diff --git a/ardac1prd/portal.ardac.org/values.yaml b/ardac1prd/portal.ardac.org/values.yaml index 9dc40c3..248c520 100644 --- a/ardac1prd/portal.ardac.org/values.yaml +++ b/ardac1prd/portal.ardac.org/values.yaml @@ -111,12 +111,15 @@ guppy: type: molecular_test - index: ardac_lab type: lab + - index: file_collect_index + type: file configIndex: - ardac_case-array-config - ardac_follow_up-array-config - ardac_biospecimen-array-config - ardac_lab_result-array-config - ardac_lab-array-config + - file_collect_index-array-config hatchery: enabled: true @@ -207,7 +210,7 @@ portal: enabled: true image: repository: bearbbhao/ardac-portal - tag: "1_1_11" + tag: "1_1_12" gitops: json: | { @@ -1199,6 +1202,124 @@ portal: ], "accessibleValidationField": "project_id" } + }, + { + "tabTitle": "Data Files", + "charts": { + "experimental_strategy": { + "chartType": "bar", + "title": "Experimental Strategy" + }, + "data_category": { + "chartType": "pie", + "title": "Data Category" + }, + "data_type": { + "chartType": "bar", + "title": "Data Type" + }, + "data_format": { + "chartType": "pie", + "title": "Data Format" + } + }, + "filters": { + "tabs": [ + { + "title": "Data File", + "fields": [ + "experimental_strategy", + "data_category", + "data_type", + "data_format" + ] + } + ] + }, + "table": { + "enabled": true, + "fields": [ + "submitter_id", + "file_name", + "experimental_strategy", + "data_category", + "data_type", + "data_format" + ] + }, + "dropdowns": { + "download": { + "title": "Download" + } + }, + "buttons": [ + { + "enabled": true, + "type": "manifest", + "title": "Download Manifest", + "leftIcon": "datafile", + "rightIcon": "download", + "fileName": "manifest.json", + "dropdownId": "download" + }, + { + "enabled": true, + "type": "data-json", + "title": "Download Metadata (JSON)", + "leftIcon": "datafile", + "rightIcon": "download", + "fileName": "data_files.json", + "dropdownId": "download" + } + ], + "guppyConfig": { + "dataType": "file", + "nodeCountTitle": "File_collections", + "fieldMapping": [ + { + "field": "pat_id", + "name": "Patient Id" + }, + { + "field": "visit_day", + "name": "Assessment Date" + }, + { + "field": "study_site", + "name": "Clinical site" + }, + { + "field": "case_arm", + "name": "Treatment Arm" + }, + { + "field": "project_id", + "name": "Project" + }, + { + "field": "observational", + "name": "Observational" + }, + { + "field": "clinical_trial", + "name": "Clinical Trial" + }, + { + "field": "gender", + "name": "sex" + } + ], + "manifestMapping": { + "resourceIndexType": "file", + "resourceIdField": "object_id", + "referenceIdFieldInResourceIndex": "_case_id", + "referenceIdFieldInDataIndex": "_case_id" + }, + "accessibleFieldCheckList": [ + "project_id" + ], + "accessibleValidationField": "project_id" + } } ], "featureFlags": { @@ -1647,7 +1768,7 @@ etl: - Heavy Drinker with Alcoholic Hepatits: AH cases - Heavy Drinker without Alcoholic Hepatits: Heavy Drinking Controls - Healthy Donor: Healthy Controls - - path: demographics[gender,race,ethnicity,year_of_birth,age_at_index] + - path: cases.demographics[gender,race,ethnicity,year_of_birth,age_at_index] value_mappings: - female: Female - male: Male @@ -1709,7 +1830,7 @@ etl: - path: follow_ups[follow_up_id:submitter_id, visit_day].cases[pat_id:submitter_id, case_arm:actarm].studies[study_name, study_id:submitter_id] - path: follow_ups.cases[pat_id:submitter_id, case_arm:actarm, case_group:cohort, study_site, aki_status, days_180_aki, days_180_survival, days_90_aki, days_90_survival, days_to_aki] - path: labs[lab_id:submitter_id, lab_name:name_of_institute, PI_name] - - path: follow_ups.demographics[gender, race, ethnicity, year_of_birth, age_at_index] + - path: follow_ups.cases.demographics[gender, race, ethnicity, year_of_birth, age_at_index] - name: ardac_lab_result doc_type: molecular_test @@ -1718,7 +1839,7 @@ etl: parent_props: - path: follow_ups[follow_up_id:submitter_id, visit_day].cases[pat_id:submitter_id, case_arm:actarm].studies[study_name, study_id:submitter_id] - path: follow_ups.cases[pat_id:submitter_id, case_arm:actarm, case_group:cohort, study_site, aki_status, days_180_aki, days_180_survival, days_90_aki, days_90_survival, days_to_aki] - - path: follow_ups.demographics[gender, race, ethnicity, year_of_birth, age_at_index] + - path: follow_ups.cases.demographics[gender, race, ethnicity, year_of_birth, age_at_index] - path: aliquots.labs[lab_id:submitter_id, lab_name:name_of_institute, PI_name] props: - name: project_id @@ -1748,3 +1869,17 @@ etl: path: aliquots.molecular_tests src: laboratory_test fn: set + + - name: file_collect_index + doc_type: file + type: collector + category: data_file + root: None + props: + - name: submitter_id + - name: file_name + - name: experimental_strategy + - name: data_category + - name: data_type + - name: data_format + - name: source_node