics', 'Transcriptomics', 'Imaging', 'Clinical'], - data_source: ['Unknown'], data_types: [ { file_count: 468, @@ -821,8 +748,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Genomics', 'Transcriptomics', 'Imaging', 'Clinical'], - expected_number_participants: 1152, experimental_strategies: [ { file_count: 2565, @@ -842,26 +767,14 @@ export const mockStudies = [ }, ], external_ids: ['phs002983'], - file_count: 2565, - guid: 'No GUID', institutions: ["Children's Hospital of Philadelphia"], investigator_names: ['Hakon Hakonarson'], is_harmonized: true, - part_lifespan_stages: ['Pediatric', 'Adult'], - participant_count: 1152, - program: 'INCLUDE', study_code: 'X01-Hakonarson', - study_name: - 'Genetic underpinnings of the multifactorial phenotype of Trisomy 21 patients unveiled by multi-omics approaches', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 436, controlled_access: ['Registered'], data_category: ['Clinical'], - data_source: ['Unknown'], data_types: [ { file_count: 0, @@ -974,8 +887,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Genomics', 'Clinical'], - expected_number_participants: 436, experimental_strategies: [ { file_count: 0, @@ -995,25 +906,14 @@ export const mockStudies = [ }, ], external_ids: ['phs002982'], - file_count: 0, - guid: 'No GUID', institutions: ['University of Oxford'], investigator_names: ['Adam de Smith'], is_harmonized: true, - part_lifespan_stages: ['Neonatal'], - participant_count: 1152, - program: 'INCLUDE', study_code: 'X01-deSmith', - study_name: 'The epidemiology of transient leukemia in newborns with Down syndrome', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 23, controlled_access: ['Registered'], data_category: ['Transcriptomics', 'Clinical'], - data_source: ['Medical Record', 'Participant or Caregiver Report'], data_types: [ { file_count: 115, @@ -1079,8 +979,6 @@ export const mockStudies = [ dataset: [], date_collection_end_year: '', date_collection_start_year: '2018', - expected_data_categories: ['Transcriptomics', 'Clinical'], - expected_number_participants: 167, experimental_strategies: [ { file_count: 253, @@ -1100,25 +998,14 @@ export const mockStudies = [ }, ], external_ids: [], - file_count: 253, - guid: 'No GUID', institutions: ['Benaroya Research Institute'], investigator_names: ['Jane Buckner'], is_harmonized: true, - part_lifespan_stages: ['Pediatric', 'Adult'], - participant_count: 167, - program: 'INCLUDE', study_code: 'BRI-DSR', - study_name: 'Benaroya Research Institute Down Syndrome Registry', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 41, controlled_access: ['Controlled'], data_category: ['Genomics', 'Clinical'], - data_source: ['Medical Record', 'Participant or Caregiver Report', 'Investigator Assessment'], data_types: [ { file_count: 0, @@ -1184,8 +1071,6 @@ export const mockStudies = [ dataset: [], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Genomics', 'Clinical'], - expected_number_participants: 600, experimental_strategies: [ { file_count: 0, @@ -1205,25 +1090,14 @@ export const mockStudies = [ }, ], external_ids: [], - file_count: 123, - guid: 'No GUID', institutions: ['Linda Crnic Institute for Down Syndrome'], investigator_names: ['Joaquin Espinosa'], is_harmonized: true, - part_lifespan_stages: ['Pediatric'], - participant_count: 41, - program: 'INCLUDE/KF', study_code: 'DS-NEXUS', - study_name: 'Nexus Translational Biobank', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 0, controlled_access: [], data_category: ['Clinical'], - data_source: ['Medical Record', 'Participant or Caregiver Report', 'Investigator Assessment'], data_types: [ { file_count: 0, @@ -1289,8 +1163,6 @@ export const mockStudies = [ dataset: [], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Clinical'], - expected_number_participants: 79, experimental_strategies: [ { file_count: 0, @@ -1310,25 +1182,14 @@ export const mockStudies = [ }, ], external_ids: [], - file_count: 0, - guid: 'NDAR', institutions: ['Geisinger Health System'], investigator_names: ['Christa Martin'], is_harmonized: true, - part_lifespan_stages: ['Pediatric', 'Adult'], - participant_count: 79, - program: 'INCLUDE', study_code: 'DS-Sleep', - study_name: 'Dimensional, Sleep, and Genomic Analyses of Down Syndrome to Elucidate Phenotypic Variability', - website: '', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 0, controlled_access: [], data_category: ['Clinical'], - data_source: ['Participant or Caregiver Report'], data_types: [ { file_count: 0, @@ -1418,8 +1279,6 @@ export const mockStudies = [ ], date_collection_end_year: '', date_collection_start_year: '2013', - expected_data_categories: ['Clinical'], - expected_number_participants: 100000, experimental_strategies: [ { file_count: 0, @@ -1439,25 +1298,14 @@ export const mockStudies = [ }, ], external_ids: [], - file_count: 0, - guid: 'NDAR', institutions: ['Eunice Kennedy Shriver National Institute of Child Health and Human Development'], investigator_names: ['Sujata Bardhan'], is_harmonized: true, - part_lifespan_stages: ['Fetal', 'Adult', 'Pediatric', 'Neonatal'], - participant_count: 3634, - program: 'INCLUDE', study_code: 'DSC', - study_name: 'DS-Connect: The Down Syndrome Registry', - website: 'https://dsconnect.nih.gov', }, { - biobank_contact: '', - biobank_request_link: '', - biospecimen_count: 0, controlled_access: [], data_category: ['Clinical'], - data_source: ['Medical Record', 'Participant or Caregiver Report', 'Investigator Assessment'], data_types: [ { file_count: 0, @@ -1523,8 +1371,6 @@ export const mockStudies = [ dataset: [], date_collection_end_year: '', date_collection_start_year: '', - expected_data_categories: ['Clinical'], - expected_number_participants: 550, experimental_strategies: [ { file_count: 0, @@ -1544,17 +1390,10 @@ export const mockStudies = [ }, ], external_ids: [], - file_count: 0, - guid: 'NDAR', institutions: ['University of Pittsburgh'], investigator_names: ['Bradley T. Christian', 'Benjamin L. Handen', 'Elizabeth Head', 'Mark Mapstone'], is_harmonized: true, - part_lifespan_stages: ['Adult'], - participant_count: 417, - program: 'INCLUDE', study_code: 'ABC-DS', - study_name: 'Alzheimer Biomarker Consortium - Down Syndrome', - website: 'https://www.nia.nih.gov/research/abc-ds', }, ]; @@ -1562,15 +1401,6 @@ const sSchema = { title: 'Study', type: 'object', properties: { - biobank_contact: { - type: 'string', - }, - biobank_request_link: { - type: 'string', - }, - biospecimen_count: { - type: 'integer', - }, data_types: { type: 'array', items: { @@ -1597,12 +1427,6 @@ const sSchema = { type: 'string', }, }, - data_source: { - type: 'array', - items: { - type: 'string', - }, - }, dataset: { type: 'array', items: { @@ -1635,9 +1459,6 @@ const sSchema = { type: 'string', }, }, - expected_data_categories: { - type: 'array', - }, expected_number_participants: { type: 'integer', }, @@ -1692,15 +1513,6 @@ const sSchema = { date_collection_start_year: { type: 'string', }, - expected_data_categories: { - type: 'array', - items: { - type: 'string', - }, - }, - expected_number_participants: { - type: 'integer', - }, experimental_strategies: { type: 'array', items: { @@ -1721,10 +1533,6 @@ const sSchema = { type: 'string', }, }, - file_count: { - type: 'integer', - }, - //FIXME in contacts? institutions: { type: 'array', items: { @@ -1740,30 +1548,9 @@ const sSchema = { type: 'string', }, }, - guid: { - type: 'string', - }, - part_lifespan_stages: { - type: 'array', - items: { - type: 'string', - }, - }, - participant_count: { - type: 'integer', - }, - program: { - type: 'string', - }, study_code: { type: 'string', }, - study_name: { - type: 'string', - }, - website: { - type: 'string', - }, }, required: ['study_code'], };