Preserve CBDS configs

ACED-IDP · Jun 14, 2024 · 0dc59e0 · 0dc59e0
1 parent 69acf02
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Showing 5 changed files with 84 additions and 133 deletions.
diff --git a/packages/sampleCommons/config/cbds/explorer.json b/packages/sampleCommons/config/cbds/explorer.json
@@ -44,76 +44,45 @@
         "disability_adjusted_life_years"
       ]
     },
-    "dropdowns": {
-      "download-table": {
-        "title": "Download 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",
+      "dataType": "patient",
       "fieldMapping": [
         {
-          "field": "project_id",
-          "name": "Project ID"
-        },
-        {
-          "field": "submitter_id",
-          "name": "Measurement ID"
+          "field": "quality_adjusted_life_years",
+          "name": "quality_adjusted_life_years"
         },
         {
-          "field": "case_ids",
-          "name": "Case ID"
+          "field": "disability_adjusted_life_years",
+          "name": "disability_adjusted_life_years"
         }
       ],
-      "accessibleFieldCheckList": ["project_id"],
+      "nodeCountTitle": "Patients",
+      "manifestMapping": {
+        "resourceIndexType": "Patient",
+        "resourceIdField": "id",
+        "referenceIdFieldInResourceIndex": "id",
+        "referenceIdFieldInDataIndex": "id"
+      },
+      "accessibleFieldCheckList": [
+        "project_id"
+      ],
       "accessibleValidationField": "project_id"
     }
   },
   {
     "tabTitle": "Observation",
     "charts": {
       "project_id": {
-        "chartType": "donut",
-        "title": "Project"
-      },
-      "category": {
         "chartType": "fullPie",
-        "title": "Category"
+        "title": "Project"
       },
       "code": {
         "chartType": "fullPie",
         "title": "Code"
+      },
+      "valueString": {
+        "chartType": "fullPie",
+        "title": "Value"
       }
     },
     "filters": {
@@ -122,17 +91,8 @@
           "title": "Observation",
           "fields": [
             "project_id",
-            "category",
-            "code"
-          ]
-        },
-        {
-          "title": "Annotations",
-          "fields": [
-            "imaging_study_annotations.midrc_mRALE_score",
-            "imaging_study_annotations.annotation_method",
-            "imaging_study_annotations.annotator_id",
-            "data_file_annotation_name"
+            "code",
+            "valueString"
           ]
         }
       ]
@@ -144,42 +104,30 @@
         "project_id",
         "category",
         "code",
-        "bodySite",
-        "effectiveDateTime",
-        "valueBoolean",
-        "valueCodeableConcept",
-        "valueDateTime",
-        "valueInteger",
-        "valueQuantity",
-        "valueRange",
-        "valueRatio",
-        "valueSampledData",
-        "valueString",
-        "interpretation"
+        "valueString"
       ]
     },
-    "dropdowns": {},
     "guppyConfig": {
       "dataType": "observation",
-      "fieldMapping":   [],
+      "fieldMapping": [],
       "nodeCountTitle": "Observations",
       "manifestMapping": {
         "resourceIndexType": "Patient",
         "resourceIdField": "_patient_id",
         "referenceIdFieldInResourceIndex": "object_id",
         "referenceIdFieldInDataIndex": "object_id"
       },
-      "accessibleFieldCheckList": ["project_id"],
+      "accessibleFieldCheckList": [
+        "project_id"
+      ],
       "accessibleValidationField": "project_id"
     }
   },
-
   {
-
     "tabTitle": "File",
     "charts": {
       "data_type": {
-        "chartType": "donut",
+        "chartType": "fullPie",
         "title": "File Type"
       },
       "data_format": {
@@ -218,14 +166,25 @@
         "type_coding"
       ]
     },
-    "dropdowns": {},
     "guppyConfig": {
       "dataType": "file",
       "fieldMapping": [
-        { "field": "object_id", "name": "Download ID" },
-        { "field": "file_name", "name": "Name" },
-        { "field": "data_type", "name": "Type" },
-        { "field": "data_format", "name": "Format" }
+        {
+          "field": "object_id",
+          "name": "Download ID"
+        },
+        {
+          "field": "file_name",
+          "name": "Name"
+        },
+        {
+          "field": "data_type",
+          "name": "Type"
+        },
+        {
+          "field": "data_format",
+          "name": "Format"
+        }
       ],
       "nodeCountTitle": "Files",
       "manifestMapping": {
@@ -234,18 +193,32 @@
         "referenceIdFieldInResourceIndex": "object_id",
         "referenceIdFieldInDataIndex": "object_id"
       },
-      "accessibleFieldCheckList": ["project_id"],
+      "accessibleFieldCheckList": [
+        "project_id"
+      ],
       "accessibleValidationField": "project_id",
       "downloadAccessor": "object_id"
     },
     "buttons": [
       {
         "enabled": true,
-        "type": "file-manifest",
+        "type": "manifest",
