Update env

Author: Yan Xu

installation/README.md

@@ -26,17 +26,24 @@ https://docs.mongodb.com/manual/installation/#mongodb-community-edition-installa
 
     - Populate the "client build" environment configuration file (i.e. `webapp/client/.env`). 
 
-        You can initialize it based upon the corresponding development/production example file:
+        You can initialize it based upon the corresponding example file:
         ```shell
-        cp webapp/client/.env.development.example \
+        cp webapp/client/.env.example \
         webapp/client/.env
         ```
         > Those environment variables are used within `webapp/client/src/config.js`.
+
+    -  Create a build directory with a production build of the client:
+        ```shell
+        cd webapp/client
+        npm run build
+        ```
+
     - Populate the server environment configuration file (i.e. `webapp/server/.env`). 
 
-        You can initialize it based upon the corresponding development/production example file:
+        You can initialize it based upon the corresponding example file:
         ```shell
-        cp webapp/server/.env.development.example \
+        cp webapp/server/.env.example \
         webapp/server/.env
         ```
         > Those environment variables are used within `webapp/server/config.js`.

installation/install.sh

@@ -51,16 +51,19 @@ do
 done
 
 echo "Setup LANL EDGE webapp ..."
-#build client
-echo "build client..."
+#install client
+echo "install client..."
 cd $app_home/webapp/client
 npm install --legacy-peer-deps
-npm run build
-#build server
-echo "build server..."
+#install server
+echo "install server..."
 cd $app_home/webapp/server
 npm install
 
 echo "LANL EDGE webapp successfully installed!"
-echo "To start the webapp in EDGEv3's root directory:"
-echo "pm2 start pm2.config.js"
+echo "Next steps:"
+echo "1. copy webapp/client/.env.example to webapp/client/.env and update settings in the .env file"
+echo "2. inside webapp/client, run command: npm run build"
+echo "3. copy webapp/server/.env.example to webapp/server/.env and update settings in the .env file"
+echo "4. start MongoDB if it's not started yet"
+echo "5. start the webapp in EDGEv3's root directory: pm2 start pm2.config.js"

webapp/README.md

@@ -8,38 +8,28 @@
 ## Install the webapp
 
     cd installation
-    ./install-local.sh
+    ./install.sh
+
+## Configure and start ui client
+
+    cd webapp/client
+    cp .env.example .env
+    (update settings in .env)
+    npm start
 
-## Start api server
+## Configure and start api server
 
     cd webapp/server
-    (change NODE_ENV=prod to NODE_ENV=dev in .env)
+    cp .env.example .env
+    (update settings in .env)
     npm start
 
-## Start ui client
-
-    cd webapp/client
-    npm start
 
 ## View the website
 
     http://localhost:3000
 
 ## Note
 
-- Have to restart the client when any changes made in client/.env.
-- Have to restart the server when any changes made in server code or server/.env.
-    
-#### Restart api server
-
-    cd webapp/server
-    use Ctrl-C to stop the webapp server
-    npm start
-
-#### Restart ui client
-
-    cd webapp/client
-    use Ctrl-C to stop the webapp client
-    npm start
-
+- Have to restart the api server when any changes made in webapp/server code or webapp/server/.env.
 

webapp/client/.env.development.example

@@ -0,0 +1,13 @@
+###############################################################################
+# Refer to `./src/config.js` to see all supported environment variables.      #
+###############################################################################
+VITE_NAME=EDGE V3
+VITE_EMAIL_NOTIFICATION_ENABLED=false
+VITE_FILEUPLOAD_ENABLED=true
+
+# for development only
+# VITE_API_URL=http://localhost:5000
+
+# ORCiD login
+VITE_IS_ORCID_AUTH_ENABLED=false
+VITE_ORCID_CLIENT_ID=="__POPULATE_ME_IF_ENABLING_ORCID_AUTH__"

webapp/client/.env.example

@@ -0,0 +1,40 @@
+# uncomment 'SYSTEM_MESSAGE' and restart pm2 to disable workflow submission
+# SYSTEM_MESSAGE=Workflow submission is temporarily unavailable. You can still browse/view your submitted projects.
+
+###############################################################################
+# Refer to `./config.js` to see all supported environment variables.          #
+###############################################################################
+
+# Networking:
+# -----------
+PORT=5000
+CRON_PORT=5555
+
+# default is 'production'
+# NODE_ENV=development
+
+# Base URL at which visitors can access the web UI server
+# Example url for development
+# APP_UI_BASE_URL=http://localhost:3000
+APP_UI_BASE_URL="__POPULATE_ME__"
+
+# Secrets:
+# --------
+#
+# Note: You can generate a secret by running the following shell command:
+#       $ node -e 'console.log(require("crypto").randomBytes(20).toString("hex"))'
+#
+JWT_SECRET="__POPULATE_ME__"
+
+# Database
+DB_NAME="__POPULATE_ME_IN_PRODUCTION__"
+
+# upload file, file extensions
+FILEUPLOAD_ALLOWED_EXTENSIONS=fastq|fq|faa|fa|fasta|fna|contigs|fastq.gz|fq.gz|fa.gz|fasta.gz|fna.gz|contigs.gz|fa.bz2|fasta.bz2|contigs.bz2|fna.bz2|fa.xz|fasta.xz|contigs.xz|fna.xz|gbk|gff|genbank|gb|xlsx|txt|bed|config|tsv|csv|raw|d|bam|sam
+
+# Email:
+# ------
+SEND_PROJECT_STATUS_EMAILS=false
+PROJECT_STATUS_SUBJECT=Your EDGE project status
+EMAIL_MAILGUN_API_KEY="__POPULATE_ME_IF_ENABLING_EMAIL__"
+EMAIL_MAILGUN_DOMAIN="__POPULATE_ME_IF_ENABLING_EMAIL__"