add Jupyter-lite to Dockerfile

uc-cdis · Nov 15, 2024 · 290ce4a · 290ce4a
1 parent bc6bda9
commit 290ce4a
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Showing 31 changed files with 3,521 additions and 168 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -16,6 +16,8 @@ WORKDIR /gen3
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
+    python \
+    pip \
     libssl1.1 \
     libgnutls30 \
     ca-certificates \
@@ -31,21 +33,17 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     && npm install -g [email protected]
 
 RUN  addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs
-COPY ./package.json ./package-lock.json ./
-COPY ./package-lock.json ./
+COPY ./package.json ./package-lock.json ./next.config.js /tsconfig.json  ./tailwind.config.js ./postcss.config.js ./start.sh ./
 COPY ./src ./src
 COPY ./public ./public
 COPY ./config ./config
-COPY ./next.config.js ./
-COPY ./tsconfig.json ./
-COPY ./.env.development ./
-COPY ./.env.production ./
-COPY ./tailwind.config.js ./
-COPY ./postcss.config.js ./
+COPY ./jupyter-lite ./jupyter-lite
 RUN npm ci
 RUN npm install \
     "@swc/core" \
-    "@napi-rs/magic-string"
+    "@napi-rs/magic-string" \
 RUN npm run build
-ENV PORT=80
-CMD ["npm", "run", "start"]
+RUN pip install -r ./jupyter-lite/requirements.txt
+RUN jupyter lite build --contents ./jupyter-lite --output-dir dist ./jupyter
+ENV PORT=3000
+CMD bash ./start.sh
diff --git a/TODO.md b/TODO.md
@@ -0,0 +1,12 @@
+# TODO For CanineDC
+
+* Create CountsPanel
+* Files Charts
+* Expandable Bar Chart List
+* Jobs Manager
+* Create Selector Facet
+* Fix Enum Badge Component
+* Create Homepage
+* Center Explorer Tabs
+* Setup/Test notebook
+* Add BAM File visualization
diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json
@@ -1,41 +1,38 @@
 [
   {
-    "tabTitle": "Cases",
+    "tabTitle": "Subjects",
     "charts": {
-      "race": {
+      "project_id": {
         "chartType": "fullPie",
-        "title": "Race"
+        "title": "Projects"
       },
-      "ethnicity": {
-        "chartType": "horizontalStacked",
-        "title": "Ethnicity"
+      "disease_type": {
+        "chartType": "fullPie",
+        "title": "Disease Type"
       },
-      "gender": {
-        "chartType": "bar",
-        "title": "Gender"
+      "data_format": {
+        "chartType": "horizontalStacked",
+        "title": "Data Format"
       }
     },
     "filters": {
       "tabs": [
         {
-          "title": "Study Selection",
-          "fields": ["project"]
+          "title": "Subject",
+          "fields":[
+            "project_id",
+            "gender",
+            "breed",
+            "data_format",
+            "data_type"
+          ]
         },
         {
-          "title": "Subjects",
-          "fields": [
-            "study",
-            "gender",
-            "race",
-            "ethnicity",
-            "vital_status",
-            "whatever_lab_result_value"
-          ],
-          "fieldsConfig": {
-            "gender" : {
-              "type" : "multiselect"
-            }
-          }
+          "title": "Diagnosis",
+          "fields":[
+            "disease_type",
+            "primary_site"
+          ]
         }
       ]
     },
@@ -44,24 +41,21 @@
       "detailsConfig": {
         "panel": "default",
         "mode" : "click",
-        "idField": "submitter_id",
+        "idField": "project_id",
         "title": "Details"
       },
       "pageLimit": {
         "limit": 10000
       },
       "fields": [
-        "project",
+        "project_id",
+        "disease_type",
+        "primary_site",
+        "breed",
         "gender",
-        "race",
-        "ethnicity",
-        "whatever_lab_result_value"
-      ],
-      "columns": {
-        "whatever_lab_result_value": {
-          "sortable": false
-        }
-      }
+        "data_format",
+        "data_type"
+      ]
     },
     "dropdowns": {
       "download-table": {
@@ -77,8 +71,7 @@
             "rightIcon": "download",
             "action": "data-json",
             "actionArgs" : {
-              "filename": "MIDRC_Series_table.json",
-              "rootPath": "gen3_discovery"
+              "filename": "canine_subjects_table.json"
             }
           },
           {
@@ -89,51 +82,29 @@
             "rightIcon": "download",
             "action": "data-csv",
             "actionArgs" : {
-              "filename": "data_table.csv"
+              "filename": "canine_subjects_table.csv"
+            }
+          },
+          {
+            "enabled": true,
+            "type": "data-tsv",
+            "title": "TSV",
+            "leftIcon": "datafile",
+            "rightIcon": "download",
+            "action": "data-tsv",
+            "actionArgs" : {
+              "filename": "canine_subjects_table.tsv"
             }
           }
         ]
       }
     },
     "buttons": [
-      {
-        "enabled": true,
-        "type": "data-json",
-        "title": "JSON",
-        "dropdownId": "download-table",
-        "leftIcon": "datafile",
-        "rightIcon": "download",
-        "actionArgs": {
-          "filename": "data_table.json"
-        }
-      },
-      {
-        "enabled": true,
-        "type": "data-tsv",
-        "title": "TSV",
-        "dropdownId": "download-table",
-        "leftIcon": "datafile",
-        "rightIcon": "download",
-        "actionArgs": {
-          "filename": "data_table.tsv"
-        }
-      },
-      {
-        "enabled": true,
-        "type": "data-csv",
-        "title": "CSV",
-        "dropdownId": "download-table",
-        "leftIcon": "datafile",
-        "rightIcon": "download",
-        "actionArgs": {
-          "filename": "data_table.csv"
-        }
-      },
       {
         "enabled": true,
         "type": "manifest",
         "action": "manifest",
-        "title": "Download File Manifest for Cases",
+        "title": "Download File Manifest for Subject",
         "leftIcon": "datafile",
         "rightIcon": "download",
         "fileName": "case_manifest.json",
@@ -177,28 +148,35 @@
         "resourceIdField": "object_id",
         "referenceIdFieldInResourceIndex": "subject_id",
         "referenceIdFieldInDataIndex": "subject_id"
-      },
-      "accessibleFieldCheckList": ["project"],
-      "accessibleValidationField": "project"
+      }
     }
   },
   {
     "tabTitle": "Data Files",
     "charts": {
-      "file_type": {
-        "chartType": "stackedBar",
-        "title": "File Type"
+      "data_type": {
+        "chartType": "horizontalStacked",
+        "title": "File Type",
+        "valueType" : "percent"
       },
-      "file_format": {
-        "chartType": "stackedBar",
-        "title": "File Format"
+      "data_format": {
+        "chartType": "horizontalStacked",
+        "title": "File Format",
+        "valueType" : "percent"
       }
     },
     "filters": {
       "tabs": [
         {
           "title": "File",
-          "fields": ["subject_id"]
+          "fields": [
+            "project_id",
+            "data_type",
+            "data_format"
+          ],
+          "searchFields": [
+            "file_name"
+          ]
         }
       ]
     },
@@ -207,10 +185,15 @@
       "detailsConfig": {
         "panel": "fileDetails",
         "mode": "click",
-        "idField": "file_name",
+        "idField": "object_id",
         "title": "File Details"
       },
-      "fields": ["subject_id", "file_type", "file_size", "object_id"]
+      "fields": [
+        "project_id",
+        "file_name",
+        "file_size",
+        "object_id"
+      ]
     },
     "guppyConfig": {
       "dataType": "file",

