diff --git a/nightly.planx-pla.net/etlMapping.yaml b/nightly.planx-pla.net/etlMapping.yaml index f943e0b95..6b606cfc1 100644 --- a/nightly.planx-pla.net/etlMapping.yaml +++ b/nightly.planx-pla.net/etlMapping.yaml @@ -1,54 +1,155 @@ mappings: - - name: bloodpac - doc_type: case + - name: gen3.biodatacatalyst.nhlbi.nih.gov_subject + doc_type: subject type: aggregator - root: case + root: subject props: - name: submitter_id - name: project_id + - name: consent_codes + - name: geographic_site flatten_props: - path: demographics props: - - name: gender - - name: race - - name: ethnicity + - name: age_at_index + - name: hispanic_subgroup + - name: subcohort + - name: weight_baseline + - name: bmi_baseline + - name: height_baseline + - path: medical_histories + props: + - name: diabetes + - name: hypertension + - name: cerebrovascular_disease + - name: chronic_respiratory_disease + - name: coronary_artery_disease + - name: asthma + - name: cabg_presence + - name: copd + - name: emphysema + - name: heart_failure + - name: myocardial_infarction + - name: stroke + - name: cac_score + - name: cac_volume + - name: carotid_plaque + - name: carotid_stenosis + - name: cimt_1 + - name: cimt_2 + - name: vte_case_status + - name: vte_followup_start_age + - name: vte_prior_history + + - path: medication_records + props: + - name: hypertension_meds + - name: antihypertensive_meds + - name: fasting_lipids + - name: lipid_lowering_medication + - path: lab_results + props: + - name: lymphocyte_ncnc_bld + - name: mch_entmass_rbc + - name: mcv_entvol_rbc + - name: mchc_mcnc_rbc + - name: monocyte_ncnc_bld + - name: neutrophil_ncnc_bld + - name: pmv_entvol_bld + - name: rbc_ncnc_bld + - name: rdw_ratio_rbc + - name: hemoglobin_mcnc_bld + - name: platelet_ncnc_bld + - name: hematocrit_vfr_bld + - name: wbc_ncnc_bld + - name: basophil_ncnc_bld + - name: eosinophil_ncnc_bld + - name: unit_triglycerides + - name: hdl + - name: ldl + - name: triglycerides + - name: total_cholesterol aggregated_props: - - name: _biospecimens_count - path: biospecimens - fn: count + - name: annotated_sex + path: demographics + src: annotated_sex + fn: set + - name: race + path: demographics + src: race + fn: set + - name: ethnicity + path: demographics + src: ethnicity + fn: set - name: _samples_count - path: biospecimens.samples + path: samples fn: count - name: _aliquots_count - path: biospecimens.samples.aliquots - fn: count - - name: _analytes_count - path: biospecimens.samples.aliquots.analytes - fn: count - - name: _cell_images_count - path: biospecimens.samples.aliquots.analytes.cell_images - fn: count - - name: _mass_cytometry_assays_count - path: biospecimens.samples.aliquots.analytes.mass_cytometry_assays - fn: count - - name: _mass_cytometry_images_count - path: biospecimens.samples.aliquots.analytes.mass_cytometry_assays.mass_cytometry_images + path: samples.aliquots fn: count - name: _read_groups_count - path: biospecimens.samples.aliquots.analytes.read_groups + path: samples.aliquots.read_groups fn: count - - name: _slide_images_count - path: biospecimens.samples.aliquots.slide_images + - name: _submitted_unaligned_reads_files_count + path: samples.aliquots.read_groups.submitted_unaligned_reads_files fn: count - name: _submitted_aligned_reads_files_count - path: biospecimens.samples.aliquots.analytes.read_groups.submitted_aligned_reads_files - fn: count - - name: _submitted_methylations_count - path: biospecimens.samples.aliquots.analytes.submitted_methylation_files + path: samples.aliquots.read_groups.submitted_aligned_reads_files fn: count - - name: _submitted_somatic_mutations_count - path: biospecimens.samples.aliquots.analytes.read_groups.submitted_somatic_mutations - fn: count - - name: _submitted_unaligned_reads_files_count - path: biospecimens.samples.aliquots.analytes.read_groups.submitted_unaligned_reads_files + - name: _simple_germline_variations_count + path: samples.aliquots.read_groups.simple_germline_variations fn: count + - name: current_smoker_baseline + path: exposures + src: current_smoker_baseline + fn: set + - name: ever_smoker_baseline + path: exposures + src: ever_smoker_baseline + fn: set + parent_props: + - path: studies[studies_submitter_id:submitter_id].projects[code] + - path: studies[studies_submitter_id:submitter_id].projects[code].programs[programs_name:name] + joining_props: + - index: file + join_on: _subject_id + props: + - name: data_format + src: data_format + fn: set + - name: data_type + src: data_type + fn: set + - name: file_count + src: _file_id + fn: count + - name: gen3.biodatacatalyst.nhlbi.nih.gov_file + doc_type: file + type: collector + root: None + category: data_file + props: + - name: object_id + - name: md5sum + - name: file_name + - name: file_size + - name: data_category + - name: data_format + - name: data_type + - name: state + - name: callset + - name: bucket_path + - name: source_node + injecting_props: + subject: + props: + - name: _subject_id + src: id + fn: set + - name: project_id + program: + props: + - name: programs_name + src: name + fn: set diff --git a/nightly.planx-pla.net/manifest.json b/nightly.planx-pla.net/manifest.json index 2f969ed21..a7fcf8b97 100644 --- a/nightly.planx-pla.net/manifest.json +++ b/nightly.planx-pla.net/manifest.json @@ -35,85 +35,22 @@ }, "sower": [ { - "name": "ingest-metadata-manifest", - "action": "ingest-metadata-manifest", - "activeDeadlineSeconds": 86400, - "serviceAccountName": "jobs-jenkins-blood-planx-pla-net", + "name": "pelican-export", + "action": "export", "container": { "name": "job-task", - "image": "quay.io/cdis/metadata-manifest-ingestion:master", + "image": "quay.io/cdis/pelican-export:master", "pull_policy": "Always", "env": [ { - "name": "GEN3_HOSTNAME", + "name": "DICTIONARY_URL", "valueFrom": { "configMapKeyRef": { "name": "manifest-global", - "key": "hostname" + "key": "dictionary_url" } } - } - ], - "volumeMounts": [ - { - "name": "creds-volume", - "readOnly": true, - "mountPath": "/creds.json", - "subPath": "creds.json" - } - ], - "cpu-limit": "1", - "memory-limit": "1Gi" - }, - "volumes": [ - { - "name": "creds-volume", - "secret": { - "secretName": "sower-jobs-g3auto" - } - } - ], - "restart_policy": "Never" - }, - { - "name": "get-dbgap-metadata", - "action": "get-dbgap-metadata", - "serviceAccountName": "jobs-jenkins-blood-planx-pla-net", - "container": { - "name": "job-task", - "image": "quay.io/cdis/get-dbgap-metadata:master", - "pull_policy": "Always", - "env": [], - "volumeMounts": [ - { - "name": "creds-volume", - "readOnly": true, - "mountPath": "/creds.json", - "subPath": "creds.json" - } - ], - "cpu-limit": "1", - "memory-limit": "1Gi" - }, - "volumes": [ - { - "name": "creds-volume", - "secret": { - "secretName": "sower-jobs-g3auto" - } - } - ], - "restart_policy": "Never" - }, - { - "name": "manifest-indexing", - "action": "index-object-manifest", - "serviceAccountName": "jobs-jenkins-blood-planx-pla-net", - "container": { - "name": "job-task", - "image": "quay.io/cdis/manifest-indexing:master", - "pull_policy": "Always", - "env": [ + }, { "name": "GEN3_HOSTNAME", "valueFrom": { @@ -122,72 +59,48 @@ "key": "hostname" } } + }, + { + "name": "ROOT_NODE", + "value": "subject" } ], "volumeMounts": [ { - "name": "sower-jobs-creds-volume", + "name": "pelican-creds-volume", "readOnly": true, - "mountPath": "/creds.json", + "mountPath": "/pelican-creds.json", + "subPath": "config.json" + }, + { + "name": "peregrine-creds-volume", + "readOnly": true, + "mountPath": "/peregrine-creds.json", "subPath": "creds.json" } ], "cpu-limit": "1", - "memory-limit": "1Gi" + "memory-limit": "12Gi" }, "volumes": [ { - "name": "sower-jobs-creds-volume", + "name": "pelican-creds-volume", "secret": { - "secretName": "sower-jobs-g3auto" - } - } - ], - "restart_policy": "Never" - }, - { - "name": "indexd-manifest", - "action": "download-indexd-manifest", - "serviceAccountName": "jobs-jenkins-blood-planx-pla-net", - "container": { - "name": "job-task", - "image": "quay.io/cdis/download-indexd-manifest:master", - "pull_policy": "Always", - "env": [ - { - "name": "GEN3_HOSTNAME", - "valueFrom": { - "configMapKeyRef": { - "name": "manifest-global", - "key": "hostname" - } - } - } - ], - "volumeMounts": [ - { - "name": "sower-jobs-creds-volume", - "readOnly": true, - "mountPath": "/creds.json", - "subPath": "creds.json" + "secretName": "pelicanservice-g3auto" } - ], - "cpu-limit": "1", - "memory-limit": "1Gi" - }, - "volumes": [ + }, { - "name": "sower-jobs-creds-volume", + "name": "peregrine-creds-volume", "secret": { - "secretName": "sower-jobs-g3auto" + "secretName": "peregrine-creds" } } ], "restart_policy": "Never" }, { - "name": "pelican-export", - "action": "export", + "name": "pelican-export-files", + "action": "export-files", "container": { "name": "job-task", "image": "quay.io/cdis/pelican-export:master", @@ -213,7 +126,11 @@ }, { "name": "ROOT_NODE", - "value": "subject" + "value": "file" + }, + { + "name": "EXTRA_NODES", + "value": "" } ], "volumeMounts": [ @@ -231,7 +148,7 @@ } ], "cpu-limit": "1", - "memory-limit": "4Gi" + "memory-limit": "12Gi" }, "volumes": [ { @@ -263,7 +180,7 @@ "environment": "qaplanetv1", "hostname": "nigthly.planx-pla.net", "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/bpadictionary/develop/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/gtexdictionary/4.4.5/schema.json", "portal_app": "gitops", "kube_bucket": "kube-qaplanetv1-gen3", "logs_bucket": "logs-qaplanetv1-gen3", @@ -271,7 +188,8 @@ "useryaml_s3path": "s3://cdis-gen3-users/qa/user.yaml", "dispatcher_job_num": "5", "pdb": "on", - "netpolicy": "on" + "netpolicy": "on", + "mutatedEnvHostname": "gen3.biodatacatalyst.nhlbi.nih.gov" }, "ssjdispatcher": { "job_images": { @@ -281,15 +199,15 @@ "guppy": { "indices": [ { - "index": "jenkins_subject_alias", + "index": "gen3.biodatacatalyst.nhlbi.nih.gov_subject", "type": "subject" }, { - "index": "jenkins_file_alias", + "index": "gen3.biodatacatalyst.nhlbi.nih.gov_file", "type": "file" } ], - "config_index": "jenkins_configs_alias", + "config_index": "gen3.biodatacatalyst.nhlbi.nih.gov_array-config", "auth_filter_field": "auth_resource_path" }, "scaling": { @@ -325,5 +243,6 @@ "guppy": { "strategy": "auto" } - } + }, + "portal": null } diff --git a/nightly.planx-pla.net/portal/gitops-createdby.png b/nightly.planx-pla.net/portal/gitops-createdby.png deleted file mode 100644 index b361a54a7..000000000 Binary files a/nightly.planx-pla.net/portal/gitops-createdby.png and /dev/null differ diff --git a/nightly.planx-pla.net/portal/gitops-favicon.ico b/nightly.planx-pla.net/portal/gitops-favicon.ico index 1b33622a8..bd02d0b17 100644 Binary files a/nightly.planx-pla.net/portal/gitops-favicon.ico and b/nightly.planx-pla.net/portal/gitops-favicon.ico differ diff --git a/nightly.planx-pla.net/portal/gitops-logo.png b/nightly.planx-pla.net/portal/gitops-logo.png index 4b3bb8f51..96609e40a 100644 Binary files a/nightly.planx-pla.net/portal/gitops-logo.png and b/nightly.planx-pla.net/portal/gitops-logo.png differ diff --git a/nightly.planx-pla.net/portal/gitops-sponsors/nhlbi.png b/nightly.planx-pla.net/portal/gitops-sponsors/nhlbi.png new file mode 100644 index 000000000..8153bbb9f Binary files /dev/null and b/nightly.planx-pla.net/portal/gitops-sponsors/nhlbi.png differ diff --git a/nightly.planx-pla.net/portal/gitops.css b/nightly.planx-pla.net/portal/gitops.css index 09a451791..4625abd6d 100644 --- a/nightly.planx-pla.net/portal/gitops.css +++ b/nightly.planx-pla.net/portal/gitops.css @@ -1 +1,170 @@ -/* gitops default css */ +:root { + --primary-color: #c0143c; + --secondary-color: #616265; + --g3-primary-btn__bg-color: #c02f42; +} + +/* Buttons */ + +.g3-button--primary, +.g3-dropdown-button__button--primary, +.data-dictionary__switch-button--active, +.popup__title { + background-color: var(--primary-color); +} + +.g3-button--primary:hover, +.g3-dropdown-button__button--primary:hover, +.data-dictionary__switch-button:hover { + background-color: var(--secondary-color) +} + +.g3-button--default:active, .g3-button--default:active svg path { + border: 1px solid var(--primary-color); + color: 1px solid var(--primary-color); + fill: 1px solid var(--primary-color); +} + +.g3-dropdown-button__button--primary:hover, +.g3-dropdown-button__button--primary:hover svg path, +.g3-dropdown-button__menu-trigger--primary:hover, +.g3-dropdown-button__menu-trigger--primary:hover svg path { + border: 1px solid black; +} + +/* fix for hard-coded orange button on File download page */ +.button-primary-orange { + background-color: var(--primary-color); +} +.button-primary-orange:hover { + background-color: var(--secondary-color); +} + +/* Nav Bars and Footer */ + +.top-bar, +.top-bar__header, +.top-icon-button.body-typo { + background-color: #616265; +} + +.top-bar__link { + border-right: 2px solid #fff; +} + +.nav-button:hover, +.button-active { + border-bottom: 3px solid var(--primary-color); +} + +.nav-bar__logo-img { + height: 110px; + margin-bottom: -30px; + margin-top: -25px; +} + +.footer__version-area { + width: 600px; +} + +/** + * hide footer versions from view, according to NIH guidelines that require + * footer to contain only links. + */ +.footer__version-area, .footer__logo-area { + display: none; +} + +.footer { + background-color: #000; +} + +.footer-container { + background-color: #000; +} + +.footer__nav { + background-color: #000; +} + +/* Data Explorer */ + +.filter-group__tab, +.g3-filter-group__tab { + border-top: 1px solid