diff --git a/.env.development b/.env.development
index 08bd4b5..cef14df 100644
--- a/.env.development
+++ b/.env.development
@@ -1,2 +1,2 @@
-GEN3_COMMONS_NAME=brh
-NEXT_PUBLIC_GEN3_API='https://brhstaging.data-commons.org'
+GEN3_COMMONS_NAME=gen3
+NEXT_PUBLIC_GEN3_API=https://brhstaging.data-commons.org
diff --git a/.env.production b/.env.production
index a2eb081..0a10ad9 100644
--- a/.env.production
+++ b/.env.production
@@ -1 +1 @@
-GEN3_COMMONS_NAME=brh
+GEN3_COMMONS_NAME=gen3
diff --git a/config/brh/colors.json b/config/brh/colors.json
deleted file mode 100644
index b339da3..0000000
--- a/config/brh/colors.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{
- "primary": "#3283C8",
- "secondary": "#3283C8",
- "accent": "#b75113",
- "base": "#c0c0c0",
- "accentWarm": "#25869b",
- "accentCool": "#1f839b",
- "chart": "#0d95A1",
- "table": "#c0c0c0"
-}
diff --git a/config/brh/discovery.json b/config/brh/discovery.json
deleted file mode 100644
index 76eff4b..0000000
--- a/config/brh/discovery.json
+++ /dev/null
@@ -1,290 +0,0 @@
-{
- "metadataConfig": [
- {
- "tableConfig": {
- "selectableRows": true,
- "expandableRows": true
- },
- "features": {
- "dataFetchFunction": "AggMDSAllLocal",
- "aiSearch": false,
- "advSearchFilters": {
- "enabled": false,
- "field": "advSearchFilters",
- "displayName": "Filters",
- "filters": [
- {
- "key": "Research Focus Area"
- },
- {
- "key": "Administering IC(s)"
- },
- {
- "key": "Simulated vs. Real Data"
- },
- {
- "key": "Year Grant Awarded"
- },
- {
- "key": "Study Description"
- }
- ]
- },
- "pageTitle": {
- "enabled": false,
- "text": "Study Discovery"
- },
- "tagsColumn": {
- "enabled": false
- },
- "tagsInDescription": {
- "enabled": true
- },
- "search": {
- "searchBar": {
- "enabled": true,
- "searchableTextFields": [
- "short_name",
- "full_name",
- "study_description",
- "study_id"
- ]
- },
- "tagSearchDropdown": {
- "enabled": true,
- "collapsibleButtonText": "Data Commons"
- },
- "exportToWorkspace": {
- "enabled": true,
- "manifestFieldName": "__manifest",
- "enableDownloadManifest": true,
- "downloadManifestButtonText": "Download",
- "documentationLinks": {
- "gen3Client": "https://gen3.org/resources/user/gen3-client/",
- "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/"
- }
- }
- },
- "authorization": {
- "enabled": true,
- "columnTooltip": "Filter by data access. Accessible indicates you are authorized to access. Not accessible indicates you are not authorized to access.",
- "supportedValues": {
- "accessible": {
- "enabled": true,
- "menuText": "Available"
- },
- "unaccessible": {
- "enabled": false,
- "menuText": "Not Accessible"
- },
- "pending": {
- "enabled": false,
- "menuText": "Pending"
- },
- "notAvailable": {
- "enabled": false,
- "menuText": "Not Available"
- }
- }
- }
- },
- "aggregations": [
- {
- "name": "Studies",
- "field": "_unique_id",
- "type": "count"
- },
- {
- "name": "Total Subjects",
- "field": "_subjects_count",
- "type": "sum"
- }
- ],
- "tagSelector": {
- "title": "Tags by category"
- },
- "studyColumns": [
- {
- "name": "Study Name",
- "field": "short_name",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a",
- "width": "157px",
- "contentType": "string"
- },
- {
- "name": "Full Name",
- "field": "full_name",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a",
- "width": "400px",
- "contentType": "string"
- },
- {
- "name": "Number of Subjects",
- "field": "_subjects_count",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a",
- "contentType": "number",
- "width": "98px"
- },
- {
- "name": "ID Number",
- "field": "study_id",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a",
- "width": "152px",
- "contentType": "string"
- },
- {
- "name": "Data Commons",
- "field": "commons",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a",
- "contentType": "link",
- "cellRenderFunction": "withURL",
- "params": {
- "hrefValueFromField": "commons_url"
- }
- },
- {
- "name": "DATA ACCESS METHOD",
- "field": "data_access_method",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "API",
- "contentType": "string"
- }
- ],
- "studyPreviewField": {
- "name": "Description",
- "field": "study_description",
- "contentType": "string",
- "includeName": false,
- "includeIfNotAvailable": true,
- "valueIfNotAvailable": "No description has been provided for this study."
- },
- "simpleDetailsView": {
- "showAllAvailableFields": false,
- "header": {
- "field": "name"
- },
- "fieldsToShow": [
- {
- "groupName": "Study Identifiers",
- "groupWidth": "half",
- "includeName": false,
- "fields": [
- {
- "name": "Number of Subjects",
- "field": "_subjects_count",
- "contentType": "number"
- },
- {
- "name": "Full Name",
- "field": "full_name",
- "contentType": "string"
- },
- {
- "name": "Short Name",
- "field": "short_name",
- "contentType": "text",
- "includeName": true,
- "includeIfNotAvailable": true,
- "valueIfNotAvailable": "N/A"
- },
- {
- "name": "dbGaP Accession Number",
- "field": "dbgap_accession",
- "contentType": "text",
- "includeName": true,
- "includeIfNotAvailable": false
- },
- {
- "name": "Project ID",
- "field": "project_id",
- "contentType": "text",
- "includeIfNotAvailable": false
- },
- {
- "name": "Data Commons",
- "field": "commons",
- "contentType": "text",
- "includeIfNotAvailable": false
- },
- {
- "name": "Tutorial Notebook",
- "field": "tutorial_notebook",
- "contentType": "text",
- "includeIfNotAvailable": true,
- "valueIfNotAvailable": "NO"
- }
- ]
- },
- {
- "groupWidth": "full",
- "fields": [
- {
- "name": "Description",
- "field": "study_description",
- "contentType": "paragraphs",
- "includeName": true,
- "includeIfNotAvailable": true,
- "valueIfNotAvailable": "No description has been provided for this study."
