Merge branch 'main' into craigrbarnes-patch-2

.env.development

@@ -1,6 +1,6 @@
-GEN3_COMMONS_NAME=gen3
+GEN3_COMMONS_NAME=brh
 NEXT_PUBLIC_GEN3_API=https://localhost
 NEXT_PUBLIC_GEN3_DOMAIN=https://localhost
-
-# set these if you want to use different endpoints
-#NEXT_PUBLIC_GEN3_GUPPY_API=
+NEXT_PUBLIC_GEN3_MDS_API=https://localhost
+#NEXT_PUBLIC_GEN3_AI_SEARCH_API=http://localhost:8089
+#NEXT_PUBLIC_GEN3_GUPPY_API=https://localhost:3010/guppy

.env.production

@@ -1,3 +1,3 @@
-GEN3_COMMONS_NAME=gen3
+GEN3_COMMONS_NAME=brh
 NEXT_PUBLIC_GEN3_API=https://localhost/
 NEXT_PUBLIC_GEN3_DOMAIN=https://localhost/

config/brh/colors.json

@@ -0,0 +1,10 @@
+{
+  "primary": "#3283C8",
+  "secondary": "#3283C8",
+  "accent": "#b75113",
+  "base": "#c0c0c0",
+  "accentWarm": "#25869b",
+  "accentCool": "#1f839b",
+  "chart": "#0d95A1",
+  "table": "#c0c0c0"
+}

config/brh/discovery.json

@@ -0,0 +1,284 @@
+{
+  "tableConfig": {
+    "selectableRows": true,
+    "expandableRows": true
+  },
+  "features": {
+    "dataFetchFunction": "MDSAllLocal",
+    "aiSearch" : true,
+    "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"
+  },
+  "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
+    }
+  ]
+}

config/brh/footer.json

@@ -0,0 +1,18 @@
+{
+  "footerRightLogos": [
+    [
+      {
+        "logo": "gen3.png",
+        "width": 132,
+        "height": 60,
+        "description": "Gen3 Logo"
+      },
+      {
+        "logo": "createdby.png",
+        "width": 170,
+        "height": 60,
+        "description": "Created by CTDS"
+      }
+      ]
+    ]
+}

config/brh/landingPage.json

@@ -0,0 +1,36 @@
+{
+  "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": "https://gen3.org/figs/kv.svg",
+              "alt": "Gen3 Data Platform"
+            }
+          }
+        ]
+      }
+    },
+    {
+      "break": "standard"
+    }
+  ]
+}

config/brh/login.json

@@ -0,0 +1,25 @@
+{
+    "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/brh/gene_bgy.png",
+    "email": "[email protected]",
+    "showCredentialsLogin" : true
+  }