var(--primary-color); + border-right: 1px solid var(--primary-color); + border-left: 1px solid var(--primary-color); + color: var(--primary-color); +} + +.tier-access-selector__radio-input:checked + .tier-access-selector__customized-radio-input::after { + background-color: var(--primary-color); +} + +.filter-group__tab--selected, +.g3-filter-group__tab--selected { + background-color: var(--primary-color); + color: #fff; +} + +.aggregation-card .bucket-item .bucket-count { + color: var(--secondary-color); +} + +.aggregation-card input[type='checkbox']:checked { + background: var(--secondary-color); +} + +.g3-single-select-filter__checkbox:checked { + background: var(--primary-color); +} + +.sqon-clear { + background-color: var(--primary-color); +} + +.sqon-value { + background-color: var(--secondary-color); +} + +.sqon-value-group, .sqon-more, .sqon-less { + color: var(--primary-color); +} + +.input-range__track--active, +.rc-slider-track, +.g3-single-select-filter__count .g3-icon--under { + background-color: var(--primary-color); +} + +/* Charts */ + +tspan.special-number, +.special-number, +.form-special-number, +.g3-single-select-filter__count { + color: var(--primary-color); +} + +.special-number { + fill: var(--primary-color); +} + +.data-explorer__charts tspan.special-number, +.data-explorer__charts .special-number, +.data-explorer__charts .form-special-number { + color: var(--secondary-color); +} + +.data-explorer__charts .special-number { + fill: var(--secondary-color); +} + +.explorer-button-group__dropdown { + margin-right: 10px; +} + +/* Other */ +.protected-content { + background-color: #f4f4f6; +} diff --git a/nightly.planx-pla.net/portal/gitops.json b/nightly.planx-pla.net/portal/gitops.json index 0c49d7a11..fc6b53ae4 100644 --- a/nightly.planx-pla.net/portal/gitops.json +++ b/nightly.planx-pla.net/portal/gitops.json @@ -1,11 +1,15 @@ { - "gaTrackingId": "UA-119127212-2", + "gaTrackingId": "UA-119127212-18", + "grafanaFaroConfig": { + "grafanaFaroEnable": true, + "grafanaFaroNamespace": "bdcatprod" + }, "graphql": { "boardCounts": [ { - "graphql": "_case_count", - "name": "Case", - "plural": "Cases" + "graphql": "_subject_count", + "name": "Subject", + "plural": "Subjects" }, { "graphql": "_study_count", @@ -20,8 +24,8 @@ ], "chartCounts": [ { - "graphql": "_case_count", - "name": "Case" + "graphql": "_subject_count", + "name": "Subject" }, { "graphql": "_study_count", @@ -31,47 +35,49 @@ "projectDetails": "boardCounts" }, "components": { - "appName": "BloodPAC Metadata Submission Portal", + "appName": "NHLBI BioData Catalyst®", "index": { "introduction": { - "heading": "BloodPAC Data Commons", - "text": "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources.", + "heading": "", + "text": "NHLBI BioData Catalyst® (BDC) supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources.", "link": "/submission" }, "buttons": [ { "name": "Define Data Field", - "icon": "data-field-define", - "body": "The BloodPAC Data Commons define the data in a general way. Please study the dictionary before you start browsing.", + "icon": "stage-planning", + "body": "BDC define the data in a general way. Please study the dictionary before you start browsing.", "link": "/DD", "label": "Learn more" }, - { - "name": "Submit Data", - "icon": "data-submit", - "body": "Submit Data based on the dictionary.", - "link": "/submission", - "label": "Submit data" - }, { "name": "Explore Data", - "icon": "data-files", - "body": "The Explorer page gives you insights and a clear overview of data.", + "icon": "stage-explore", + "body": "The Exploration Page gives you insights and a clear overview under selected factors.", "link": "/explorer", "label": "Explore data" + } + ], + "homepageChartNodesExcludeFiles": true, + "homepageChartNodes": [ + { + "node": "subject", + "name": "Subjects" }, { - "name": "Access Data", - "icon": "data-access", - "body": "Getting metadata and other clinical variables exposed by API in our secure cloud environment.", - "link": "/query", - "label": "Query data" + "node": "study", + "name": "Studies" } ] }, "navigation": { - "title": "BloodPAC Data Commons", "items": [ + { + "icon": "query", + "link": "/discovery", + "color": "#a2a2a2", + "name": "Discovery" + }, { "icon": "dictionary", "link": "/DD", @@ -84,18 +90,6 @@ "color": "#a2a2a2", "name": "Exploration" }, - { - "icon": "query", - "link": "/query", - "color": "#a2a2a2", - "name": "Query" - }, - { - "icon": "workspace", - "link": "/workspace", - "color": "#a2a2a2", - "name": "Workspace" - }, { "icon": "profile", "link": "/identity", @@ -112,900 +106,1093 @@ "name": "Submit Data" }, { - "link": "https://www.synapse.org/#!Synapse:syn8011461/wiki/411591", + "link": "https://bdcatalyst.gitbook.io/biodata-catalyst-documentation/explore_data/gen3-discovering-data", "name": "Documentation" } ] }, "login": { - "title": "BloodPAC Data Commons", + "title": "NHLBI BioData Catalyst", "subTitle": "Explore, Analyze, and Share Data", - "text": "This website combines liquid biopsy data from academic, government, and industry partners and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for the treatment and prevention of cancer.", + "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.", "contact": "If you have any questions about access or the registration process, please contact ", - "email": "bpa-support@gen3.org" - } + "contact_link": { + "href": "https://biodatacatalyst.nhlbi.nih.gov/contact" + }, + "image": "stage-icons/stage-gene" + }, + "footerLogos": [ + { + "src": "/src/img/gen3.png", + "href": "https://ctds.uchicago.edu/gen3", + "alt": "Gen3 Data Commons" + }, + { + "src": "/src/img/createdby.png", + "href": "https://ctds.uchicago.edu/", + "alt": "Center for Translational Data Science at the University of Chicago" + }, + { + "src": "/src/img/sponsors/nhlbi.png", + "href": "https://www.nhlbi.nih.gov", + "alt": "NHLBI" + } + ], + "footer": { + "links": [ + { + "href": "https://biodatacatalyst.nhlbi.nih.gov/privacy/", + "text": "Privacy Policy" + }, + { + "href": "https://osp.od.nih.gov/scientific-sharing/policies/", + "text": "Data Sharing Policy" + }, + { + "text": "HHS Vulnerability Disclosure", + "href": "https://www.hhs.gov/vulnerability-disclosure-policy/index.html" + }, + { + "text": "Freedom of Information Act (FOIA)", + "href": "https://www.nhlbi.nih.gov/about/foia-fee-for-service-office" + }, + { + "text": "Accessibility", + "href": "https://biodatacatalyst.nhlbi.nih.gov/accessibility" + }, + { + "text": "U.S. Department of Health & Human Services", + "href": "https://www.hhs.gov" + }, + { + "text": "National Institutes of Health", + "href": "https://www.nih.gov" + }, + { + "text": "National Heart, Lung, and Blood