+        "action": "manifest",
         "title": "Download Manifest",
-        "leftIcon": "datafile",
-        "rightIcon": "download",
-        "fileName": "file-manifest.json"
+        "leftIcon": "gen3:datafile",
+        "rightIcon": "gen3:download",
+        "fileName": "manifest.json",
+        "actionArgs": {
+          "resourceIndexType": "Patient",
+          "resourceIdField": "_patient_id",
+          "referenceIdFieldInDataIndex": "object_id",
+          "fileFields": [
+            "file_name",
+            "file_size",
+            "md5sum",
+            "object_id"
+          ]
+        }
       }
     ]
   }

diff --git a/packages/sampleCommons/config/cbds/footer.json b/packages/sampleCommons/config/cbds/footer.json
@@ -2,11 +2,11 @@
   "footerRightLogos": [
     [
       {
-        "logo": "/icons/ACED_PARTNERS.jpg",
-        "width": 791,
-        "height": 94,
-        "description": "ACED partners"
+        "logo": "/icons/knight.png",
+        "width": 150,
+        "height": 70,
+        "description": "Knight Cancer Institute"
       }
     ]
   ]
-}
+}
diff --git a/packages/sampleCommons/config/cbds/landingPage.json b/packages/sampleCommons/config/cbds/landingPage.json
@@ -9,6 +9,14 @@
     {
       "splitarea": {
         "left": [
+          {
+            "image": {
+              "src": "/icons/cbds.png",
+              "alt": "CBDS Icon"
+            }
+          }
+        ],
+        "right": [
           {
             "text": "The CBDS Integrated Data Platform is built to empower researchers by providing a robust suite of tools designed to streamline the analysis and sharing of critical research data. With a focus on collaboration and innovation, our platform stands aims to assist analysts and principle investigators with accelerating discoveries and fostering partnerships across labs."
           },
@@ -18,23 +26,6 @@
               "linkType": "portal",
               "text": "Explore Gen3 Data"
             }
-          },
-          {
-            "text": "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Etiam elit dui, commodo a tortor ut, vestibulum consectetur tellus. Aliquam erat volutpat. Aenean sodales lacus quis venenatis fermentum. Phasellus varius tempor odio a elementum. Aliquam sed diam molestie, ornare neque in, porttitor mi. Aliquam hendrerit libero volutpat, bibendum ante at, auctor velit. Nulla eget augue a turpis facilisis dictum. Nulla vulputate accumsan aliquam. Fusce imperdiet arcu nibh, nec vehicula nisi placerat at. Phasellus eget magna elementum, tincidunt urna at, venenatis nulla. Cras ullamcorper ante sed ex porttitor, at elementum ligula dapibus. Sed malesuada mi turpis, eu venenatis lorem convallis in. "
-          },
-          {
-            "link": {
-              "href": "https://gen3.datacommons.io",
-              "text": "Learn More"
-            }
-          }
-        ],
-        "right": [
-          {
-            "image": {
-              "src": "https://www.cancerresearchuk.org/sites/default/files/aced_website_header.jpg",
-              "alt": "Gen3 Data Platform"
-            }
           }
         ]
       }
@@ -69,4 +60,4 @@
       }
     }
   ]
-}
+}
diff --git a/packages/sampleCommons/config/cbds/login.json b/packages/sampleCommons/config/cbds/login.json
@@ -19,6 +19,5 @@
       "className": "text-center text-sm"
     }
   ],
-  "image": "images/gene.svg",
-  "showCredentialsLogin" : true
-}
+  "showCredentialsLogin": false
+}
diff --git a/packages/sampleCommons/config/cbds/navigation.json b/packages/sampleCommons/config/cbds/navigation.json
@@ -6,9 +6,9 @@
       "navigationPanel": "bg-base-max text-primary"
     },
     "logo": {
-      "src": "/icons/logo_small_2.png",
+      "src": "/icons/cbds.png",
       "height": 220,
-      "href": "/"
+      "href": "/cbdsLandingPage"
     },
     "items": [
       {
@@ -17,24 +17,12 @@
         "name": "Exploration",
         "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder."
       },
-      {
-        "icon": "gen3:exploration",
-        "href": "/SamplePage",
-        "name": "DEMO",
-        "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder."
-      },
       {
         "icon": "gen3:exploration",
         "href": "/GRIPREF",
         "name": "GRIPREF",
         "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder."
       },
-      {
-        "icon": "gen3:exploration",
-        "href": "/SMMART",
-        "name": "SMMART",
-        "tooltip": "SMMART"
-      },
       {
         "icon": "gen3:query",
         "href": "/Query",
@@ -52,10 +40,10 @@
   "topBar": {
     "items": [
       {
-        "href": "https://www.cancerresearchuk.org/funding-for-researchers/research-opportunities-in-early-detection-and-diagnosis/international-alliance-for-cancer-early-detection",
-        "name": "ACED"
+        "href": "https://www.ohsu.edu/knight-cancer-institute",
+        "name": "CBDS"
       }
     ],
     "showLogin": true
   }
-}
+}