- }
- ]
- }
- ]
- },
- "minimalFieldMapping": {
- "tagsListFieldName": "tags",
- "authzField": "authz",
- "uid": "_unique_id"
- },
- "tags": {
- "tagCategories": [
- {
- "name": "Commons",
- "displayName": "Data Commons",
- "color": "rgba(129, 211, 248, 1)",
- "display": true
- },
- {
- "name": "Program",
- "color": "rgba(129, 211, 248, 1)",
- "display": false
- },
- {
- "name": "Study Registration",
- "color": "rgba(236, 128, 141, 1)",
- "display": false
- },
- {
- "name": "Data Type",
- "color": "rgba(112, 182, 3, 1)",
- "display": false
- },
- {
- "name": "primary_site",
- "color": "rgba(112, 182, 3, 1)",
- "display": false
- },
- {
- "name": "disease_type",
- "color": "rgba(112, 182, 3, 1)",
- "display": false
- },
- {
- "name": "data_type",
- "color": "rgba(112, 182, 3, 1)",
- "display": false
- },
- {
- "name": "clinical_study_type",
- "color": "rgba(112, 182, 3, 1)",
- "display": false
- }
- ]
- }
- }
- ]
-}
diff --git a/config/brh/footer.json b/config/brh/footer.json
deleted file mode 100644
index 6bbf956..0000000
--- a/config/brh/footer.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
- "classNames": {
- "root": "bg-base-darker",
- "layout": "flex items-center justify-end"
- },
- "rightSection":
- {
- "columns": [
- {
- "rows": [
- {
- "Icon": {
- "logo": "/icons/gen3.png",
- "width": 132,
- "height": 60,
- "description": "Gen3 Logo"
- }
- }
- ]
- },
- {
- "rows": [
- {
- "Icon": {
- "logo": "/icons/createdby.png",
- "width": 170,
- "height": 60,
- "description": "Created by CTDS"
- }
- }
- ]
- }
- ]
- }
-
-}
diff --git a/config/brh/landingPage.json b/config/brh/landingPage.json
deleted file mode 100644
index 306be39..0000000
--- a/config/brh/landingPage.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
- "body": [
- {
- "title": {
- "text": "Biomedical Research Hub",
- "level": 2
- }
- },
- {
- "splitarea": {
- "left": [
- {
- "text": "The Biomedical Research Hub (BRH) is a standard-based data ecosystem for securely managing, analyzing and sharing biomedical data to support research communities and collaborations."
- },
- {
- "link": {
- "href": "/Discovery",
- "text": "Discovery Data"
- }
- }
- ],
- "right": [
- {
- "image": {
- "src": "/images/kv.svg",
- "alt": "Gen3 Data Platform"
- }
- }
- ]
- }
- },
- {
- "break": "standard"
- }
- ]
-}
diff --git a/config/brh/login.json b/config/brh/login.json
deleted file mode 100644
index 15da29a..0000000
--- a/config/brh/login.json
+++ /dev/null
@@ -1,25 +0,0 @@
-{
- "topContent": [
- {
- "text": "Biomedical Research Hub",
- "className": "text-center text-3xl font-bold"
- },
- {
- "text": "Discover, Analyze, and Share Data",
- "className": "text-center text-xl font-medium"
- },
- {
- "text": "The Biomedical Research Hub (BRH) is a standard-based data ecosystem for securely managing, analyzing and sharing biomedical data to support research communities and collaborations.",
- "className": "text-center text-sm"
- }
- ],
- "bottomContent": [
- {
- "text": "If you have any questions about access or the registration process, please contact ",
- "className": "text-center text-sm"
- }
- ],
- "image": "/images/gene_side_texture.svg",
- "email": "brhsupport@datacommons.io",
- "showCredentialsLogin" : true
-}
diff --git a/config/brh/navigation.json b/config/brh/navigation.json
deleted file mode 100644
index 33f06f6..0000000
--- a/config/brh/navigation.json
+++ /dev/null
@@ -1,79 +0,0 @@
-{
- "navigation": {
- "classNames": {
- "root": "pl-1 mr-6 bg-base-max text-primary opacity-100 hover:opacity-100",
- "item": "py-2 px-4 hover:bg-base-lightest hover:text-base-contrast",
- "navigationPanel": "bg-base-max text-primary"
- },
- "logo": {
- "src": "/images/brh/logo.png",
- "height": 256,
- "width": 320,
- "href": "/"
- },
- "items": [
- {
- "icon": "gen3:query",
- "href": "/Discovery",
- "name": "Discovery",
- "tooltip": "Use free-text search and tags to rapidly find relevant studies, discover new datasets across multiple resources, and easily export selected data files to the analysis workspace."
- },
- {
- "name": "Workspace",
- "href": "/Workspace",
- "icon": "gen3:workspace",
- "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources."
- },
- {
- "name": "Notebooks",
- "href": "/NotebookLite",
- "icon": "gen3:notebook",
- "tooltip": "Notebooks for basic analysis"
- },
- {
- "icon": "gen3:profile",
- "href": "/Profile",
- "name": "Profile",
- "tooltip": "Create API keys for programmatic data access, and review your authorization privileges to datasets and services."
- }
- ]
- },
- "topBar": {
- "items": [
- {
- "link": "https://uc-cdis.github.io/BRH-documentation/",
- "name": "Documentation",
- "classNames": {
- "root": "border-base-light",
- "label": "text-white",
- "button": "hover:border-white"
- }
- },
- {
- "link": "brhsupport@datacommons.io",
- "name": "Email Support",
- "classNames": {
- "root": "border-base-light",
- "label": "text-white",
- "button": "hover:border-white"
- }
- },
- {
- "link": "https://uc-cdis.github.io/platform-citation/brh-cite/",
- "name": "Cite BRH",
- "classNames": {
- "root": "border-base-light",
- "label": "text-white",
- "button": "hover:border-white"
- }
- }
- ],
- "loginButtonVisibility": "visible",
- "classNames": {
- "root": "border-base-light text-primary-contrast-dark",
- "label": "text-primary-contrast",
- "button": "hover:border-white",
- "login" : "hover:border-white text-white"
- }
- }
-}
diff --git a/config/brh/profile.json b/config/brh/profile.json
deleted file mode 100644
index 9428194..0000000
--- a/config/brh/profile.json
+++ /dev/null
@@ -1,52 +0,0 @@
-{
- "hasExternalLogins" : true,
- "resourceTable": {
- "serviceColors": {
- "guppy": {
- "service": "guppy",
- "color": "red.4",
- "label": "Guppy"
- },
- "requestor": {
- "service": "requestor",
- "color": "yellow.5",
- "label": "Requestor"
- },
- "dictionary_page": {
- "service": "dictionary_page",
- "color": "blue.5",
- "label": "Dictionary Page"
- },
- "job": {
- "service": "job",
- "color": "indigo.7",
- "label": "Job"
- },
- "kayako": {
- "service": "kayako",
- "color": "yellow.6",
- "label": "Kayako"
- },
- "fence": {
- "service": "fence",
- "color": "teal.4",
- "label": "Fence"
- },
- "sheepdog": {
- "service": "sheepdog",
- "color": "grape.7",
- "label": "Sheepdog"
- },
- "peregrine": {
- "service": "peregrine",
- "color": "lime.7",
- "label": "Peregrine"
- },
- "jupyterhub": {
- "service": "jupyterhub",
- "color": "lime.4",
- "label": "JuptyerHub"
- }
- }
- }
-}
diff --git a/config/brh/query.json b/config/brh/query.json
deleted file mode 100644
index 2c63c08..0000000
--- a/config/brh/query.json
+++ /dev/null
@@ -1,2 +0,0 @@
-{
-}
diff --git a/config/gen3/colors.json b/config/gen3/colors.json
index 9ac464a..b339da3 100644
--- a/config/gen3/colors.json
