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submission.html
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<!doctype html>
<html lang="en-us">
<head>
<!-- Meta -->
<meta charset="utf-8">
<meta http-equiv="x-ua-compatible" content="ie=edge">
<meta name="viewport" content="width=device-width,initial-scale=1">
<title>Submission</title>
<meta name="description" content="Local EGA in Norway">
<!-- The compiled CSS file -->
<link rel="stylesheet" href="css/production.css">
<!-- Web fonts -->
<link href="https://fonts.googleapis.com/css?family=Montserrat:400,400i,700|Source+Serif+Pro:700" rel="stylesheet">
<!-- favicon.ico. Place these in the root directory. -->
<link rel="shortcut icon" href="/img/favicon.ico">
</head>
<body class="has-animations">
<div class="container pt3 mt2 text--gray align--center">
<div class="grid-column align--left">
<a href="/" class="link"><img class="logo" style="max-height: 100px; vertical-align: -2em; margin: 20px;" src="/img/EGA_submarcas_Norway.svg" alt="Federated EGA Norway node"></a>
<a href="/docs.html" class="link link--text" style="margin: 8px;">Docs and Info</a>
<a href="/pp.html" class="link link--text" style="margin: 8px;">Privacy Policy</a>
<a href="/tos.html" class="link link--text" style="margin: 8px;">Terms of Service</a>
<a href="mailto:[email protected]" class="link link--text" style="margin: 8px;">Contact Us</a>
<a href="/about.html" class="link link--text" style="margin: 8px;">About</a>
</div>
</div>
<!-- Header -->
<header class="align--center pt3">
<div class="container--lg border--bottom pb3">
<h1 class="mb2">Federated EGA Norway node</h1>
<h2 class="mt3">Submission</h2>
</div>
</header>
<main>
<!-- Feature list -->
<div class="container pt3 mt2 text--gray align--center">
<p class="mb3">
This page documents the practical steps to upload data files and meta-data
describing your dataset. Before an actual submission you should send us an
email at [email protected] expressing your interest to submit a dataset to
Federated EGA Norway, and you will receive detailed instructions to guide you
through the submission process.
</p>
<p class="mb3">
Before you start, please, make sure that you have all the required software installed.
All the required tools are open-source and developed by Elixir developers.
Please, avoid using any third-party tools that are not listed on this page.
</p>
<div class="border--bottom grid-row">
<div class="grid-column span-half mb3 reveal-on-scroll is-revealing">
<img class="illustration--small mb1" src="/img/encryption.svg" alt="Encryption tool">
<p><a class="link link--text" target="_blank" href="https://github.com/elixir-oslo/crypt4gh">Encryption tool</a></p>
</div>
<div class="grid-column span-half mb3 reveal-on-scroll is-revealing">
<img class="illustration--small mb1" src="/img/uploading.svg" alt="Put in a vault">
<p><a class="link link--text" target="_blank" href="https://github.com/elixir-oslo/lega-commander">File manager</a></p>
</div>
</div>
</div>
<!-- Focus -->
<div class="container--lg pt1 pb1">
<div class="grid-row grid-row--center">
<div class="grid-column span-1"></div>
<div class="grid-column mt3 mb2">
<div class="mb2">
<a id="requirements"></a><h2><a href="#requirements" class="link link--text">1. Formal requirements</a></h2>
<p class="mt2">
The most prominent first action needed, is that we enter into a Data Processing Agreement
together, with your home organisation as the Data Controller and the University of Oslo as
the Data Processor and Service Provider of the Federated EGA Norway node. A generic
researcher guide can be found <a class="link link--text" target="_blank" href="researcher_guide.html">here</a>.
</p>
</div>
</div>
<div class="grid-column mt3 mb2 reveal-on-scroll is-revealing">
<img src="/img/requirements.svg" alt="Registration">
</div>
</div>
<div class="grid-row grid-row--center">
<div class="grid-column mt3 mb2 reveal-on-scroll is-revealing">
<img src="/img/registration.svg" alt="Registration">
</div>
<div class="grid-column span-1"></div>
<div class="grid-column mt3 mb2">
<div class="border--bottom pb2 mb2">
<a id="registration"></a><h2><a target="_blank" href="#registration" class="link link--text">2. Registering</a></h2>
<p class="mt2">
You will need to obtain a Central EGA account prepared for submission to the Federated EGA Norway node. Follow these instructions to <a class="link link--text" target="_blank" href="/registration.html">register</a>.
