24 disable workflows

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.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/src/edge/common/Dialogs.js

@@ -12,7 +12,7 @@ import { colors } from './util'
 export const ConfirmDialog = (props) => {
   return (
     <Modal isOpen={props.isOpen} centered>
-      <ModalHeader>{props.title}</ModalHeader>
+      <ModalHeader>{props.header}</ModalHeader>
       <ModalBody>{props.message}</ModalBody>
       <ModalFooter>
         <Button color="primary" onClick={props.handleClickYes}>

webapp/client/src/edge/common/util.js

@@ -167,12 +167,16 @@ export const notify = (type, msg, timeout) => {
     toast.success(msg, {
       position: 'top-center',
       autoClose: timeout,
+      rtl: false,
+      hideProgressBar: false,
     })
   }
   if (type === 'error') {
     toast.error(msg, {
       position: 'top-center',
       autoClose: false,
+      rtl: false,
+      hideProgressBar: false,
     })
   }
 }

webapp/client/src/edge/um/user/JobQueue.js

@@ -15,10 +15,6 @@ const JobQueue = () => {
         accessorKey: 'name', //access nested data with dot notation
         header: 'project',
       },
-      {
-        accessorKey: 'owner',
-        header: 'Owner',
-      },
       {
         accessorKey: 'type', //normal accessorKey
         header: 'Type',
@@ -79,8 +75,8 @@ const JobQueue = () => {
         data={tableData}
         enableFullScreenToggle={false}
         enableColumnActions={false}
-        enableSorting={false}
-        enableColumnFilters={false}
+        enableSorting={true}
+        enableColumnFilters={true}
         state={{
           isLoading: loading,
         }}

webapp/client/src/edge/um/user/UploadFiles.js

@@ -28,6 +28,9 @@ const UploadFiles = (props) => {
   const [allowedExtensions, setAllowedExtensions] = useState([])
   const [files, setFiles] = useState([])
   const [updateSize, setUpdateSize] = useState(0)
+  const [files2upload, setFiles2Upload] = useState(0)
+  const [filesUploaded, setFilesUploaded] = useState(0)
+  let uploaded = 0
 
   useEffect(() => {
     //get upload info
@@ -124,6 +127,8 @@ const UploadFiles = (props) => {
     }
 
     //upload files
+    setFiles2Upload(files.length)
+
     let promises = []
     for (var i = 0; i < files.length; i++) {
       let curr = files[i]
@@ -143,9 +148,13 @@ const UploadFiles = (props) => {
             },
           })
             .then((response) => {
+              uploaded += 1
+              setFilesUploaded(uploaded)
               resolve('Upload ' + curr.meta.name + ' successfully!')
             })
             .catch((error) => {
+              uploaded += 1
+              setFilesUploaded(uploaded)
               resolve('Upload ' + curr.meta.name + ' failed! ' + error)
             })
         }),
@@ -155,13 +164,19 @@ const UploadFiles = (props) => {
     Promise.all(promises)
       .then((response) => {
         allFiles.forEach((f) => f.remove())
+        let errors = 0
         response.forEach((e) => {
           if (e.includes('failed')) {
             notify('error', e)
+            errors += 1
           } else {
-            notify('success', e)
+            //notify('success', e)
           }
         })
+        if (errors === 0) {
+          notify('success', 'Files uploaded successfully!', 2000)
+          //setTimeout(() => props.history.push("/user/files"), 2000);
+        }
         setSubmitting(false)
         props.reloadTableData()
       })
@@ -173,7 +188,10 @@ const UploadFiles = (props) => {
 
   return (
     <>
-      <LoaderDialog loading={submitting} text="Uploading..." />
+      <LoaderDialog
+        loading={submitting}
+        text={'Uploading...' + Math.round((filesUploaded / files2upload) * 100) + '%'}
+      />
       <ToastContainer />
       <div className="clearfix">
         <h4 className="pt-3">Upload Files</h4>

webapp/client/src/edge/um/user/forms/RegisterForm.js

@@ -71,7 +71,7 @@ const RegisterForm = (props) => {
 
   return (
     <Form onSubmit={handleSubmit(props.onSubmit)}>
-      <h1>Register</h1>
+      <h1>Sign Up</h1>
       <p className="text-muted">Create your account</p>
       <InputGroup className="mb-3">
         <InputGroupText className="text-muted"> First Name </InputGroupText>

webapp/client/src/edge/workflows/sra/Main.js

@@ -109,10 +109,7 @@ const Main = (props) => {
   }, [])
 
   return (
-    <div
-      className="animated fadeIn"
-      style={disabled ? { pointerEvents: 'none', opacity: '0.4' } : {}}
-    >
+    <div className="animated fadeIn">
       <MessageDialog
         className="modal-lg modal-danger"
         title="System Message"
@@ -128,7 +125,7 @@ const Main = (props) => {
           e.preventDefault()
         }}
       >
-        <div className="clearfix">
+        <div className="clearfix" style={disabled ? { pointerEvents: 'none', opacity: '0.4' } : {}}>
           <h4 className="pt-3">Retrieve SRA Data</h4>
           {workflow && (
             <>

webapp/client/src/scss/_custom.scss

@@ -77,6 +77,15 @@ button:hover {
 .modal-success .modal-header {
   background-color: $success;
 }
+.modal-warning .modal-header {
+  background-color: $warning;
+}
+.modal-danger .modal-header {
+  background-color: $danger;
+}
+.modal-info .modal-header {
+  background-color: $info;
+}
 
 // EDGE
 .edge-header {

webapp/server/.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__"

webapp/server/edge-api/controllers/auth-user-controller.js

@@ -11,11 +11,11 @@ const sysError = config.APP.API_ERROR;
 const info = async (req, res) => {
   try {
     logger.debug(`/api/auth-user/info: ${JSON.stringify(req.user.email)}`);
-    if (config.SYSTEM_MESSAGE) {
+    if (config.APP.SYSTEM_MESSAGE) {
       return res.send({
         info: {
           allowNewRuns: false,
-          message: config.SYSTEM_MESSAGE,
+          message: config.APP.SYSTEM_MESSAGE,
         },
         message: 'Action successful',
         success: true,