+++ b/config/gen3/colors.json
@@ -1,9 +1,10 @@
{
- "primary": "#345948",
- "secondary": "#BF7E06",
- "accent": "#8C0404",
- "base": "#CCCCCC",
- "accentWarm": "#594B04",
- "accentCool": "#908719",
- "chart": "#0d95A1"
+ "primary": "#3283C8",
+ "secondary": "#3283C8",
+ "accent": "#b75113",
+ "base": "#c0c0c0",
+ "accentWarm": "#25869b",
+ "accentCool": "#1f839b",
+ "chart": "#0d95A1",
+ "table": "#c0c0c0"
}
diff --git a/config/brh/dataLibrary.json b/config/gen3/dataLibrary.json
similarity index 100%
rename from config/brh/dataLibrary.json
rename to config/gen3/dataLibrary.json
diff --git a/config/gen3/discovery.json b/config/gen3/discovery.json
index e49aaf3..76eff4b 100644
--- a/config/gen3/discovery.json
+++ b/config/gen3/discovery.json
@@ -1,350 +1,290 @@
{
- "tableConfig": {
- "selectableRows": true,
- "expandableRows": true
- },
- "features": {
- "advSearchFilters": {
- "enabled": true,
- "field": "advSearchFilters",
- "displayName": "Filters",
- "filters": [
- {
- "key": "Study Type"
+ "metadataConfig": [
+ {
+ "tableConfig": {
+ "selectableRows": true,
+ "expandableRows": true
+ },
+ "features": {
+ "dataFetchFunction": "AggMDSAllLocal",
+ "aiSearch": false,
+ "advSearchFilters": {
+ "enabled": false,
+ "field": "advSearchFilters",
+ "displayName": "Filters",
+ "filters": [
+ {
+ "key": "Research Focus Area"
+ },
+ {
+ "key": "Administering IC(s)"
+ },
+ {
+ "key": "Simulated vs. Real Data"
+ },
+ {
+ "key": "Year Grant Awarded"
+ },
+ {
+ "key": "Study Description"
+ }
+ ]
},
- {
- "key": "Data Type"
+ "pageTitle": {
+ "enabled": false,
+ "text": "Study Discovery"
},
- {
- "key": "Subject Type"
+ "tagsColumn": {
+ "enabled": false
+ },
+ "tagsInDescription": {
+ "enabled": true
+ },
+ "search": {
+ "searchBar": {
+ "enabled": true,
+ "searchableTextFields": [
+ "short_name",
+ "full_name",
+ "study_description",
+ "study_id"
+ ]
+ },
+ "tagSearchDropdown": {
+ "enabled": true,
+ "collapsibleButtonText": "Data Commons"
+ },
+ "exportToWorkspace": {
+ "enabled": true,
+ "manifestFieldName": "__manifest",
+ "enableDownloadManifest": true,
+ "downloadManifestButtonText": "Download",
+ "documentationLinks": {
+ "gen3Client": "https://gen3.org/resources/user/gen3-client/",
+ "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/"
+ }
+ }
},
+ "authorization": {
+ "enabled": true,
+ "columnTooltip": "Filter by data access. Accessible indicates you are authorized to access. Not accessible indicates you are not authorized to access.",
+ "supportedValues": {
+ "accessible": {
+ "enabled": true,
+ "menuText": "Available"
+ },
+ "unaccessible": {
+ "enabled": false,
+ "menuText": "Not Accessible"
+ },
+ "pending": {
+ "enabled": false,
+ "menuText": "Pending"
+ },
+ "notAvailable": {
+ "enabled": false,
+ "menuText": "Not Available"
+ }
+ }
+ }
+ },
+ "aggregations": [
{
- "key": "Gender"
+ "name": "Studies",
+ "field": "_unique_id",
+ "type": "count"
},
{
- "key": "Age"
+ "name": "Total Subjects",
+ "field": "_subjects_count",
+ "type": "sum"
}
- ]
- },
- "tagsColumn": {
- "enabled": false
- },
- "tagsInDescription": {
- "enabled": true
- },
- "exportToWorkspace": {
- "enabled": true,
- "manifestFieldName": "__manifest",
- "enableDownloadManifest": true,
- "enableDownloadZip": true,
- "downloadZipButtonText": "Download Zip",
- "downloadManifestButtonText": "Download Manifest",
- "documentationLinks": {
- "gen3Client": "https://gen3.org/resources/user/gen3-client/",
- "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/"
+ ],
+ "tagSelector": {
+ "title": "Tags by category"
},
- "verifyExternalLogins": true
- },
- "pageTitle": {
- "enabled": false
- },
- "search": {
- "searchBar": {
- "enabled": true,
- "inputSubtitle": "Examples: pain, buprenorphine, intervention",
- "searchableTextFields": [
- "study_metadata.minimal_info.study_description",
- "institutions",
- "investigators_name",
- "study_metadata.minimal_info.study_name",
- "project_number",
- "study_metadata.metadata_location.nih_application_id",
- "_hdp_uid",
- "dataset_1_title",
- "dataset_2_title",
- "dataset_3_title",
- "dataset_4_title",
- "administering_ic",
- "research_program",
- "doi_identifier",
- "doi_resolvable_link"
- ]
- },
- "tagSearchDropdown": {
- "enabled": true,
- "collapsibleButtonText": "Data Repository"
- }
- },
- "authorization": {
- "enabled": true,
- "columnTooltip": "Filter by data access",
- "supportedValues": {
- "accessible": {
- "enabled": true,
- "menuText": "Available"
+ "studyColumns": [
+ {
+ "name": "Study Name",
+ "field": "short_name",
+ "errorIfNotAvailable": false,
+ "valueIfNotAvailable": "n/a",
+ "width": "157px",
+ "contentType": "string"
},
- "unaccessible": {
- "enabled": false,
- "menuText": "Not Accessible"
+ {
+ "name": "Full Name",
+ "field": "full_name",
+ "errorIfNotAvailable": false,
+ "valueIfNotAvailable": "n/a",
+ "width": "400px",
+ "contentType": "string"
},
- "pending": {
- "enabled": true,
- "menuText": "Pending"
+ {
+ "name": "Number of Subjects",
+ "field": "_subjects_count",
+ "errorIfNotAvailable": false,
+ "valueIfNotAvailable": "n/a",
+ "contentType": "number",
+ "width": "98px"
},
- "notAvailable": {
- "enabled": true,
- "menuText": "Not Available"
+ {
+ "name": "ID Number",
+ "field": "study_id",
+ "errorIfNotAvailable": false,
+ "valueIfNotAvailable": "n/a",
+ "width": "152px",
+ "contentType": "string"
+ },
+ {
+ "name": "Data Commons",
+ "field": "commons",
+ "errorIfNotAvailable": false,
+ "valueIfNotAvailable": "n/a",
+ "contentType": "link",
+ "cellRenderFunction": "withURL",
+ "params": {
+ "hrefValueFromField": "commons_url"
+ }
+ },
+ {
+ "name": "DATA ACCESS METHOD",
+ "field": "data_access_method",
+ "errorIfNotAvailable": false,
+ "valueIfNotAvailable": "API",
+ "contentType": "string"
}
- }
- }
- },
- "aggregations": [
- {
- "name": "Studies",
- "field": "_hdp_uid",
- "type": "count"
- }
- ],
- "tagSelector": {
- "showTagCategoryNames": true
- },
- "studies": [],
- "studyColumns": [
- {
- "name": "Project Title",
- "field": "study_metadata.minimal_info.study_name",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a"
- },
- {
- "name": "HEAL Research Focus Area",
- "field": "research_focus_area",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a"
- },
- {
- "name": "HEAL Research Program",
- "field": "research_program",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a"
- },
- {
- "name": "Investigator(s)",
- "field": "investigators_name",
- "errorIfNotAvailable": false,
- "valueIfNotAvailable": "n/a"
- }
- ],
- "studyPreviewField": {
- "name": "Summary",
- "field": "study_metadata.minimal_info.study_description",
- "contentType": "string",
- "includeName": false,
- "includeIfNotAvailable": true,
- "valueIfNotAvailable": "No summary has been provided for this study."