Institute", + "href": "https://www.nhlbi.nih.gov" + }, + { + "text": "USA.gov", + "href": "https://www.usa.gov" + } + ] + }, + "categorical9Colors": [ + "#c0143c", + "#616265", + "#59CD90", + "#F2DC5D", + "#40476D", + "#FFA630", + "#AE8799", + "#1A535C", + "#462255" + ], + "categorical2Colors": [ + "#616265", + "#c0143c" + ] }, + "requiredCerts": [], "featureFlags": { - "explorer": true + "explorer": true, + "discovery": true }, - "explorerConfig": [ - { - "tabTitle": "Studies", - "charts": { - "project_id": { - "chartType": "count", - "title": "Projects" - }, - "study_setup": { - "chartType": "bar", - "title": "Study Setup" - }, - "study_objective": { - "chartType": "bar", - "title": "Study Objective" - }, - "study_design": { - "chartType": "bar", - "title": "Study Design" - } - }, - "filters": { - "tabs": [ - { - "title": "Studies", - "fields":[ - "project_id", - "study_setup", - "study_objective", - "study_design" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "study_description", - "data_description", - "study_setup", - "study_objective", - "study_design", - "associated_study", - "_cases_count", - "_biospecimens_count", - "_samples_count", - "_aliquots_count", - "_analytes_count", - "_immunoassays_count", - "_pcr_assays_count", - "_pcr_assay_files_count", - "_read_groups_count", - "_cell_images_count", - "_mass_cytometry_assays_count", - "_mass_cytometry_images_count", - "_slide_images_count", - "_submitted_unaligned_reads_files_count", - "_submitted_aligned_reads_files_count", - "_submitted_somatic_mutations_count", - "_submitted_methylations_count" - ] - }, - "buttons": [ - { - "enabled": true, - "type": "data", - "title": "Download Studies", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "studies.json" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "arrangerConfig": { - "projectId": "search", - "graphqlField": "study", - "index": "", - "nodeCountField": "project_id" - }, - "guppyConfig": { - "dataType": "study", - "nodeCountTitle": "Studies", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } + "dataExplorerConfig": { + "charts": { + "project_id": { + "chartType": "count", + "title": "Projects" + }, + "annotated_sex": { + "chartType": "pie", + "title": "Annotated Sex" + }, + "race": { + "chartType": "bar", + "title": "Race" + } }, - { - "tabTitle": "Cases", - "charts": { - "project_id": { - "chartType": "count", - "title": "Projects" - }, - "gender": { - "chartType": "pie", - "title": "Gender" - }, - "race": { - "chartType": "bar", - "title": "Race" - }, - "ethnicity": { - "chartType": "bar", - "title": "Ethnicity" - } - }, - "filters": { - "tabs": [ - { - "title": "Cases", - "fields":[ - "project_id", - "index_date", - "lost_to_followup", - "gender", - "days_to_birth", - "race", - "ethnicity" - ] - } + "filters": { + "tabs": [ + { + "title": "Project", + "fields": [ + "programs_name", + "project_id", + "consent_codes", + "studies_submitter_id", + "geographic_site", + "data_type", + "data_format" ] }, - "table": { - "enabled": true, + { + "title": "Subject", + "searchFields": [ + "submitter_id" + ], "fields": [ - "project_id", - "submitter_id", - "index_date", - "lost_to_followup", - "gender", - "days_to_birth", + "annotated_sex", "race", "ethnicity", - "data_format", + "hispanic_subgroup", + "subcohort", + "current_smoker_baseline", + "ever_smoker_baseline" + ] + }, + { + "title": "Harmonized Variables", + "fields": [ + "fasting_lipids", + "lipid_lowering_medication", + "carotid_plaque", + "carotid_stenosis", + "antihypertensive_meds", + "vte_case_status", + "vte_prior_history" + ] + } + ] + }, + "table": { + "enabled": true, + "fields": [ + "project_id", + "data_format", + "race", + "annotated_sex", + "ethnicity", + "hdl", + "ldl" + ] + }, + "dropdowns": { + "sevenBridges": { + "title": "Export to Seven Bridges" + } + }, + "buttons": [ + { + "enabled": true, + "type": "export-pfb-to-url", + "targetURLTemplate": "https://cgc.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc", + "title": "Export to CGC", + "rightIcon": "external-link", + "dropdownId": "sevenBridges" + }, + { + "enabled": true, + "type": "export-pfb-to-url", + "targetURLTemplate": "https://cavatica.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc", + "title": "Export to CAVATICA", + "rightIcon": "external-link", + "dropdownId": "sevenBridges" + }, + { + "enabled": true, + "type": "export-pfb-to-url", + "targetURLTemplate": "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/pfb?URL={{PRESIGNED_URL}}&source=bdc", + "title": "Export to BDC (Seven Bridges)", + "rightIcon": "external-link", + "dropdownId": "sevenBridges" + }, + { + "enabled": true, + "type": "export", + "title": "Export All to Terra", + "rightIcon": "external-link" + }, + { + "enabled": true, + "type": "export-to-pfb", + "title": "Export to PFB", + "leftIcon": "datafile", + "rightIcon": "download" + } + ], + "arrangerConfig": { + "projectId": "search", + "graphqlField": "subject", + "index": "", + "manifestMapping": { + "resourceIndexType": "file", + "resourceIdField": "object_id", + "referenceIdFieldInResourceIndex": "_subject_id", + "referenceIdFieldInDataIndex": "_subject_id" + }, + "nodeCountField": "_subject_id" + }, + "guppyConfig": { + "dataType": "subject", + "nodeCountTitle": "Subjects", + "fileCountField": "file_count", + "fieldMapping": [ + { + "field": "_subject_id", + "name": "Subject ID" + }, + { + "field": "consent_codes", + "name": "data use restriction" + }, + { + "field": "cac_score", + "name": "CAC Score" + }, + { + "field": "cac_volume", + "name": "CAC Volume" + }, + { + "field": "cimt_1", + "name": "CIMT 1" + }, + { + "field": "cimt_2", + "name": "CIMT 2" + }, + { + "field": "vte_case_status", + "name": "VTE Case Status" + }, + { + "field": "vte_followup_start_age", + "name": "VTE Followup Start Age" + }, + { + "field": "vte_prior_history", + "name": "VTE Prior History" + }, + { + "field": "basophil_ncnc_bld", + "name": "Basophils Number Concentration Bld" + }, + { + "field": "eosinophil_ncnc_bld", + "name": "Eosinophils Number Concentration Bld" + }, + { + "field": "hdl", + "name": "HDL" + }, + { + "field": "hematocrit_vfr_bld", + "name": "Hematocrit Fraction of Volume Bld" + }, + { + "field": "hemoglobin_mcnc_bld", + "name": "Hemoglobin Mass Concentration Bld" + }, + { + "field": "ldl", + "name": "LDL" + }, + { + "field": "lymphocyte_ncnc_bld", + "name": "Lymphocytes Number Concentration Bld" + }, + { + "field": "mch_entmass_rbc", + "name": "MCH Average Mass Rbc" + }, + { + "field": "mchc_mcnc_rbc", + "name": "MCHC Mass Concentration Rbc" + }, + { + "field": "mcv_entvol_rbc", + "name": "MCV Average Volume Rbc" + }, + { + "field": "monocyte_ncnc_bld", + "name": "Monocytes Number Concentration Bld" + }, + { + "field": "neutrophil_ncnc_bld", + "name": "Neutrophils Number Concentration