mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-09-15 12:47:59 +08:00
124 lines
4.1 KiB
HTML
124 lines
4.1 KiB
HTML
<!--
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Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
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under the Apache License, Version 2.0 (the "License"); you may not use
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this file except in compliance with the License. You may obtain a copy
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of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
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required by applicable law or agreed to in writing, software distributed
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under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
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OR CONDITIONS OF ANY KIND, either express or implied. See the License for
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the specific language governing permissions and limitations under the License.
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-->
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<html>
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<head>
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<title>Cellxgene Gateway</title>
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
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<link rel="stylesheet" href="{{ url_for('static', filename='css/homepagestyle.css') }}">
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<link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
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{% for script in extra_scripts %}
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<script src="{{ script }}"></script>
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{% endfor %}
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<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
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<style>
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li {
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font-size: 20px;
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}
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</style>
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</head>
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<body>
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<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
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<h3>Cellxgene Gateway - HOME</h3>
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</header>
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<br>
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<h1 style="padding-left:35px">
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Links:
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</h1>
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<div class="list-group" style="width:50%;padding-left:65px">
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<a target="_blank" href="/filecrawl.html" class="list-group-item list-group-item-action">
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<u>File Crawler: Allows you to view all uploaded data.</u></a>
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</div>
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<br>
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<h1 style="padding-left:35px">
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How To Upload Data:
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</h1>
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<ol style="padding-left:85px;">
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<li>
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Create a folder for your Username:
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</li>
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<br>
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<form action="{{ url_for('make_user') }}" method="post">
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Username <input type="text" name="directory">
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<input type="submit" value="Create">
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</form>
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<li>
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Create a subdirectory under the selected Folder:
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</li>
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<br>
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<form action="{{ url_for('make_subdir') }}" method="post">
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<select name="usernames" id="usernames">
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{% for user in users %}
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<option value="{{ user }}">{{ user }}</option>
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{% endfor %}
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</select>
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<br>
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Subdirectory Name <input type="text" name="directory">
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<input type="submit" value="Create">
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</form>
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<li>Choose a folder to copy your data to, then upload your data file (must be in .h5ad format).</li>
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<br>
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<form action="{{ url_for('upload_file') }}" method="post" enctype="multipart/form-data">
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Type in the name of the directory and subdirectory you wish to upload to, i.e. "USER/cells". <input type="text" name="path">
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<br>
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File: <input type="file" name="file"><br>
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<input style="position:relative; top:10px;" type="submit" value="Upload">
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</form>
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<br>
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<li>Take a look at your data using the file crawler link above</li>
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</ol>
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<br>
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<h1 style="padding-left:35px">
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How To Upload Data via SSH and SCP (Linux):
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</h1>
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<ol style="padding-left:85px;">
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<li>
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Confirm that your ssh key has been properly added. Running the following command should connect you to the server:
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</li>
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<pre>ssh ec2-user@{{ ip }}</pre>
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<li>
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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:
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</li>
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<pre>- USER
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- hpc.h5ad
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- pbmc3k.h5ad</pre>
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<li>Copy your data to the server (replace USER with your username):</li>
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<pre>ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/'
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ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/DATA/'
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scp -r pbmc3k.h5ad ec2-user@{{ ip }}:{{ cellxgene_data }}/USER/DATA/</pre>
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<li>Take a look at your data using the file crawler link above</li>
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</ol>
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<br>
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<br>
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<script>
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if (NIBRIam && NIBRIam.NIBR521 !== undefined) {
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var usernames = document.getElementById("usernames")
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var options = usernames.options
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for (i = 0; i < options.length; i++) {
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if (options[i].value.toLowerCase() == currentUser.toLowerCase()) {
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options[i].setAttribute("selected", "selected")
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}
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}
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}
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</script>
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</body>
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</html>
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