- },
- "detailView": {
- "headerField": "study_metadata.minimal_info.study_name",
- "tabs": [
- {
- "tabName": "Summary",
- "groups": [
- {
- "header": "Study Description Summary",
- "fields": [
- {
- "type": "block",
- "sourceField": "study_metadata.minimal_info.study_description"
- }
- ]
- },
+ ],
+ "studyPreviewField": {
+ "name": "Description",
+ "field": "study_description",
+ "contentType": "string",
+ "includeName": false,
+ "includeIfNotAvailable": true,
+ "valueIfNotAvailable": "No description has been provided for this study."
+ },
+ "simpleDetailsView": {
+ "showAllAvailableFields": false,
+ "header": {
+ "field": "name"
+ },
+ "fieldsToShow": [
{
- "header": "HEAL Research Initiative/Award Administration",
+ "groupName": "Study Identifiers",
+ "groupWidth": "half",
+ "includeName": false,
"fields": [
{
- "type": "text",
- "label": "Project Number",
- "sourceField": "project_number",
- "default": ""
- },
- {
- "type": "text",
- "label": "HEAL Research Program",
- "sourceField": "research_program",
- "default": "Not specified"
- },
- {
- "type": "text",
- "label": "Institution(s)",
- "sourceField": "institutions"
- },
- {
- "type": "text",
- "label": "Investigator(s)",
- "sourceField": "investigators_name"
- },
- {
- "type": "text",
- "label": "Administering IC(s)",
- "sourceField": "administering_ic"
+ "name": "Number of Subjects",
+ "field": "_subjects_count",
+ "contentType": "number"
},
{
- "type": "text",
- "label": "Year Grant Awarded",
- "sourceField": "year_awarded"
+ "name": "Full Name",
+ "field": "full_name",
+ "contentType": "string"
},
{
- "type": "link",
- "label": "NIH RePORTER Link",
- "sourceField": "study_metadata.metadata_location.nih_reporter_link"
+ "name": "Short Name",
+ "field": "short_name",
+ "contentType": "text",
+ "includeName": true,
+ "includeIfNotAvailable": true,
+ "valueIfNotAvailable": "N/A"
},
{
- "type": "text",
- "label": "Clinical Trial ID",
- "sourceField": "study_metadata.metadata_location.clinical_trials_study_ID"
+ "name": "dbGaP Accession Number",
+ "field": "dbgap_accession",
+ "contentType": "text",
+ "includeName": true,
+ "includeIfNotAvailable": false
},
{
- "type": "link",
- "label": "Clinical Trial Link",
- "sourceField": "study_metadata.metadata_location.clinical_trials_study_link"
+ "name": "Project ID",
+ "field": "project_id",
+ "contentType": "text",
+ "includeIfNotAvailable": false
},
{
- "type": "text",
- "label": "DOI",
- "sourceField": "doi_identifier"
+ "name": "Data Commons",
+ "field": "commons",
+ "contentType": "text",
+ "includeIfNotAvailable": false
},
{
- "type": "link",
- "label": "DOI Link",
- "sourceField": "doi_resolvable_link"
+ "name": "Tutorial Notebook",
+ "field": "tutorial_notebook",
+ "contentType": "text",
+ "includeIfNotAvailable": true,
+ "valueIfNotAvailable": "NO"
}
]
},
{
- "header": "Study Characteristics",
+ "groupWidth": "full",
"fields": [
{
- "type": "tags",
- "sourceField": "tags"
+ "name": "Description",
+ "field": "study_description",
+ "contentType": "paragraphs",
+ "includeName": true,
+ "includeIfNotAvailable": true,
+ "valueIfNotAvailable": "No description has been provided for this study."
}
]
}
]
},
- {
- "tabName": "Data",
- "groups": [
+ "minimalFieldMapping": {
+ "tagsListFieldName": "tags",
+ "authzField": "authz",
+ "uid": "_unique_id"
+ },
+ "tags": {
+ "tagCategories": [
{
- "fields": [
- {
- "type": "accessDescriptor"
- }
- ]
+ "name": "Commons",
+ "displayName": "Data Commons",
+ "color": "rgba(129, 211, 248, 1)",
+ "display": true
},
{
- "header": "Repository",
- "fields": [
- {
- "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_study_link",
- "type": "linkList",
- "label": ""
- }
- ]
- }
- ]
- },
- {
- "tabName": "Cite",
- "groups": [
+ "name": "Program",
+ "color": "rgba(129, 211, 248, 1)",
+ "display": false
+ },
{
- "header": "Citation Requirements",
- "fields": [
- {
- "type": "text",
- "label": "Cite the study on the HEAL Data Platform",
- "sourceField": "study_metadata.citation.heal_platform_citation"
- },
- {
- "type": "text",
- "label": "Cite the study at the local repository",
- "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_citation"
- }
- ]
- }
- ]
- },
- {
- "tabName": "Related Studies",
- "groups": [
+ "name": "Study Registration",
+ "color": "rgba(236, 128, 141, 1)",
+ "display": false
+ },
{
- "header": "Related Studies",
- "fields": [
- {
- "type": "linkList",
- "sourceField": "related_studies",
- "label": "",
- "renderFunction": "linkWithTitle"
- }
- ]
+ "name": "Data Type",
+ "color": "rgba(112, 182, 3, 1)",
+ "display": false
+ },
+ {
+ "name": "primary_site",
+ "color": "rgba(112, 182, 3, 1)",
+ "display": false
+ },
+ {
+ "name": "disease_type",
+ "color": "rgba(112, 182, 3, 1)",
+ "display": false
+ },
+ {
+ "name": "data_type",
+ "color": "rgba(112, 182, 3, 1)",
+ "display": false
+ },
+ {
+ "name": "clinical_study_type",
+ "color": "rgba(112, 182, 3, 1)",
+ "display": false
}
]
}
- ]
- },
- "tagsDisplayName": "Study Filters",
- "tagColumnWidth": "500px",
- "minimalFieldMapping": {
- "authzField": "authz",
- "tagsListFieldName": "tags",
- "dataAvailabilityField": "data_availability",
- "uid": "_hdp_uid"
- },
- "tagCategories": [
- {
- "name": "Study Type",
- "color": "#532565",
- "display": false
- },
- {
- "name": "Data Type",
- "color": "#982568",
- "display": false
- },
- {
- "name": "Subject Type",
- "color": "#981f32",
- "display": false
- },
- {
- "name": "Gender",
- "color": "#bf362e",
- "display": false
- },
- {
- "name": "Age",
- "color": "#e07c3e",
- "display": false
- },
- {
- "name": "Research Program",
- "color": "#532565",
- "display": false
- },
- {
- "name": "Commons",
- "displayName": "Data Resources",
- "color": "#981f32",
- "display": false
- },
- {
- "name": "Other",
- "color": "#bf362e",
- "display": false
- },
- {
- "name": "Data Repository",
- "color": "#bf362e",
- "display": true
}
]
}
diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json
deleted file mode 100644
index afee5ea..0000000
--- a/config/gen3/explorer.json
+++ /dev/null
@@ -1,785 +0,0 @@
-[
- {
- "tabTitle": "Cases",
- "charts": {
- "covid19_positive": {
- "chartType": "fullPie",
- "title": "COVID-19 Positive"
- },
- "sex": {
- "chartType": "fullPie",
- "title": "Sex"
- },
- "race": {
- "chartType": "fullPie",
- "title": "Race"
- }
- },
- "filters": {
- "tabs": [
- {
- "title": "Demographics",
- "fields": [
- "sex",
- "race",
- "ethnicity",
- "age_at_index",
- "index_event",
- "zip",
- "covid19_positive",
- "project_id"
- ]
- },
- {
- "title": "COVID Tests",