Bld" + }, + { + "field": "platelet_ncnc_bld", + "name": "Platelets Number Concentration Bld" + }, + { + "field": "pmv_entvol_bld", + "name": "PMV Mean Volume Bld" + }, + { + "field": "rbc_ncnc_bld", + "name": "Red Blood Cells Number Concentration Bld" + }, + { + "field": "rdw_ratio_rbc", + "name": "Red Cell Distribution Width Ratio Rbc" + }, + { + "field": "wbc_ncnc_bld", + "name": "White Blood Cells Number Concentration Bld" + }, + { + "field": "bmi_baseline", + "name": "BMI Baseline" + }, + { + "field": "current_smoker_baseline", + "name": "Current Smoker Baseline" + }, + { + "field": "ever_smoker_baseline", + "name": "Ever Smoker Baseline" + }, + { + "field": "geographic_site", + "name": "Geographic Site" + }, + { + "field": "height_baseline", + "name": "Height Baseline" + }, + { + "field": "total_cholesterol", + "name": "Total Cholesterol" + }, + { + "field": "triglycerides", + "name": "Triglycerides" + }, + { + "field": "studies_submitter_id", + "name": "Study" + }, + { + "field": "programs_name", + "name": "Program" + } + ], + "manifestMapping": { + "resourceIndexType": "file", + "resourceIdField": "object_id", + "referenceIdFieldInResourceIndex": "_subject_id", + "referenceIdFieldInDataIndex": "_subject_id" + }, + "accessibleFieldCheckList": [ + "project_id" + ], + "accessibleValidationField": "project_id" + }, + "getAccessButtonLink": "https://dbgap.ncbi.nlm.nih.gov/", + "terraExportURL": "https://terra.biodatacatalyst.nhlbi.nih.gov/#import-data", + "terraTemplate": [ + "bdc", + "gen3" + ], + "sevenBridgesExportURL": "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/windmill" + }, + "fileExplorerConfig": { + "charts": { + "data_type": { + "chartType": "stackedBar", + "title": "File Type" + }, + "data_format": { + "chartType": "stackedBar", + "title": "File Format" + } + }, + "filters": { + "tabs": [ + { + "title": "File", + "fields": [ + "programs_name", + "project_id", + "data_category", "data_type", - "_biospecimens_count", - "_samples_count", - "_aliquots_count", - "_analytes_count", - "_immunoassays_count", - "_pcr_assays_count", - "_pcr_assay_files_count", - "_read_groups_count", - "_cell_images_count", - "_mass_cytometry_assays_count", - "_mass_cytometry_images_count", - "_slide_images_count", - "_submitted_unaligned_reads_files_count", - "_submitted_aligned_reads_files_count", - "_submitted_somatic_mutations_count", - "_submitted_methylations_count" + "data_format", + "callset" + ], + "searchFields": [ + "file_name" + ] + } + ] + }, + "table": { + "enabled": true, + "fields": [ + "project_id", + "file_name", + "file_size", + "object_id", + "callset" + ] + }, + "guppyConfig": { + "dataType": "file", + "fieldMapping": [ + { + "field": "object_id", + "name": "GUID" + }, + { + "field": "programs_name", + "name": "Program" + } + ], + "nodeCountTitle": "Files", + "manifestMapping": { + "resourceIndexType": "subject", + "resourceIdField": "_subject_id", + "referenceIdFieldInResourceIndex": "object_id", + "referenceIdFieldInDataIndex": "object_id" + }, + "accessibleFieldCheckList": [ + "project_id" + ], + "accessibleValidationField": "project_id", + "downloadAccessor": "object_id" + }, + "dropdowns": { + "sevenBridges": { + "title": "Export to Seven Bridges" + } + }, + "buttons": [ + { + "enabled": true, + "type": "export-file-pfb-to-url", + "targetURLTemplate": "https://cgc.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc", + "title": "Export to CGC", + "rightIcon": "external-link", + "dropdownId": "sevenBridges" + }, + { + "enabled": true, + "type": "export-file-pfb-to-url", + "targetURLTemplate": "https://cavatica.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc", + "title": "Export to CAVATICA", + "rightIcon": "external-link", + "dropdownId": "sevenBridges" + }, + { + "enabled": true, + "type": "export-file-pfb-to-url", + "targetURLTemplate": "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/pfb?URL={{PRESIGNED_URL}}&source=bdc", + "title": "Export to BDC (Seven Bridges)", + "rightIcon": "external-link", + "dropdownId": "sevenBridges" + }, + { + "enabled": true, + "type": "file-manifest", + "title": "Download Manifest", + "leftIcon": "datafile", + "rightIcon": "download", + "fileName": "file-manifest.json" + }, + { + "enabled": true, + "type": "export-files-to-pfb", + "title": "Export All to PFB", + "rightIcon": "external-link" + }, + { + "enabled": true, + "type": "export-files", + "title": "Export All to Terra", + "rightIcon": "external-link" + } + ], + "terraExportURL": "https://terra.biodatacatalyst.nhlbi.nih.gov/#import-data", + "terraTemplate": [ + "bdc", + "gen3" + ], + "sevenBridgesExportURL": "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/windmill", + "enableLimitedFilePFBExport": { + "sourceNodeField": "source_node" + } + }, + "discoveryConfig": { + "features": { + "pageTitle": { + "enabled": false, + "text": "Study Discovery" + }, + "tagsColumn": { + "enabled": false + }, + "tagsInDescription": { + "enabled": true + }, + "search": { + "searchBar": { + "enabled": true, + "searchableTextFields": [ + "name", + "full_name", + "_subjects_count", + "study_id", + "released", + "study_description", + "doi_titles", + "doi_version_information", + "doi_citation", + "doi_creators", + "doi_publisher", + "doi_identifier", + "doi_alternateIdentifiers", + "doi_contributors", + "doi_descriptions", + "doi_publication_year", + "doi_resolvable_link", + "doi_fundingReferences", + "doi_relatedIdentifiers" ] }, - "buttons": [ - { + "tagSearchDropdown": { + "enabled": true, + "collapsibleButtonText": "Study Filters" + } + }, + "authorization": { + "enabled": true, + "supportedValues": { + "accessible": { "enabled": true, - "type": "data", - "title": "Download Cases", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "cases.json" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" + "menuText": "Accessible" }, - { + "unaccessible": { "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" + "menuText": "Not Accessible" } - ], - "arrangerConfig": { - "projectId": "search", - "graphqlField": "case", - "index": "", - "nodeCountField": "project_id" - }, - "guppyConfig": { - "dataType": "case", - "nodeCountTitle": "Cases", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" } + } + }, + "aggregations": [ + { + "name": "Studies", + "field": "study_id", + "type": "count" }, { - "tabTitle": "Biospecimens", - "charts": { - "project_id": { - "chartType": "count", - "title": "Projects" - }, - "biospecimen_anatomic_site": { - "chartType": "bar", - "title": "Anatomic Site" + "name": "Total Subjects", + "field": "_subjects_count", + "type": "sum" + } + ], + "tagSelector": { + "title": "Tags by category", + "showTagCategoryNames": true + }, + "studyColumns": [ + { + "name": "Study Name", + "field": "name" + }, + { + "name": "Full