mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-10-04 11:18:11 +08:00
the first commit
This commit is contained in:
Alok Saldanha
@@ -0,0 +1,40 @@
|
||||
<!--
|
||||
Copyright 2019 Novartis Institutes for BioMedical Research Inc. 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.
|
||||
-->
|
||||
|
||||
<html>
|
||||
<head>
|
||||
<title>Cellxgene Gateway - Error</title>
|
||||
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
|
||||
<link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
|
||||
{% for script in extra_scripts %}
|
||||
<script src="{{ script }}"></script>
|
||||
{% endfor %}
|
||||
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
|
||||
</head>
|
||||
<body>
|
||||
<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
|
||||
<h3>Cellxgene Gateway - Error</h3>
|
||||
</header>
|
||||
<br>
|
||||
<div style="margin-left:20px">
|
||||
|
||||
<h4>{{ message }}</h4>
|
||||
|
||||
<a href="/filecrawl.html">
|
||||
Please click here to be redirected to the file directory.
|
||||
</a>
|
||||
<br>
|
||||
<a href="/">
|
||||
Please click here to return to the homepage.
|
||||
</a>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,34 @@
|
||||
<!--
|
||||
Copyright 2019 Novartis Institutes for BioMedical Research Inc. 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.
|
||||
-->
|
||||
|
||||
<html>
|
||||
<head>
|
||||
<title>Cellxgene Gateway - FILE CRAWLER</title>
|
||||
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
|
||||
<link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
|
||||
{% for script in extra_scripts %}
|
||||
<script src="{{ script }}"></script>
|
||||
{% endfor %}
|
||||
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
|
||||
</head>
|
||||
<body>
|
||||
<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
|
||||
<h3>Cellxgene Gateway - FILE CRAWLER</h3>
|
||||
</header>
|
||||
<br>
|
||||
|
||||
<h4>Please wait until a dataset is done loading before trying to launch a different one</h4>
|
||||
|
||||
<br>
|
||||
{{ rendered_html|safe }}
|
||||
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,123 @@
|
||||
<!--
|
||||
Copyright 2019 Novartis Institutes for BioMedical Research Inc. 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.
|
||||
-->
|
||||
|
||||
<html>
|
||||
<head>
|
||||
<title>Cellxgene Gateway</title>
|
||||
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
|
||||
<link rel="stylesheet" href="{{ url_for('static', filename='css/homepagestyle.css') }}">
|
||||
<link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
|
||||
{% for script in extra_scripts %}
|
||||
<script src="{{ script }}"></script>
|
||||
{% endfor %}
|
||||
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
|
||||
<style>
|
||||
li {
|
||||
font-size: 20px;
|
||||
}
|
||||
</style>
|
||||
</head>
|
||||
<body>
|
||||
<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
|
||||
<h3>Cellxgene Gateway - HOME</h3>
|
||||
</header>
|
||||
<br>
|
||||
|
||||
<h1 style="padding-left:35px">
|
||||
Links:
|
||||
</h1>
|
||||
<div class="list-group" style="width:50%;padding-left:65px">
|
||||
<a target="_blank" href="/filecrawl.html" class="list-group-item list-group-item-action">
|
||||
<u>File Crawler: Allows you to view all uploaded data.</u></a>
|
||||
|
||||
</div>
|
||||
|
||||
<br>
|
||||
|
||||
<h1 style="padding-left:35px">
|
||||
How To Upload Data:
|
||||
</h1>
|
||||
<ol style="padding-left:85px;">
|
||||
<li>
|
||||
Create a folder for your Username:
|
||||
</li>
|
||||
<br>
|
||||
<form action="{{ url_for('make_user') }}" method="post">
|
||||
Username <input type="text" name="directory">
|
||||
<input type="submit" value="Create">
|
||||
</form>
|
||||
<li>
|
||||
Create a subdirectory under the selected Folder:
|
||||
</li>
|
||||
<br>
|
||||
<form action="{{ url_for('make_subdir') }}" method="post">
|
||||
<select name="usernames" id="usernames">
|
||||
{% for user in users %}
|
||||
<option value="{{ user }}">{{ user }}</option>
|
||||
{% endfor %}
|
||||
</select>
|
||||
<br>
|
||||
Subdirectory Name <input type="text" name="directory">
|
||||
<input type="submit" value="Create">
|
||||
</form>
|
||||
<li>Choose a folder to copy your data to, then upload your data file (must be in .h5ad format).</li>
|
||||
<br>
|
||||
<form action="{{ url_for('upload_file') }}" method="post" enctype="multipart/form-data">