- "fields": [
- "measurements.test_name",
- "measurements.test_result_text",
- "measurements.test_method",
- "measurements.test_days_from_index"
- ]
- },
- {
- "title": "Medications",
- "fields": [
- "medications.days_to_medication_start",
- "medications.days_to_medication_end",
- "medications.dose_sequence_number",
- "medications.medication_code",
- "medications.medication_code_system",
- "medications.medication_manufacturer",
- "medications.medication_name",
- "medications.medication_status",
- "medications.medication_type"
- ]
- },
- {
- "title": "Procedures",
- "fields": [
- "procedures.breathing_support_type",
- "procedures.days_to_procedure_start",
- "procedures.days_to_procedure_end",
- "procedures.procedure_name"
- ]
- },
- {
- "title": "Conditions",
- "fields": [
- "conditions.condition_name",
- "conditions.condition_code_system",
- "conditions.condition_code",
- "conditions.days_to_condition_start",
- "conditions.days_to_condition_end"
- ]
- }
- ]
- },
- "table": {
- "enabled": true,
- "fields": [
- "submitter_id",
- "sex",
- "age_at_index",
- "index_event",
- "race",
- "ethnicity",
- "zip",
- "covid19_positive",
- "measurements.test_name",
- "measurements.test_result_text",
- "measurements.test_method",
- "measurements.test_days_from_index",
- "medications.days_to_medication_start",
- "medications.days_to_medication_end",
- "medications.dose_sequence_number",
- "medications.medication_code",
- "medications.medication_code_system",
- "medications.medication_manufacturer",
- "medications.medication_name",
- "medications.medication_status",
- "medications.medication_type",
- "procedures.breathing_support_type",
- "procedures.days_to_procedure_start",
- "procedures.days_to_procedure_end",
- "procedures.procedure_name",
- "conditions.condition_name",
- "conditions.condition_code_system",
- "conditions.condition_code",
- "conditions.days_to_condition_start",
- "conditions.days_to_condition_end",
- "_imaging_studies_count",
- "_ct_series_file_count",
- "_dx_series_file_count",
- "_cr_series_file_count",
- "_mr_series_file_count",
- "project_id"
- ],
- "columns": {
- "measurements.test_name": {
- "title": "Test Name",
- "type": "array",
- "accessorPath": "measurements[*].test_name"
- },
- "measurements.test_result_text": {
- "title": "Test Results Text",
- "type": "array",
- "accessorPath": "measurements[*].test_result_text",
- "cellRenderFunction": "NegativePositive"
- },
- "measurements.test_method": {
- "title": "Test Method",
- "type": "array",
- "accessorPath": "measurements[*].test_method"
- },
- "measurements.test_days_from_index": {
- "title": "Test Days from Index",
- "type": "array",
- "accessorPath": "measurements[*].test_days_from_index"
- }
- }
- },
- "dropdowns": {
- "download-table": {
- "title": "Download Case Metadata Table"
- }
- },
- "buttons": [
- {
- "enabled": true,
- "type": "data-json",
- "title": "JSON",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Cases_table.json"
- },
- {
- "enabled": true,
- "type": "data-tsv",
- "title": "TSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Cases_table.tsv"
- },
- {
- "enabled": true,
- "type": "data-csv",
- "title": "CSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Cases_table.csv"
- },
- {
- "enabled": true,
- "type": "manifest",
- "title": "Download File Manifest for Cases",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_case_manifest.json"
- },
- {
- "enabled": false,
- "type": "export-to-workspace",
- "title": "Export to Workspace",
- "leftIcon": "datafile",
- "rightIcon": "download"
- }
- ],
- "loginForDownload": true,
- "guppyConfig": {
- "dataType": "case",
- "nodeCountTitle": "Cases",
- "fieldMapping": [
- {
- "field": "project_id",
- "name": "Project ID"
- },
- {
- "field": "submitter_id",
- "name": "Case ID"
- },
- {
- "field": "_imaging_studies_count",
- "name": "Imaging Studies Count"
- },
- {
- "field": "_ct_series_file_count",
- "name": "CT Series Count"
- },
- {
- "field": "_dx_series_file_count",
- "name": "DX Series Count"
- },
- {
- "field": "_cr_series_file_count",
- "name": "CR Series Count"
- },
- {
- "field": "_mr_series_file_count",
- "name": "MR Series Count"
- }
- ],
- "manifestMapping": {
- "resourceIndexType": "imaging_data_file",
- "resourceIdField": "object_id",
- "referenceIdFieldInResourceIndex": "_case_id",
- "referenceIdFieldInDataIndex": "_case_id"
- },
- "accessibleFieldCheckList": [
- "project_id"
- ],
- "accessibleValidationField": "project_id"
- }
- },
- {
- "tabTitle": "Measurements",
- "charts": {
- "test_method": {
- "chartType": "fullPie",
- "title": "Test Method"
- },
- "test_result_text": {
- "chartType": "fullPie",
- "title": "COVID-19 Test Result"
- },
- "test_name": {
- "chartType": "donut",
- "title": "Test Name"
- }
- },
- "filters": {
- "tabs": [
- {
- "title": "COVID-19 Tests",
- "fields": [
- "test_method",
- "test_result_text",
- "test_name",
- "test_days_from_index",
- "project_id"
- ]
- }
- ]
- },
- "table": {
- "enabled": true,
- "fields": [
- "case_ids",
- "test_method",
- "test_result_text",
- "test_name",
- "test_days_from_index",
- "submitter_id",
- "project_id"
- ]
- },
- "dropdowns": {
- "download-table": {
- "title": "Download Measurements Metadata Table"
- }
- },
- "buttons": [
- {
- "enabled": true,
- "type": "data-json",
- "title": "JSON",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Measurements_table.json"
- },
- {
- "enabled": true,
- "type": "data-tsv",
- "title": "TSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Measurements_table.tsv"
- },
- {
- "enabled": true,
- "type": "data-csv",
- "title": "CSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Measurements_table.csv"
- }
- ],
- "loginForDownload": true,
- "guppyConfig": {
- "dataType": "measurement",
- "nodeCountTitle": "Measurements",
- "fieldMapping": [
- {
- "field": "project_id",
- "name": "Project ID"
- },
- {
- "field": "submitter_id",
- "name": "Measurement ID"
- },
- {
- "field": "case_ids",
- "name": "Case ID"
- }
- ],
- "accessibleFieldCheckList": [
- "project_id"
- ],
- "accessibleValidationField": "project_id"
- }
- },
- {
- "tabTitle": "Imaging Studies",
- "charts": {
- "study_modality": {
- "chartType": "fullPie",
- "title": "Study Modality"
- },
- "sex": {
- "chartType": "fullPie",
- "title": "Case Sex"
- }
- },
- "filters": {
- "tabs": [
- {
- "title": "Study Properties",
- "fields": [
- "study_modality",
- "study_description",
- "age_at_imaging",
- "study_year",
- "study_year_shifted",
- "body_part_examined",
- "study_location",
- "days_from_study_to_pos_covid_test",