Name", + "field": "full_name", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "", + "contentType": "string" + }, + { + "name": "Number of Subjects", + "field": "_subjects_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a", + "contentType": "number" + }, + { + "name": "dbGaP Accession Number", + "field": "study_id" + }, + { + "name": "Released", + "field": "released", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + } + ], + "studyPreviewField": { + "name": "Description", + "field": "study_description", + "contentType": "string", + "includeName": false, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "No description has been provided for this study." + }, + "studyPageFields": { + "showAllAvailableFields": false, + "header": { + "field": "name" + }, + "fieldsToShow": [ + { + "groupName": "Study Identifiers", + "includeName": false, + "fields": [ + { + "name": "Number of Subjects", + "field": "_subjects_count", + "contentType": "number" }, - "biospecimen_type": { - "chartType": "pie", - "title": "Biospecimen Type" + { + "name": "Full Name", + "field": "full_name", + "contentType": "string" }, - "blood_tube_type": { - "chartType": "bar", - "title": "Blood Tube Type" - } - }, - "filters": { - "tabs": [ - { - "title": "Biospecimens", - "fields":[ - "project_id", - "biospecimen_anatomic_site", - "biospecimen_type", - "blood_tube_type", - "days_to_collection", - "days_to_procurement", - "method_of_procurement", - "procured_or_purchased", - "tissue_type", - "disease_type", - "shipping_temperature", - "tumor_code", - "tumor_morphology", - "days_to_collection_other", - "days_to_procurement_other", - "biospecimen_volume", - "blood_draw_method", - "clinical_site", - "primary_site", - "tumor_descriptor", - "procurement_temperature", - "metastatic_bone", - "metastatic_visceral", - "metastatic_lymph_node", - "biospecimen_weight" - ] - }, - { - "title": "Samples", - "fields":[ - "composition", - "hours_to_fractionation_lower", - "hours_to_fractionation_upper", - "blood_fractionation_method", - "sample_volume", - "storage_agitation", - "storage_agitation_hours" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "biospecimen_anatomic_site", - "biospecimen_type", - "blood_tube_type", - "days_to_collection", - "days_to_procurement", - "method_of_procurement", - "procured_or_purchased", - "tissue_type", - "disease_type", - "shipping_temperature", - "tumor_code", - "tumor_morphology", - "days_to_collection_other", - "days_to_procurement_other", - "biospecimen_volume", - "blood_draw_method", - "clinical_site", - "primary_site", - "tumor_descriptor", - "procurement_temperature", - "metastatic_bone", - "metastatic_visceral", - "metastatic_lymph_node", - "biospecimen_weight", - "composition", - "hours_to_fractionation_lower", - "hours_to_fractionation_upper", - "blood_fractionation_method", - "sample_volume", - "storage_agitation", - "storage_agitation_hours" - ] - }, - "buttons": [ { - "enabled": true, - "type": "data", - "title": "Download Biospecimens", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "biospecimens.json" + "name": "Short Name", + "field": "short_name", + "contentType": "string", + "includeName": true, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "N/A" }, { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" + "name": "dbGaP Study Accession", + "field": "dbgap_accession", + "contentType": "string", + "includeName": true, + "includeIfNotAvailable": false }, { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" + "name": "Project ID", + "field": "project_id", + "contentType": "string", + "includeIfNotAvailable": false } - ], - "arrangerConfig": { - "projectId": "search", - "graphqlField": "biospecimen", - "index": "", - "nodeCountField": "project_id" - }, - "guppyConfig": { - "dataType": "biospecimen", - "nodeCountTitle": "Biospecimens", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } + ] }, { - "tabTitle": "Aliquots", - "charts": { - "aliquot_container": { - "chartType": "bar", - "title": "Aliquot Container" - }, - "clinical_or_contrived": { - "chartType": "pie", - "title": "Clinical vs. Contrived" - }, - "analyte_type": { - "chartType": "bar", - "title": "Analyte Type" - } - }, - "filters": { - "tabs": [ - { - "title": "Aliquots", - "fields":[ - "project_id", - "aliquot_container", - "clinical_or_contrived", - "preservation_method", - "storage_temperature", - "aliquot_volume", - "methanol_added", - "hours_to_freezer_lower", - "hours_to_freezer_lower_other", - "hours_to_freezer_upper", - "hours_to_freezer_upper_other", - "aliquot_quantity", - "contrivance_method" - ] - }, - { - "title": "Analytes", - "fields":[ - "analyte_isolation_method", - "analyte_type", - "cell_type", - "cell_identifier", - "frame_identifier", - "run_identifier", - "days_to_assay" - ] + "fields": [ + { + "name": "Description", + "field": "study_description", + "contentType": "paragraphs", + "includeName": false, + "includeIfNotAvailable": true, + "valueIfNotAvailable": "No description has been provided for this study." + } + ] + } + ] + }, + "detailView": { + "headerField": "project_id", + "tabs": [ + { + "tabName": "DOI", + "groups": [ + { + "header": "Dataset Information", + "fields": [ + { + "type": "block", + "label": "", + "sourceField": "doi_disclaimer", + "default": "" + }, + { + "type": "text", + "label": "Title:", + "sourceField": "doi_titles", + "default": "Not specified" + }, + { + "type": "link", + "label": "DOI:", + "sourceField": "doi_resolvable_link", + "default": "None" + }, + { + "type": "text", + "label": "Data available:", + "sourceField": "doi_is_available", + "default": "None" + }, + { + "type": "text", + "label": "Creators:", + "sourceField": "doi_creators", + "default": "Not specified" + }, + { + "type": "text", + "label": "Citation:", + "sourceField": "doi_citation", + "default": "Not specified" + }, + { + "type": "link", + "label": "Contact:", + "sourceField": "doi_contact", + "default": "Not specified" } ] }, - "table": { - "enabled": true, + { + "header": "How to Access the Data", "fields": [ - "project_id", - "submitter_id", - "aliquot_container", - "clinical_or_contrived", - "preservation_method", - "storage_temperature", - "aliquot_volume", - "methanol_added", - "hours_to_freezer_lower", - "hours_to_freezer_lower_other", - "hours_to_freezer_upper", - "hours_to_freezer_upper_other", - "aliquot_quantity", - "contrivance_method", - "analyte_isolation_method", - "analyte_type", - "cell_type", - "cell_identifier", - "frame_identifier", - "run_identifier", - "days_to_assay" + { + "type": "block", + "label": "How to access the data:", + "sourceField": "doi_access_information", + "default": "Not specified" + }, + { + "type": "link", + "label": "Data and access