Merge branch 'master' into snyk-fix-66646c6d6d40244903616a664e35a8c4

.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 }}

.github/workflows/integration_tests.yaml

@@ -0,0 +1,27 @@
+name: Integration Tests
+
+on: pull_request
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  integration_tests:
+    name: Integration tests
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    with:
+      SERVICE_TO_TEST: portal
+    secrets:
+      CI_AWS_ACCESS_KEY_ID: ${{ secrets.CI_AWS_ACCESS_KEY_ID }}
+      CI_AWS_SECRET_ACCESS_KEY: ${{ secrets.CI_AWS_SECRET_ACCESS_KEY }}
+      JENKINS_API_TOKEN: ${{ secrets.JENKINS_API_TOKEN }}
+      QA_DASHBOARD_S3_PATH: ${{ secrets.QA_DASHBOARD_S3_PATH }}
+      CI_TEST_ORCID_USERID: ${{ secrets.CI_TEST_ORCID_USERID }}
+      CI_TEST_ORCID_PASSWORD: ${{ secrets.CI_TEST_ORCID_PASSWORD }}
+      CI_TEST_RAS_USERID: ${{ secrets.CI_TEST_RAS_USERID }}
+      CI_TEST_RAS_PASSWORD: ${{ secrets.CI_TEST_RAS_PASSWORD }}
+      CI_TEST_RAS_2_USERID: ${{ secrets.CI_TEST_RAS_2_USERID }}
+      CI_TEST_RAS_2_PASSWORD: ${{ secrets.CI_TEST_RAS_2_PASSWORD }}
+      CI_SLACK_BOT_TOKEN: ${{ secrets.CI_SLACK_BOT_TOKEN }}
+      CI_SLACK_CHANNEL_ID: ${{ secrets.CI_SLACK_CHANNEL_ID }}

.gitignore

@@ -17,6 +17,7 @@ data/schema.graphql
 data/schema.json
 src/params.js
 src/css/themeoverrides.css
+public/*
 src/img/sponsors/gitops-sponsors/
 __generated__/
 *.log

.nvmrc

@@ -0,0 +1 @@
+16

.secrets.baseline

@@ -3,7 +3,7 @@
     "files": "package-lock.json|.*/dictionary.json|.*/schema.json",
     "lines": ".*integrity.*"
   },
-  "generated_at": "2021-10-08T03:14:20Z",
+  "generated_at": "2024-11-19T16:49:52Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -81,7 +81,7 @@
         "hashed_secret": "abd9c7ed80fd61f97a190e059555269a6ff69b94",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 16,
+        "line_number": 17,
         "type": "Secret Keyword"
       }
     ],

.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 [email protected]
+# 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/[email protected]' \
+    && 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/[email protected]'
+RUN NODE_OPTIONS=--max-old-space-size=3584 NODE_ENV=production npx webpack build
 
-CMD bash ./dockerStart.sh
+CMD [ "bash", "./dockerStart.sh" ]

boot.js

@@ -19,18 +19,9 @@
   scriptNode.src = buildSrc;
   scriptNode.type = 'text/javascript';
   document.body.appendChild(scriptNode);
-  // create theme override node in body
-  const themeOverridesSrc = (basename && basename !== '/') ? `${basename}/src/css/themeoverrides.css?_=${cssVersion}` : `/src/css/themeoverrides.css?_=${cssVersion}`;
-  let linkNode = document.createElement('link');
-  linkNode.href = themeOverridesSrc;
-  linkNode.type = 'text/css';
-  linkNode.id = 'gen3-theme-overrides';
-  linkNode.rel = 'stylesheet';
-  document.body.appendChild(linkNode);
   // create local theme override node in body
-  const localThemeOverridesSrc = (basename && basename !== '/') ? `https://localhost:9443${basename}/src/css/themeoverrides.css` : 'https://localhost:9443/src/css/themeoverrides.css';
   linkNode = document.createElement('link');
-  linkNode.href = localThemeOverridesSrc;
+  linkNode.href = 'https://localhost:9443/src/css/themeoverrides.css';
   linkNode.type = 'text/css';
   linkNode.rel = 'stylesheet';
   document.body.appendChild(linkNode);

custom/customize.sh

@@ -29,7 +29,10 @@ fi
 
 if [ -f custom/css/$APP.css ]; then
   cp custom/css/$APP.css src/css/themeoverrides.css
+  mkdir -p public/src/css/
+  cp custom/css/$APP.css public/src/css/themeoverrides.css
 else
+  rm -rf public/src
   echo "/* generated file - see customize.sh */" > src/css/themeoverrides.css
 fi
 

data/config/acct.json

@@ -112,7 +112,7 @@
       "title": "ACCOuNT Data Commons",
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website provides a centralized, cloud-based discovery portal for African American pharmacogenomics data and aims to accelerate discovery of novel genetic variants in African Americans related to clinically actionable cardiovascular phenotypes.",
-      "contact": "If you have any questions about access or the registration process, please contact support@datacommons.io"
+      "contact": "If you have any questions about access or the registration process, please contact support@gen3.org"
     }
   },
   "featureFlags": {

data/config/anvil.json

@@ -102,7 +102,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "categorical9Colors": [
       "#035C94",

data/config/bpa.json

@@ -116,7 +116,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website combines liquid biopsy data from academic, government, and industry partners and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for the treatment and prevention of cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "bpa-support@datacommons.io"
+      "email": "bpa-support@gen3.org"
     },
     "certs": {
       "security_quiz": {

data/config/canine.json

@@ -119,7 +119,7 @@
       "subTitle": "explore, analyze, and share research data",
       "text": "This website analyzes and shares genomic architecture of modern dog breeds and runs analysis for canine cancer to create clean, easy to navigate visualizations for data-driven discovery for canine cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/dcf.json