- "days_from_study_to_neg_covid_test",
- "project_id"
- ]
- },
- {
- "title": "LOINC Properties",
- "fields": [
- "loinc_long_common_name",
- "loinc_method",
- "loinc_system",
- "loinc_contrast",
- "loinc_code"
- ]
- },
- {
- "title": "Imaging Properties",
- "fields": [
- "data_format",
- "data_category",
- "data_type"
- ]
- },
- {
- "title": "Case Demographics",
- "fields": [
- "covid19_positive",
- "age_at_index",
- "sex",
- "race",
- "ethnicity",
- "zip",
- "index_event"
- ]
- }
- ]
- },
- "table": {
- "enabled": true,
- "fields": [
- "submitter_id",
- "study_modality",
- "study_description",
- "body_part_examined",
- "age_at_imaging",
- "days_to_study",
- "study_year",
- "study_year_shifted",
- "loinc_long_common_name",
- "loinc_method",
- "loinc_system",
- "loinc_contrast",
- "loinc_code",
- "days_from_study_to_pos_covid_test",
- "days_from_study_to_neg_covid_test",
- "covid19_positive",
- "age_at_index",
- "index_event",
- "sex",
- "race",
- "ethnicity",
- "zip",
- "_ct_series_file_count",
- "_dx_series_file_count",
- "_cr_series_file_count",
- "_mr_series_file_count",
- "data_format",
- "data_category",
- "data_type",
- "study_uid",
- "case_ids",
- "object_id",
- "project_id"
- ],
- "dicomViewerId": "submitter_id",
- "linkFields": [
- "submitter_id"
- ]
- },
- "dropdowns": {
- "download-table": {
- "title": "Download Imaging Studies Table"
- }
- },
- "buttons": [
- {
- "enabled": true,
- "type": "data-json",
- "title": "JSON",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Studies_table.json"
- },
- {
- "enabled": true,
- "type": "data-tsv",
- "title": "TSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Studies_table.tsv"
- },
- {
- "enabled": true,
- "type": "data-csv",
- "title": "CSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Studies_table.csv"
- },
- {
- "enabled": true,
- "type": "manifest",
- "title": "Download File Manifest for Imaging Studies",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_imaging_study_manifest.json"
- },
- {
- "enabled": false,
- "type": "export-to-workspace",
- "title": "Export to Workspace",
- "leftIcon": "datafile",
- "rightIcon": "download"
- }
- ],
- "loginForDownload": true,
- "guppyConfig": {
- "dataType": "imaging_study",
- "nodeCountTitle": "Imaging Studies",
- "fieldMapping": [
- {
- "field": "project_id",
- "name": "Project ID"
- },
- {
- "field": "submitter_id",
- "name": "Browse in DICOM viewer"
- },
- {
- "field": "case_ids",
- "name": "Patient ID"
- },
- {
- "field": "_ct_series_file_count",
- "name": "CT Series Count"
- },
- {
- "field": "_dx_series_file_count",
- "name": "DX Series Count"
- },
- {
- "field": "_cr_series_file_count",
- "name": "CR Series Count"
- },
- {
- "field": "_mr_series_file_count",
- "name": "MR Series Count"
- },
- {
- "field": "loinc_long_common_name",
- "name": "Long Common Name (Study description)"
- },
- {
- "field": "loinc_contrast",
- "name": "Contrast"
- },
- {
- "field": "loinc_code",
- "name": "LOINC Code"
- },
- {
- "field": "loinc_method",
- "name": "Method (Modality)"
- },
- {
- "field": "loinc_system",
- "name": "System (Body region)"
- }
- ],
- "manifestMapping": {
- "resourceIndexType": "imaging_data_file",
- "resourceIdField": "object_id",
- "referenceIdFieldInResourceIndex": "_imaging_study_id",
- "referenceIdFieldInDataIndex": "_imaging_study_id",
- "useFilterForCounts": true
- },
- "accessibleFieldCheckList": [
- "project_id"
- ],
- "accessibleValidationField": "project_id"
- }
- },
- {
- "tabTitle": "Imaging Series",
- "charts": {
- "sex": {
- "chartType": "fullPie",
- "title": "Case Sex"
- },
- "covid19_positive": {
- "chartType": "fullPie",
- "title": "Cases that ever had COVID-19"
- }
- },
- "filters": {
- "tabs": [
- {
- "title": "Study Properties",
- "fields": [
- "study_description",
- "age_at_imaging",
- "study_year",
- "study_year_shifted",
- "study_location",
- "days_from_study_to_pos_covid_test",
- "days_from_study_to_neg_covid_test",
- "project_id"
- ]
- },
- {
- "title": "Series Properties",
- "fields": [
- "acquisition_type",
- "angio_flag",
- "contrast_bolus_agent",
- "convolution_kernel",
- "detector_type",
- "diffusion_b_value",
- "diffusion_gradient_orientation",
- "echo_number",
- "echo_time",
- "echo_train_length",
- "exposure_modulation_type",
- "image_type",
- "imaged_nucleus",
- "imager_pixel_spacing",
- "lossy_image_compression",
- "manufacturer",
- "manufacturer_model_name",
- "modality",
- "multiframe_images",
- "number_of_temporal_positions",
- "patient_position",
- "pixel_spacing",
- "radiopharmaceutical",
- "repetition_time",
- "scan_options",
- "sequence_variant",
- "series_description",
- "slice_thickness",
- "software_version",
- "spacing_between_slices",
- "spatial_resolution",
- "transducer_type",
- "view_position",
- "data_format",
- "data_category",
- "data_type"
- ]
- },
- {
- "title": "Case Demographics",
- "fields": [
- "covid19_positive",
- "age_at_index",
- "sex",
- "race",
- "zip",
- "index_event"
- ]
- }
- ]
- },
- "table": {
- "enabled": true,
- "fields": [
- "acquisition_type",
- "angio_flag",
- "contrast_bolus_agent",
- "convolution_kernel",
- "detector_type",
- "diffusion_b_value",
- "diffusion_gradient_orientation",
- "echo_number",
- "echo_time",
- "echo_train_length",
- "exposure_modulation_type",
- "image_type",
- "imaged_nucleus",
- "imager_pixel_spacing",
- "lossy_image_compression",
- "manufacturer",
- "manufacturer_model_name",
- "modality",
- "multiframe_images",
- "number_of_temporal_positions",
- "patient_position",
- "pixel_spacing",
- "radiopharmaceutical",
- "repetition_time",
- "scan_options",
- "sequence_variant",
- "series_description",
- "slice_thickness",
- "software_version",
- "spacing_between_slices",
- "spatial_resolution",
- "transducer_type",
- "view_position",
- "study_description",
- "age_at_imaging",
- "days_to_study",
- "study_year",
- "study_year_shifted",
- "days_from_study_to_pos_covid_test",
- "days_from_study_to_neg_covid_test",
- "data_format",
- "covid19_positive",
- "age_at_index",
- "index_event",
- "sex",
- "race",
- "zip",
- "data_format",
- "data_category",
- "data_type",
- "series_uid",
- "study_uid",
- "case_ids",
- "object_id",
- "submitter_id",
- "project_id"
- ],
- "columns": {
- "object_id": {
- "title": "Object Id2",
- "type": "link",
- "accessorPath": "object_id",
- "params": {
- "baseURL": "/browse/series/"
- }
- }
- },
- "dicomViewerId": "submitter_id",
- "linkFields": [
- "submitter_id"
- ]
- },
- "dropdowns": {
- "download-table": {
- "title": "Download Table"
- }
- },