information:", + "sourceField": "doi_access_information_link", + "default": "Not specified" + } ] }, - "buttons": [ - { - "enabled": true, - "type": "data", - "title": "Download Aliquots", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "aliquots.json" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "arrangerConfig": { - "projectId": "search", - "graphqlField": "aliquot", - "index": "", - "nodeCountField": "project_id" + { + "header": "Additional Information", + "fields": [ + { + "type": "text", + "label": "Publisher:", + "sourceField": "doi_publisher", + "default": "Not specified" + }, + { + "type": "text", + "label": "Funded by:", + "sourceField": "doi_fundingReferences", + "default": "Not specified" + }, + { + "type": "text", + "label": "Publication Year:", + "sourceField": "doi_publication_year", + "default": "Not specified" + }, + { + "type": "text", + "label": "Resource Type:", + "sourceField": "doi_resource_type", + "default": "Not specified" + }, + { + "type": "text", + "label": "Version:", + "sourceField": "doi_version_information", + "default": "Not specified" + }, + { + "type": "text", + "label": "Contributors:", + "sourceField": "doi_contributors", + "default": "Not specified" + }, + { + "type": "text", + "label": "Related Identifiers:", + "sourceField": "doi_relatedIdentifiers", + "default": "Not specified" + } + ] }, - "guppyConfig": { - "dataType": "aliquot", - "nodeCountTitle": "Aliquots", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" + { + "header": "Description", + "fields": [ + { + "type": "block", + "label": "Description:", + "sourceField": "doi_descriptions", + "default": "Not specified" + } + ] } + ] }, { - "tabTitle": "Read Groups", - "charts": { - "instrument_model": { - "chartType": "bar", - "title": "Instrument Model" - }, - "library_preparation_kit_name": { - "chartType": "bar", - "title": "Library Prep Kit" - }, - "library_strategy": { - "chartType": "bar", - "title": "Library Strategy" - }, - "platform": { - "chartType": "bar", - "title": "Platform" - } - }, - "filters": { - "tabs": [ - { - "title": "Read Groups", - "fields":[ - "project_id", - "instrument_model", - "is_paired_end", - "library_preparation_kit_name", - "library_preparation_kit_vendor", - "library_preparation_kit_version", - "library_strategy", - "platform", - "read_group_name", - "read_length_lower", - "read_length_upper", - "barcoding_applied", - "target_capture_kit_name", - "library_name", - "library_selection", - "sequencing_center", - "library_strand", - "flow_cell_barcode", - "adapter_sequence", - "library_preparation_kit_catalog_number", - "cycles" - ] + "tabName": "Study", + "groups": [ + { + "header": "Study Information", + "fields": [ + { + "type": "text", + "label": "Full Name:", + "sourceField": "full_name", + "default": "Not specified" + }, + { + "type": "text", + "label": "Short Name:", + "sourceField": "short_name", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number Of Subjects:", + "sourceField": "_subjects_count", + "default": "Not specified" + }, + { + "type": "text", + "label": "dbGaP Accession Number:", + "sourceField": "dbgap_accession", + "default": "Not specified" + }, + { + "type": "link", + "label": "dbGaP URL:", + "sourceField": "dbgap_url", + "default": "Not specified" + }, + { + "type": "text", + "label": "Released:", + "sourceField": "released", + "default": "Not specified" + }, + { + "type": "tags" } ] }, - "table": { - "enabled": true, + { + "header": "Study Description", "fields": [ - "project_id", - "submitter_id", - "instrument_model", - "is_paired_end", - "library_preparation_kit_name", - "library_preparation_kit_vendor", - "library_preparation_kit_version", - "library_strategy", - "platform", - "read_group_name", - "read_length_lower", - "read_length_upper", - "barcoding_applied", - "target_capture_kit_name", - "library_name", - "library_selection", - "sequencing_center", - "library_strand", - "flow_cell_barcode", - "adapter_sequence", - "library_preparation_kit_catalog_number", - "cycles" + { + "type": "block", + "sourceField": "study_description" + } ] - }, - "buttons": [ - { - "enabled": true, - "type": "data", - "title": "Download Read Groups", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "read_groups.json" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "arrangerConfig": { - "projectId": "search", - "graphqlField": "read_group", - "index": "", - "nodeCountField": "project_id" - }, - "guppyConfig": { - "dataType": "read_group", - "nodeCountTitle": "Read Groups", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" } + ] }, { - "tabTitle": "Medical History", - "charts": { - "primary_diagnosis": { - "chartType": "bar", - "title": "Primary Diagnoses" - }, - "comorbidity": { - "chartType": "bar", - "title": "Comorbidities" - }, - "analyte_name": { - "chartType": "bar", - "title": "Diagnostic Tests" - }, - "therapeutic_agents": { - "chartType": "bar", - "title": "Treatments" - } + "tabName": "dbGaP FHIR", + "groups": [ + { + "header": "Disclaimer", + "fields": [ + { + "type": "block", + "sourceField": "DBGAP_FHIR_Disclaimer", + "default": "This information was retrieved from dbGaP's FHIR API for discoverability purposes and may not contain fully up-to-date information. Please refer to the official FHIR server for up-to-date FHIR data." + }, + { + "type": "link", + "label": "dbGaP FHIR Research Study URL:", + "sourceField": "DBGAP_FHIR_ResearchStudyURL", + "default": "Not specified" + } + ] }, - "filters": { - "tabs": [ - { - "title": "Projects", - "fields":[ - "project_id" - ] - }, - { - "title": "Comorbidities", - "fields":[ - "comorbidity", - "days_to_comorbidity" - ] - }, - { - "title": "Diagnoses", - "fields":[ - "age_at_diagnosis", - "best_overall_response", - "classification_of_tumor", - "days_to_best_overall_response", - "days_to_diagnosis", - "morphology", - "primary_diagnosis", - "prior_treatment", - "tissue_or_organ_of_origin", - "tumor_grade", - "ajcc_clinical_stage", - "overall_survival", - "progression_free_survival", - "ajcc_pathologic_stage", - "method_of_diagnosis", - "ajcc_pathologic_n", - "ajcc_pathologic_t", - "ajcc_pathologic_m" - ] - }, - { - "title": "Diagnostic Tests", - "fields":[ - "analyte_name", - "days_to_test", - "test_result", - "test_sample_composition", - "test_type", - "test_units", - "test_value" - ] - }, - { - "title": "Followups", - "fields":[ - "days_to_followup", - "time_from_alcohol", - "time_from_biopsy", - "time_from_exercise", - "time_from_food", - "time_from_physical_trauma", - "time_from_recreational_drugs", - "time_from_tobacco", - "time_from_treatment" - ] - }, - { - "title": "Treatments", - "fields":[ - "therapeutic_agents", - "treatment_intent_type", - "treatment_type", - "days_to_treatment_start", - "regimen_or_line_of_therapy", - "days_to_treatment_end", - "treatment_class", - "dosage", - "dosage_units" - ] + { + "header": "General