merge from develop

Author: craigrbarnes

.dockerignore

@@ -1,9 +1,15 @@
 node_modules
 packages/core/node_modules
+packages/core/dist
 packages/frontend/node_modules
+packages/frontend/dist
 packages/tools/node_modules
+packages/tools/dist
 packages/sampleCommons/node_modules
 packages/sampleCommons/.next
+packages/sampleCommons/.swc
 .git
 .nx
 .next
+.nx
+docs

.github/workflows/ci.yaml

@@ -4,16 +4,14 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-node@v3.4.1
-      with:
-        node-version: 20.11.0
-    - name: install npm version
-      run: npm install -g npm
-    - name: Get Version
-      run: npm -v
-    - name: Install modules
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v4.1.0
+        with:
+          node-version: 20.17.0
+      - name: Get Version
+        run: npm -v
+      - name: Install modules
 
-      run: npm ci
-    - name: Run ESLint
-      run: npm run lint
+        run: npm ci --include=optional
+      - name: Run ESLint
+        run: npm run lint

.gitignore

@@ -19,6 +19,8 @@ packages/sampleCommons/.next/
 .DS_Store
 *.pem
 .vscode
+.nx
+.idea
 
 # debug
 npm-debug.log*
@@ -31,11 +33,10 @@ yarn-error.log*
 .env.test.local
 .env.production.local
 
-
-# Ignore DevSpace cache and log folder
-.devspace/
-
 # sample configs
 packages/sampleCommons/config/canine
 packages/sampleCommons/config/midrc
 packages/sampleCommons/config/heal
+packages/sampleCommons/config/bdc
+/packages/frontend/.rollup.cache/
+/packages/sampleCommons/.swc/

.nvmrc

@@ -1 +1 @@
- v20.17.0
+v20.17.0

Dockerfile

@@ -1,3 +1,5 @@
+# docker build -t ff .
+# docker run -p 3000:3000 -it ff
 # Build stage
 FROM quay.io/cdis/ubuntu:20.04 AS builder
 
@@ -38,7 +40,7 @@ COPY packages/frontend/package.json ./packages/frontend/
 COPY packages/sampleCommons/package.json ./packages/sampleCommons/
 
 # Install dependencies
-RUN npm ci
+RUN npm ci --include=optional
 
 # Install additional dependencies
 RUN npm install \
@@ -57,7 +59,7 @@ RUN lerna run --scope @gen3/core build && \
     lerna run --scope @gen3/samplecommons build
 
 # Production stage
-FROM node:20-slim AS production
+FROM node:20.18.2-alpine3.20 AS production
 
 WORKDIR /gen3
 
@@ -67,7 +69,7 @@ RUN addgroup --system --gid 1001 nextjs && \
 
 # Copy built artifacts from builder
 COPY --from=builder --chown=nextjs:nextjs /gen3 .
-
+RUN apk add --no-cache bash
 # Set environment variables
 ENV PORT=3000
 ENV NODE_ENV=production

NOTICE

@@ -0,0 +1,7 @@
+Copyright 2022-2025 University of Chicago
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

docs/Configuration/Discovery.md

@@ -15,7 +15,9 @@ The configuration for the Discovery Page is divided into several sections:
 - `tagsDisplayName`: Name for the tag categories displayed.
 - `tagColumnWidth`: Width settings for the tag columns.
 - `minimalFieldMapping`: Essential field mappings required by the page.
-- `tagCategories`: Definitions for the categorization and display of tags.
+- `tags`: Definitions for the categorization and display of tags.
+  - `tagCategories`: Definitions for the categorization and display of tags.
+  - `showUnknownTags`: Defaults to False
 
 ### 2. Detailed Configuration Sections
 

docs/Configuration/Explorer.md

@@ -57,6 +57,31 @@ and
 https://localhost/Explorer/files
 ```
 
+### Charts
+The charts section configures data visualizations for the explorer page. Each chart is defined by its `chartType` and `title`.
+
+```json    
+"charts": {
+      "race": {
+        "chartType": "fullPie",
+        "title": "Race"
+      },
+      "ethnicity": {
+        "chartType": "horizontalStacked",
+        "title": "Ethnicity"
+      },
+      "gender": {
+        "chartType": "bar",
+        "title": "Gender"
+      }
+    }
+```
+    
+The currently supported chart types are:
+* `bar`: a regular vertical bar chart.
+* `horizontalStacked`: horizontal stacked bar chart.
+* `fullPie`: full pie chart.
+* `donut`: pie chart with a hole.
 
 ### Download Table Data
 

docs/Configuration/Login.md

@@ -0,0 +1,38 @@
+# Login Configuration Guide
+
+The login page configuration consists of two main sections:
+* Top Content
+* Bottom Content
+
+and example configuration:
+```json
+{
+  "topContent": [
+    {
+      "text": "Gen3 Data Commons",
+      "className": "text-center text-3xl font-bold"
+    },
+    {
+      "text": "DISCOVER, ANALYZE, AND SHARE DATA",
+      "className": "text-center text-xl font-medium"
+    }
+  ],
+  "bottomContent": [
+ {
+      "type" : "textWithEmail",
+      "text": "If you have any questions about access or the registration process, please contact",
+      "email": "gen3@datacommons.io",
+      "className": "text-center text-sm"
+    }
+  ],
+  "image": "images/gene_side_texture.svg",
+  "showCredentialsLogin" : true
+}
+
+```
+
+Both topContent and bottomContent are arrays of the [TextContent](../../packages/frontend/docs/components/TextContent.md) component.
+
+* image: the side image for the login page
+* showCredentialsLogin: is for development and allows logins using a credentials file instead of logging in which
+usually will not work because fence will not allow redirects back to https://localhost

docs/Configuration/Navigation.md

@@ -73,7 +73,7 @@ Example of a top bar item:
 where:
  * 'visible' - always shown, if logged in shows userId and a logout button
  * 'logoutOnly' - only show the logoutButton when logged in
- * 'hidded' - never show
+ * 'hide' - never show
 
 ```json
   "loginButtonVisibility": "logoutOnly"