|
||||
Type in the name of the directory and subdirectory you wish to upload to, i.e. "USER/cells". <input type="text" name="path">
|
||||
<br>
|
||||
File: <input type="file" name="file"><br>
|
||||
<input style="position:relative; top:10px;" type="submit" value="Upload">
|
||||
</form>
|
||||
<br>
|
||||
<li>Take a look at your data using the file crawler link above</li>
|
||||
</ol>
|
||||
|
||||
|
||||
<br>
|
||||
|
||||
<h1 style="padding-left:35px">
|
||||
How To Upload Data via SSH and SCP (Linux):
|
||||
</h1>
|
||||
<ol style="padding-left:85px;">
|
||||
<li>
|
||||
Confirm that your ssh key has been properly added. Running the following command should connect you to the server:
|
||||
</li>
|
||||
<pre>ssh ec2-user@{{ ip }}</pre>
|
||||
<li>
|
||||
Prepare your data on your own machine. They should be in a common folder called 'USER' and should look <br>similar to the following structure:
|
||||
</li>
|
||||
<pre>- USER
|
||||
- hpc.h5ad
|
||||
- pbmc3k.h5ad</pre>
|
||||
<li>Copy your data to the server (replace USER with your username):</li>
|
||||
<pre>ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/'
|
||||
ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/DATA/'
|
||||
scp -r pbmc3k.h5ad ec2-user@{{ ip }}:{{ cellxgene_data }}/USER/DATA/</pre>
|
||||
<li>Take a look at your data using the file crawler link above</li>
|
||||
</ol>
|
||||
|
||||
<br>
|
||||
<br>
|
||||
|
||||
<script>
|
||||
if (NIBRIam && NIBRIam.NIBR521 !== undefined) {
|
||||
var usernames = document.getElementById("usernames")
|
||||
var options = usernames.options
|
||||
|
||||
for (i = 0; i < options.length; i++) {
|
||||
if (options[i].value.toLowerCase() == currentUser.toLowerCase()) {
|
||||
options[i].setAttribute("selected", "selected")
|
||||
}
|
||||
}
|
||||
}
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,53 @@
|
||||
<!--
|
||||
Copyright 2019 Novartis Institutes for BioMedical Research Inc. 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.
|
||||
-->
|
||||
|
||||
<html>
|
||||
<head>
|
||||
<title>Cellxgene Gateway - Loading</title>
|
||||
<link rel="icon" type="image/png" href="nibr.png">
|
||||
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
|
||||
|
||||
<meta http-equiv="refresh" content="5">
|
||||
</head>
|
||||
<body>
|
||||
<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
|
||||
<h3>Cellxgene Gateway - Loading<span id='dots'></span></h3>
|
||||
</header>
|
||||
|
||||
<br>
|
||||
<div style="margin-left:20px">
|
||||
|
||||
<br>
|
||||
<h4>Output:</h4>
|
||||
<pre>{{ all_output }}</pre>
|
||||
<p>
|
||||
Launch Time: <span id="launch_time"> {{ launchtime.isoformat(' ') }} </span>
|
||||
</p>
|
||||
<p>
|
||||
The page will refresh shortly.
|
||||
</p>
|
||||
|
||||
<a href="/filecrawl.html">
|
||||
Please click here to be redirected to the file directory.
|
||||
</a>
|
||||
<br>
|
||||
<a href="/">
|
||||
Please click here to return to the homepage.
|
||||
</a>
|
||||
</div>
|
||||
<script>
|
||||
window.setInterval(function(){
|
||||
var dots = document.getElementById('dots');
|
||||
dots.textContent = dots.textContent + '.';
|
||||
}, 1000);
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,43 @@
|
||||
<!--
|
||||
Copyright 2019 Novartis Institutes for BioMedical Research Inc. 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.
|
||||
-->
|
||||
|
||||
<html>
|
||||
<head>
|
||||
<title>Cellxgene Gateway - Process Error</title>
|
||||
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
|
||||
<link rel="icon" type="image/png" href="nibr.png">
|
||||
{% for script in extra_scripts %}
|
||||
<script src="{{ script }}"></script>
|
||||
{% endfor %}
|
||||
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
|
||||
</head>
|
||||
<body>
|
||||
<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
|
||||
<h3>Cellxgene Gateway - Process Error</h3>
|
||||
</header>
|
||||
<br>
|
||||
<div style="margin-left:20px">
|
||||
|
||||
<h4>{{ message[0] }}</h4>
|
||||
<h4>{{ message[1] }}</h4>
|
||||
<h4>{{ message[2] }}</h4>
|
||||
<h4>{{ message[3] }}</h4>
|
||||
|
||||
<a href="/filecrawl.html">
|
||||
Please click here to be redirected to the file directory.
|
||||
</a>
|
||||
<br>
|
||||
<a href="/">
|
||||
Please click here to return to the homepage.
|
||||
</a>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
Reference in New Issue
Block a user