Information", + "fields": [ + { + "type": "text", + "label": "Title:", + "sourceField": "DBGAP_FHIR_Title", + "default": "Not specified" + }, + { + "type": "text", + "label": "ID:", + "sourceField": "DBGAP_FHIR_Id", + "default": "Not specified" + }, + { + "type": "text", + "label": "Focus:", + "sourceField": "DBGAP_FHIR_Focus", + "default": "Not specified" + }, + { + "type": "text", + "label": "Identifier:", + "sourceField": "DBGAP_FHIR_Identifier", + "default": "Not specified" + }, + { + "type": "text", + "label": "Category:", + "sourceField": "DBGAP_FHIR_Category", + "default": "Not specified" + }, + { + "type": "text", + "label": "Status:", + "sourceField": "DBGAP_FHIR_Status", + "default": "Not specified" + }, + { + "type": "text", + "label": "Release Date:", + "sourceField": "DBGAP_FHIR_ReleaseDate", + "default": "Not specified" } ] }, - "table": { - "enabled": true, + { + "header": "Counts", "fields": [ - "project_id", - "submitter_id", - "comorbidity", - "days_to_comorbidity", - "age_at_diagnosis", - "best_overall_response", - "classification_of_tumor", - "days_to_best_overall_response", - "days_to_diagnosis", - "morphology", - "primary_diagnosis", - "prior_treatment", - "tissue_or_organ_of_origin", - "tumor_grade", - "ajcc_clinical_stage", - "overall_survival", - "progression_free_survival", - "ajcc_pathologic_stage", - "method_of_diagnosis", - "ajcc_pathologic_n", - "ajcc_pathologic_t", - "ajcc_pathologic_m", - "analyte_name", - "days_to_test", - "test_result", - "test_sample_composition", - "test_type", - "test_units", - "test_value", - "days_to_followup", - "time_from_alcohol", - "time_from_biopsy", - "time_from_exercise", - "time_from_food", - "time_from_physical_trauma", - "time_from_recreational_drugs", - "time_from_tobacco", - "time_from_treatment", - "therapeutic_agents", - "treatment_intent_type", - "treatment_type", - "days_to_treatment_start", - "regimen_or_line_of_therapy", - "days_to_treatment_end", - "treatment_class", - "dosage", - "dosage_units" + { + "type": "text", + "label": "Number of Samples:", + "sourceField": "DBGAP_FHIR_NumSamples", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number of Molecular Datasets:", + "sourceField": "DBGAP_FHIR_NumMolecularDatasets", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number Of Variables:", + "sourceField": "DBGAP_FHIR_NumVariables", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number of Subjects:", + "sourceField": "DBGAP_FHIR_NumSubjects", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number of Documents:", + "sourceField": "DBGAP_FHIR_NumDocuments", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number of Analyses:", + "sourceField": "DBGAP_FHIR_NumAnalysis", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number of Phenotype Datasets:", + "sourceField": "DBGAP_FHIR_NumPhenotypeDatasets", + "default": "Not specified" + }, + { + "type": "text", + "label": "Number of Sub Studies:", + "sourceField": "DBGAP_FHIR_NumSubStudies", + "default": "Not specified" + } ] }, - "buttons": [ - { - "enabled": true, - "type": "data", - "title": "Download Medical History", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "medical_history.json" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "arrangerConfig": { - "projectId": "search", - "graphqlField": "case", - "index": "", - "nodeCountField": "project_id" + { + "header": "Description", + "fields": [ + { + "type": "block", + "sourceField": "DBGAP_FHIR_Description" + } + ] }, - "guppyConfig": { - "dataType": "medical_history", - "nodeCountTitle": "Medical History", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Files", - "charts": { - "data_type": { - "chartType": "stackedBar", - "title": "File Type" - }, - "data_format": { - "chartType": "stackedBar", - "title": "File Format" - } - }, - "filters": { - "tabs": [ { - "title": "File", + "header": "Additional Information", "fields": [ - "project_id", - "data_type", - "data_format" + { + "type": "text", + "label": "Conditions:", + "sourceField": "DBGAP_FHIR_Condition", + "default": "Not specified" + }, + { + "type": "text", + "label": "Keywords:", + "sourceField": "DBGAP_FHIR_Keyword", + "default": "Not specified" + }, + { + "type": "link", + "label": "Study Overview URL:", + "sourceField": "DBGAP_FHIR_StudyOverviewUrl", + "default": "Not specified" + }, + { + "type": "text", + "label": "Part Of:", + "sourceField": "DBGAP_FHIR_PartOf", + "default": "Not specified" + }, + { + "type": "text", + "label": "Enrollment:", + "sourceField": "DBGAP_FHIR_Enrollment", + "default": "Not specified" + }, + { + "type": "text", + "label": "Sponsor:", + "sourceField": "DBGAP_FHIR_Sponsor", + "default": "Not specified" + } ] } ] }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "file_name", - "file_size", - "object_id" + { + "tabName": "Access", + "groups": [ + { + "fields": [ + { + "type": "accessDescriptor" + } + ] + }, + { + "header": "Study Access", + "fields": [ + { + "type": "text", + "sourceField": "study_data_requires_access_request", + "label": "Study Data Requires Access Request" + } + ] + } ] - }, - "guppyConfig": { - "dataType": "file", - "fieldMapping": [ - { "field": "object_id", "name": "GUID" } - ], - "nodeCountTitle": "Files", - "manifestMapping": { - "resourceIndexType": "case", - "resourceIdField": "case_id", - "referenceIdFieldInResourceIndex": "object_id", - "referenceIdFieldInDataIndex": "object_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id", - "downloadAccessor": "object_id" - }, - "buttons": [ - { - "enabled": true, - "type": "file-manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "file-manifest.json", - "dropdownId": "download" - }, - { - "enabled": true, - "type": "export-files-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "dropdowns": {} + } + ] + }, + "minimalFieldMapping": { + "tagsListFieldName": "tags", + "authzField": "authz", + "uid": "study_id" + }, + "tagCategories": [ + { + "name": "Program", + "color": "rgba(129, 211, 248, 1)", + "display": true + }, + { + "name": "Study Registration", + "color": "rgba(236, 128, 141, 1)", + "display": true + }, + { + "name": "Data Type", + "color": "rgba(112, 182, 3, 1)", + "display": true } - ] + ] + }, + "useArboristUI": true, + "terraExportWarning": { + "subjectThreshold": 120000, + "title": "Warning: Data Transfer May Fail in Terra", + "message": "Warning: Your selected cohort contains more subjects than are currently supported for import by Terra. It is recommended that you slice your data into segments of no more than 120,000 subjects and then export each segment separately. Would you like to continue anyway?" + }, + "ddUrl": "ddog-gov.com" }