diff --git a/config/gen3/footer.json b/config/gen3/footer.json
@@ -1,18 +1,34 @@
 {
-  "footerRightLogos": [
-    [
+  "classNames": {
+    "root": "bg-base-darker",
+    "layout": "flex items-center justify-end"
+  },
+  "rightSection": {
+    "columns": [
       {
-        "logo": "/images/gen3.png",
-        "width": 132,
-        "height": 60,
-        "description": "Gen3 Logo"
+        "rows": [
+          {
+            "Icon": {
+              "logo": "/icons/gen3.png",
+              "width": 132,
+              "height": 60,
+              "description": "Gen3 Logo"
+            }
+          }
+        ]
       },
       {
-        "logo": "/images/createdby.png",
-        "width": 170,
-        "height": 60,
-        "description": "Created by CTDS"
+        "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
@@ -10,17 +10,7 @@
       "splitarea": {
         "left": [
           {
-            "text": "The <strong>Gen3 Data Platform</strong> is a single web interface which allows visitors to <strong>discover, access and analyze data</strong>. Making data easily findable enables secondary, cross-study analyses, promotes dissemination of research and accelerates new discoveries."
-          },
-          {
-            "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."
+            "text": "The Canine Data Commons supports the management and sharing of genomics data for the canine research community and aims to accelerate opportunities for discovery and development for the treatment and prevention of canine 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": {
@@ -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."
-      }
     }
   ]
 }