- "buttons": [
- {
- "enabled": true,
- "type": "data-json",
- "title": "JSON",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Series_table.json"
- },
- {
- "enabled": true,
- "type": "data-tsv",
- "title": "TSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Series_table.tsv"
- },
- {
- "enabled": true,
- "type": "data-csv",
- "title": "CSV",
- "dropdownId": "download-table",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Series_table.csv"
- },
- {
- "enabled": true,
- "type": "file-manifest",
- "title": "Download File Manifest",
- "leftIcon": "datafile",
- "rightIcon": "download",
- "fileName": "MIDRC_Imaging_Series_manifest.json"
- },
- {
- "enabled": false,
- "type": "export-to-workspace",
- "title": "Export to Workspace",
- "leftIcon": "datafile",
- "rightIcon": "download"
- }
- ],
- "loginForDownload": true,
- "guppyConfig": {
- "dataType": "imaging_data_file",
- "nodeCountTitle": "Imaging Series",
- "fieldMapping": [
- {
- "field": "project_id",
- "name": "Project ID"
- },
- {
- "field": "case_ids",
- "name": "Patient ID"
- }
- ],
- "manifestMapping": {
- "referenceIdFieldInResourceIndex": "object_id",
- "referenceIdFieldInDataIndex": "object_id"
- },
- "downloadAccessor": "object_id",
- "accessibleFieldCheckList": [
- "project_id"
- ],
- "accessibleValidationField": "project_id"
- }
- }
-]
diff --git a/config/gen3/footer.json b/config/gen3/footer.json
index 9bcdfb8..6bbf956 100644
--- a/config/gen3/footer.json
+++ b/config/gen3/footer.json
@@ -1,18 +1,36 @@
{
- "footerRightLogos": [
- [
- {
- "logo": "gen3.png",
- "width": 132,
- "height": 60,
- "description": "Gen3 Logo"
- },
- {
- "logo": "createdby.png",
- "width": 170,
- "height": 60,
- "description": "Created by CTDS"
- }
- ]
- ]
+ "classNames": {
+ "root": "bg-base-darker",
+ "layout": "flex items-center justify-end"
+ },
+ "rightSection":
+ {
+ "columns": [
+ {
+ "rows": [
+ {
+ "Icon": {
+ "logo": "/icons/gen3.png",
+ "width": 132,
+ "height": 60,
+ "description": "Gen3 Logo"
+ }
+ }
+ ]
+ },
+ {
+ "rows": [
+ {
+ "Icon": {
+ "logo": "/icons/createdby.png",
+ "width": 170,
+ "height": 60,
+ "description": "Created by CTDS"
+ }
+ }
+ ]
+ }
+ ]
+ }
+
}
diff --git a/config/gen3/landingPage.json b/config/gen3/landingPage.json
index 9f1d633..306be39 100644
--- a/config/gen3/landingPage.json
+++ b/config/gen3/landingPage.json
@@ -2,7 +2,7 @@
"body": [
{
"title": {
- "text": "Gen3 Data Platform",
+ "text": "Biomedical Research Hub",
"level": 2
}
},
@@ -10,29 +10,19 @@
"splitarea": {
"left": [
{
- "text": "The Gen3 Data Platform is a single web interface which allows visitors to discover, access and analyze data. Making data easily findable enables secondary, cross-study analyses, promotes dissemination of research and accelerates new discoveries."
+ "text": "The Biomedical Research Hub (BRH) is a standard-based data ecosystem for securely managing, analyzing and sharing biomedical data to support research communities and collaborations."
},
{
"link": {
- "href": "/discovery",
- "linkType": "portal",
- "text": "Explore Gen3 Data"
- }
- },
- {
- "text": "The Gen3 platform consists of open-source software services that support the emergence of healthy data ecosystems by enabling the interoperation and creation of cloud-based data resources, including data commons and analysis workspaces. Gen3 aims to accelerate and democratize the process of scientific discovery by making it easy to manage, analyze, harmonize, and share large and complex datasets in the cloud."
- },
- {
- "link": {
- "href": "https://gen3.datacommons.io",
- "text": "Learn More"
+ "href": "/Discovery",
+ "text": "Discovery Data"
}
}
],
"right": [
{
"image": {
- "src": "https://gen3.org/figs/kv.svg",
+ "src": "/images/kv.svg",
"alt": "Gen3 Data Platform"
}
}
@@ -41,32 +31,6 @@
},
{
"break": "standard"
- },
- {
- "cardsArea": {
- "title": "",
- "cards": [
- {
- "icon": "MdOutlineSearch",
- "bodyText": "Search studies and related datasets for download or analysis in a workspace.",
- "btnText": "Discover",
- "href": "/Discovery",
- "linkType": "portal"
- },
- {
- "icon": "MdOutlineBarChart",
- "bodyText": "Explore Tutorials and Example Analysis.",
- "btnText": "Analyze",
- "href": "/resource-browser",
- "linkType": "portal"
- }
- ]
- }
- },
- {
- "quoteArea": {
- "quote": "Our vision is a world in which researchers have ready access to the data needed and the tools required to make data-driven discoveries that increase our scientific knowledge and improve the quality of life."
- }
}
]
}
diff --git a/config/gen3/login.json b/config/gen3/login.json
index 8ea514a..15da29a 100644
--- a/config/gen3/login.json
+++ b/config/gen3/login.json
@@ -1,19 +1,25 @@
{
"topContent": [
{
- "text": "Gen3 Data Commons",
+ "text": "Biomedical Research Hub",
"className": "text-center text-3xl font-bold"
},
{
- "text": "DISCOVER, ANALYZE, AND SHARE DATA",
+ "text": "Discover, Analyze, and Share Data",
"className": "text-center text-xl font-medium"
+ },
+ {
+ "text": "The Biomedical Research Hub (BRH) is a standard-based data ecosystem for securely managing, analyzing and sharing biomedical data to support research communities and collaborations.",
+ "className": "text-center text-sm"
}
],
"bottomContent": [
{
- "text": "If you have any questions about access or the registration process, please contact gen3@datacommons.io.",
+ "text": "If you have any questions about access or the registration process, please contact ",
"className": "text-center text-sm"
}
],
- "image": "images/sideTexture.png"
+ "image": "/images/gene_side_texture.svg",
+ "email": "brhsupport@datacommons.io",
+ "showCredentialsLogin" : true
}
diff --git a/config/brh/modals.json b/config/gen3/modals.json
similarity index 100%
rename from config/brh/modals.json
rename to config/gen3/modals.json
diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json
index 949162b..33f06f6 100644
--- a/config/gen3/navigation.json
+++ b/config/gen3/navigation.json
@@ -1,9 +1,14 @@
{
- "type": "horizontal",
"navigation": {
+ "classNames": {
+ "root": "pl-1 mr-6 bg-base-max text-primary opacity-100 hover:opacity-100",
+ "item": "py-2 px-4 hover:bg-base-lightest hover:text-base-contrast",
+ "navigationPanel": "bg-base-max text-primary"
+ },
"logo": {
- "src": "/icons/gen3-dark.svg",
- "height": 128,
+ "src": "/images/brh/logo.png",
+ "height": 256,
+ "width": 320,
"href": "/"
},
"items": [
@@ -11,61 +16,64 @@
"icon": "gen3:query",
"href": "/Discovery",
"name": "Discovery",
- "tooltip": "Use free-text search and tags to rapidly find relevant studies."