@@ -132,7 +132,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/default.json

@@ -132,7 +132,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "certs": {
       "security_quiz": {
@@ -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/config/gtex.json

@@ -123,7 +123,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io",
+      "email": "support@gen3.org",
       "image": "stage-icons/stage-gene"
     },
     "footerLogos": [

data/config/ibdgc.json

@@ -75,7 +75,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "The Inflammatory Bowel Disease Genetics Consortium Data Commons supports the management, analysis, and sharing of genetic data to support the vision and mission of the IBD genetics consortium.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/ncrdc-demo.json

@@ -112,7 +112,7 @@
       "subTitle": "explore, analyze, and share research data",
       "text": "The Data Common Frameworks (DCF) supports the management, analysis and sharing of many different types of biomedical data for the research community with the goal of accelerating research in the molecular basis for disease and matching targeted therapies that factor in each patient's unique biology.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/ndh.json

@@ -114,7 +114,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "The website combines government datasets from 3 divisions of NIAID to create clean, easy to navigate visualizations for data-driven discovery within Allergy and Infectious Diseases.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "footerLogos": [
       {

data/config/va.json

@@ -125,7 +125,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "The Veterans Data Commons supports the management, analysis and sharing of veteran oncologic data for the research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for precision oncology.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "footerLogos": [
       {

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 };
+            }
+          }
         }
       }
     },

dev.html

@@ -11,7 +11,7 @@
       - https://atlas.qa-mickey.planx-pla.net for Atlas iframe in VHDC qa-mickey
       - https://*.quicksight.aws.amazon.com for loading AWS Quicksight dashboards into COVID-19 Home page
     -->
-    <meta http-equiv="Content-Security-Policy" content="default-src 'self' https://login.bionimbus.org https://wayf.incommonfederation.org; child-src blob:; connect-src 'self' blob: localhost https://localhost:9443 wss://localhost:9443 https://*.s3.amazonaws.com https://*.mapbox.com https://opendata.datacommons.io https://static.planx-pla.net https://*.logs.datadoghq.com https://classic.clinicaltrials.gov https://*.google-analytics.com https://*.analytics.google.com; img-src 'self' https://opendata.datacommons.io https://static.planx-pla.net https://www.google-analytics.com data: https://*.s3.amazonaws.com https://www.google-analytics.com; script-src 'self' 'unsafe-eval' https://*.google-analytics.com https://www.googletagmanager.com localhost https://localhost:9443; worker-src 'self' blob:; style-src 'self' 'unsafe-inline' https://fonts.googleapis.com localhost https://localhost:9443; object-src 'none'; font-src 'self' data: https://fonts.googleapis.com https://fonts.gstatic.com; frame-src 'self' https://auspice.planx-pla.net https://auspice.pandemicresponsecommons.org https://atlas.qa-mickey.planx-pla.net https://*.quicksight.aws.amazon.com; ">
+    <meta http-equiv="Content-Security-Policy" content="default-src 'self' https://login.bionimbus.org https://wayf.incommonfederation.org; child-src blob:; connect-src 'self' blob: localhost https://localhost:9443 wss://localhost:9443 https://*.s3.amazonaws.com https://*.mapbox.com https://opendata.datacommons.io https://static.planx-pla.net https://faro.planx-pla.net https://*.logs.datadoghq.com https://clinicaltrials.gov https://*.google-analytics.com https://*.analytics.google.com https://*.zendesk.com; img-src 'self' https://opendata.datacommons.io https://static.planx-pla.net https://www.google-analytics.com data: https://*.s3.amazonaws.com https://www.google-analytics.com; script-src 'self' 'unsafe-eval' https://*.google-analytics.com https://www.googletagmanager.com localhost https://localhost:9443; worker-src 'self' blob:; style-src 'self' 'unsafe-inline' https://fonts.googleapis.com localhost https://localhost:9443; object-src 'none'; font-src 'self' data: https://fonts.googleapis.com https://fonts.gstatic.com; frame-src 'self' https://auspice.planx-pla.net https://auspice.pandemicresponsecommons.org https://atlas.qa-mickey.planx-pla.net https://*.quicksight.aws.amazon.com; ">
     <meta name="viewport" content="width=device-width" />
     <link href="https://fonts.googleapis.com/icon?family=Source+Sans+Pro" rel="stylesheet">
     <link href="https://fonts.googleapis.com/css2?family=Roboto:ital,wght@0,400;0,700;1,700&display=swap" rel="stylesheet">