Merge branch 'master' into feat/vadc_sprint24

Author: tianj7

.github/workflows/ci.yaml

@@ -21,6 +21,8 @@ jobs:
   ci:
     name: Build Image and Push
     uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      BUILD_PLATFORMS: "linux/amd64"
     secrets:
       ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
       ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}

.storybook/main.js

@@ -3,10 +3,6 @@ module.exports = {
       "../src/**/*.stories.mdx",
       "../src/**/*.stories.@(js|jsx|ts|tsx)"
     ],
-    "addons": [
-      "@storybook/addon-links",
-      "@storybook/addon-essentials",
-      "@storybook/addon-interactions"
-    ],
+    "addons": [],
     "framework": "@storybook/react"
   }

Dockerfile

@@ -1,40 +1,45 @@
 # To run: docker run -d --name=dataportal -p 80:80 quay.io/cdis/data-portal
 # To check running container: docker exec -it dataportal /bin/bash
 
-FROM quay.io/cdis/ubuntu:20.04
+FROM quay.io/cdis/nodejs-base:master
 
-ENV DEBIAN_FRONTEND=noninteractive
 ENV REACT_APP_PROJECT_ID=search
 
-# disable npm 7's brand new update notifier to prevent Portal from stuck at starting up
-# see https://github.com/npm/cli/issues/3163
-ENV NPM_CONFIG_UPDATE_NOTIFIER=false
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential \
-    libssl1.1 \
-    libgnutls30 \
-    ca-certificates \
-    curl \
-    git \
-    nginx \
-    python3 \
-    time \
-    vim \
-    && curl -sL https://deb.nodesource.com/setup_16.x | bash - \
-    && apt-get install -y --no-install-recommends nodejs \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && ln -sf /dev/stdout /var/log/nginx/access.log \
-    && ln -sf /dev/stderr /var/log/nginx/error.log \
-    && npm install -g npm@8.5
+# Install nginx
+RUN yum install nginx -y && \
+    # allows nginx to run on port 80 without being root user
+    setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx && \
+    chown -R gen3:gen3 /var/log/nginx && \
+    # pipe nginx logs to stdout/stderr
+    ln -sf /dev/stdout /var/log/nginx/access.log && \
+    ln -sf /dev/stderr /var/log/nginx/error.log && \
+    mkdir -p /var/lib/nginx/tmp/client_body && \
+    chown -R gen3:gen3 /var/lib/nginx/ && \
+    mkdir -p /var/cache/nginx && \
+    chown -R gen3:gen3 /var/cache/nginx \
+    && touch /var/run/nginx.pid \
+    && chown -R gen3:gen3 /var/run/nginx.pid
 
 ARG APP=dev
 ARG BASENAME
 
 RUN mkdir -p /data-portal
 COPY . /data-portal
+RUN cp /data-portal/nginx.conf /etc/nginx/conf.d/nginx.conf \
+    && chown -R gen3:gen3 /etc/nginx/conf.d \
+    && chown -R gen3:gen3 /data-portal
+
+# In standard prod these will be overwritten by volume mounts
+# Provided here for ease of use in development and
+# non-standard deployment environments
+
+RUN mkdir /mnt/ssl \
+    && openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout /mnt/ssl/nginx.key -out /mnt/ssl/nginx.crt -subj '/countryName=US/stateOrProvinceName=Illinois/localityName=Chicago/organizationName=CDIS/organizationalUnitName=PlanX/commonName=localhost/emailAddress=ops@cdis.org' \
+    && chmod 755 /mnt/ssl/nginx.crt \
+    && chmod 755 /mnt/ssl/nginx.key
+
 WORKDIR /data-portal
+USER gen3
 RUN COMMIT=`git rev-parse HEAD` && echo "export const portalCommit = \"${COMMIT}\";" >src/versions.js \
     && VERSION=`git describe --always --tags` && echo "export const portalVersion =\"${VERSION}\";" >>src/versions.js \
     && /bin/rm -rf .git \
@@ -44,15 +49,6 @@ RUN npm config set unsafe-perm=true \
     && npm run relay \
     && npm run params
     # see https://stackoverflow.com/questions/48387040/nodejs-recommended-max-old-space-size
-RUN NODE_OPTIONS=--max-old-space-size=3584 NODE_ENV=production time npx webpack build
-RUN cp nginx.conf /etc/nginx/conf.d/nginx.conf \
-    && rm /etc/nginx/sites-enabled/default
-
-# In standard prod these will be overwritten by volume mounts
-# Provided here for ease of use in development and
-# non-standard deployment environments
-
-RUN mkdir /mnt/ssl \
-    && openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout /mnt/ssl/nginx.key -out /mnt/ssl/nginx.crt -subj '/countryName=US/stateOrProvinceName=Illinois/localityName=Chicago/organizationName=CDIS/organizationalUnitName=PlanX/commonName=localhost/emailAddress=ops@cdis.org'
+RUN NODE_OPTIONS=--max-old-space-size=3584 NODE_ENV=production npx webpack build
 
 CMD [ "bash", "./dockerStart.sh" ]

data/config/default.json

@@ -187,7 +187,7 @@
     "explorer": true,
     "analysis": false
   },
-  "dataExplorerConfig": {
+  "explorerConfig": [{
     "charts": {
       "project": {
         "chartType": "count",
@@ -277,7 +277,7 @@
         "file_format"
       ]
     }
-  },
+  }],
   "useArboristUI": false,
   "showArboristAuthzOnProfile": false,
   "showFenceAuthzOnProfile": true,

data/getTexts.js

@@ -65,6 +65,7 @@ function doStringify(value, variables, indent = 0, spaces = 0) {
     const objs = value.map(
       (item) => `${insertSpace(indent + spaces)}${doStringify(item, variables, indent + spaces, spaces)}`,
     ).join(`,${ending}`);
+    // console.log(doWrapping(objs, '[', ']', indent, spaces));
     return doWrapping(objs, '[', ']', indent, spaces);
   }
   if (typeof value === 'string') {
@@ -102,15 +103,23 @@ function buildConfig(appIn, data) {
   const app = appIn || process.env.APP || 'default';
   const appConfig = data[app] || {};
   const defaultConfig = data.default || {};
+  // don't copy 'explorerConfig' over from default config since that is a non-working example
+  delete defaultConfig.explorerConfig;
   const result = { ...defaultConfig, ...appConfig };
   delete result.components;
   Object.keys(result).forEach(
     (k) => {
       if (typeof result[k] === 'object') {
         const defaultVal = defaultConfig[k];
         const appVal = appConfig[k];
-        if (defaultVal && appVal && typeof defaultVal === 'object' && typeof appVal === 'object') {
-          result[k] = { ...defaultVal, ...appVal };
+        if (defaultVal && appVal) {
+          if (typeof defaultVal === 'object' && typeof appVal === 'object') {
+            if (Array.isArray(defaultVal) && Array.isArray(appVal)) {
+              result[k] = defaultVal.concat(appVal);
+            } else if (!Array.isArray(defaultVal) && !Array.isArray(appVal)) {
+              result[k] = { ...defaultVal, ...appVal };
+            }
+          }
         }
       }
     },