- },
- {
- "icon": "gen3:dictionary",
- "href": "/DataDictionary",
- "name": "Dictionary",
- "tooltip": "The Data Dictionary serves to inform the data model and is updated as new data is ingested."
- },
- {
- "icon": "gen3:exploration",
- "href": "/Explorer",
- "name": "Exploration",
- "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder."
- },
- {
- "icon": "gen3:query",
- "href": "/Query",
- "name": "Query",
- "tooltip": "Query the databases using GraphiQL."
- },
- {
- "icon": "gen3:analysis",
- "href": "/resource-browser",
- "name": "Analysis",
- "tooltip": "Learn how to use Jupyter Notebooks to explore and visualize data available by running a tutorial notebook, or use one of these examples as a launching point for your own custom analysis."
+ "tooltip": "Use free-text search and tags to rapidly find relevant studies, discover new datasets across multiple resources, and easily export selected data files to the analysis workspace."
},
{
- "icon": "gen3:workspace",
- "href": "/#hostname#workspace/",
"name": "Workspace",
+ "href": "/Workspace",
+ "icon": "gen3:workspace",
"tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources."
},
+ {
+ "name": "Notebooks",
+ "href": "/NotebookLite",
+ "icon": "gen3:notebook",
+ "tooltip": "Notebooks for basic analysis"
+ },
{
"icon": "gen3:profile",
"href": "/Profile",
"name": "Profile",
- "tooltip": "Create API keys for programmatic data access, and review your authorization privileges to datasets and services.",
- "classNames": {
- "root": "flex flex-col flex-nowrap px-1 py-2 pt-4 items-center hover:text-accent opacity-80 hover:opacity-100 pr-10"
- }
+ "tooltip": "Create API keys for programmatic data access, and review your authorization privileges to datasets and services."
}
]
},
"topBar": {
"items": [
{
- "rightIcon": "gen3:upload",
- "href": "/submission",
- "name": "Browse Data"
+ "link": "https://uc-cdis.github.io/BRH-documentation/",
+ "name": "Documentation",
+ "classNames": {
+ "root": "border-base-light",
+ "label": "text-white",
+ "button": "hover:border-white"
+ }
+ },
+ {
+ "link": "brhsupport@datacommons.io",
+ "name": "Email Support",
+ "classNames": {
+ "root": "border-base-light",
+ "label": "text-white",
+ "button": "hover:border-white"
+ }
},
{
- "href": "https://gen3.org/resources/user/",
- "name": "Documentation"
+ "link": "https://uc-cdis.github.io/platform-citation/brh-cite/",
+ "name": "Cite BRH",
+ "classNames": {
+ "root": "border-base-light",
+ "label": "text-white",
+ "button": "hover:border-white"
+ }
}
],
- "showLogin": true
+ "loginButtonVisibility": "visible",
+ "classNames": {
+ "root": "border-base-light text-primary-contrast-dark",
+ "label": "text-primary-contrast",
+ "button": "hover:border-white",
+ "login" : "hover:border-white text-white"
+ }
}
}
diff --git a/config/gen3/profile.json b/config/gen3/profile.json
index df4c924..9428194 100644
--- a/config/gen3/profile.json
+++ b/config/gen3/profile.json
@@ -1,51 +1,52 @@
{
- "resourceTable": {
- "serviceColors": {
- "guppy": {
- "service": "guppy",
- "color": "red.4",
- "label": "Guppy"
- },
- "requestor": {
- "service": "requestor",
- "color": "yellow.5",
- "label": "Requestor"
- },
- "dictionary_page": {
- "service": "dictionary_page",
- "color": "blue.5",
- "label": "Dictionary Page"
- },
- "job": {
- "service": "job",
- "color": "indigo.7",
- "label": "Job"
- },
- "kayako": {
- "service": "kayako",
- "color": "yellow.6",
- "label": "Kayako"
- },
- "fence": {
- "service": "fence",
- "color": "teal.4",
- "label": "Fence"
- },
- "sheepdog": {
- "service": "sheepdog",
- "color": "grape.7",
- "label": "Sheepdog"
- },
- "peregrine": {
- "service": "peregrine",
- "color": "lime.7",
- "label": "Peregrine"
- },
- "jupyterhub": {
- "service": "jupyterhub",
- "color": "lime.4",
- "label": "JuptyerHub"
+ "hasExternalLogins" : true,
+ "resourceTable": {
+ "serviceColors": {
+ "guppy": {
+ "service": "guppy",
+ "color": "red.4",
+ "label": "Guppy"
+ },
+ "requestor": {
+ "service": "requestor",
+ "color": "yellow.5",
+ "label": "Requestor"
+ },
+ "dictionary_page": {
+ "service": "dictionary_page",
+ "color": "blue.5",
+ "label": "Dictionary Page"
+ },
+ "job": {
+ "service": "job",
+ "color": "indigo.7",
+ "label": "Job"
+ },
+ "kayako": {
+ "service": "kayako",
+ "color": "yellow.6",
+ "label": "Kayako"
+ },
+ "fence": {
+ "service": "fence",
+ "color": "teal.4",
+ "label": "Fence"
+ },
+ "sheepdog": {
+ "service": "sheepdog",
+ "color": "grape.7",
+ "label": "Sheepdog"
+ },
+ "peregrine": {
+ "service": "peregrine",
+ "color": "lime.7",
+ "label": "Peregrine"
+ },
+ "jupyterhub": {
+ "service": "jupyterhub",
+ "color": "lime.4",
+ "label": "JuptyerHub"
+ }
}
}
- }
}
diff --git a/config/brh/session.json b/config/gen3/session.json
similarity index 100%
rename from config/brh/session.json
rename to config/gen3/session.json
diff --git a/config/brh/submission.json b/config/gen3/submission.json
similarity index 100%
rename from config/brh/submission.json
rename to config/gen3/submission.json
diff --git a/config/brh/themeColors.json b/config/gen3/themeColors.json
similarity index 100%
rename from config/brh/themeColors.json
rename to config/gen3/themeColors.json
diff --git a/config/brh/themeFonts.json b/config/gen3/themeFonts.json
similarity index 100%
rename from config/brh/themeFonts.json
rename to config/gen3/themeFonts.json
diff --git a/config/brh/workspace.json b/config/gen3/workspace.json
similarity index 100%
rename from config/brh/workspace.json
rename to config/gen3/workspace.json