</p>
<p class="mt2">
You will also need a <a class="link link--text" target="_blank" href="https://lifescience-ri.eu/ls-login/">Life Science</a> login (a.k.a. ELIXIR AAI) identity to submit data to the Federated EGA Norway node. If you don't have one already,
you can easily associate your home institution identity from FEIDE (or other user supported identities) to a LS Login (ELIXIR AAI) user
profile during first login, see the login button on our <a class="link link--text" target="_blank" href="https://ega.elixir.no">front page</a>.
</p>
</div>
<p class="italic text--gray mb1">
If you have any questions regarding identities/accounts needed for FEGA Norway, please contact the <a href="mailto:[email protected]" class="link link--text">FEGA Norway helpdesk</a>.
</p>
</div>
</div>
<div class="grid-row grid-row--center">
<div class="grid-column mt3 mb2 order-2">
<div class="border--bottom pb2 mb2">
<a id="encryption"></a><h2><a href="#encryption" class="link link--text">3. Encryption</a></h2>
<p class="mt2">
In order to deposit your data, it must me encrypted first with <code>crypt4gh</code> tool.
</p>
<p class="mt2">
The <a class="link link--text" target="_blank" href="/ega.pub.pem">public key</a> of our Federated EGA Norway service should be downloaded first. Then your own key-pair should be generated.
</p>
<p class="mt2">
Finally, the encryption can be performed.
</p>
</div>
<p class="italic text--gray mb1">
You can find more details on the tool <a class="link link--text" target="_blank" href="https://github.com/elixir-oslo/crypt4gh">page</a> at the GitHub.
</p>
</div>
<div class="grid-column span-1"></div>
<div class="grid-column mt3 mb2 order-1 reveal-on-scroll is-revealing">
<script src="https://gist.github.com/dtitov/ee546faa4036477217f7548b46f7e1b7.js"></script>
</div>
</div>
<div class="grid-row grid-row--center">
<div class="grid-column mt3 mb2 reveal-on-scroll is-revealing">
<script src="https://gist.github.com/dtitov/d09b5e7be0fd5f3571125500047f631f.js"></script>
</div>
<div class="grid-column span-1"></div>
<div class="grid-column mt3 mb2">
<div class="border--bottom pb2 mb2">
<a id="authentication"></a><h2><a href="#authentication" class="link link--text">4. Authentication</a></h2>
<p class="mt2">
Before uploading the data, you need to set the authentication environment variables.
</p>
<p class="mt2">
First, you must set <code>CENTRAL_EGA_USERNAME</code> and <code>CENTRAL_EGA_PASSWORD</code>. This is your <a class="link link--text" target="_blank" href="https://ega-archive.org/">EGA</a> credentials.
</p>
<p class="mt2">
Second, you have to set <code>ELIXIR_AAI_TOKEN</code>. This is a JWT token that can be generated on this website after successful LS login/Elixir AAI authentication: <a class="link link--text" target="_blank" href="https://ega.elixir.no/token.html">https://ega.elixir.no/token.html</a>
</p>
</div>
<p class="italic text--gray mb1">
Note that <code>ELIXIR_AAI_TOKEN</code> has an expiration time of nearly two hours, so one would need to re-obtain and re-set it upon expiration.
</p>
</div>
</div>
<div class="grid-row grid-row--center">
<div class="grid-column mt3 mb2 order-2">
<div class="border--bottom pb2 mb2">
<a id="uploading"></a><h2><a href="#uploading" class="link link--text">5. Uploading</a></h2>
<p class="mt2">
At last, you can perform the actual upload of the previously encrypted data, using <code>lega-commander</code> tool.
</p>
<p class="mt2">
Uploads are processed in chunks, so it is possible to resume the upload in case of unexpected interruption.
</p>
<p class="mt2">
It is also possible to upload directories with files. In this case one must specify a folder name instead of the filename.
Please, keep in mind that the hierarchy of the subfolders is not preserved, i.e. if you have files in multiple nested folders, they all will end up in one folder on the server.
</p>
</div>
<p class="italic text--gray mb1">
You can find more details on the tool <a class="link link--text" target="_blank" href="https://github.com/elixir-oslo/lega-commander">page</a> at the GitHub.
</p>
</div>
<div class="grid-column span-1"></div>
<div class="grid-column mt3 mb2 order-1 reveal-on-scroll is-revealing">
<script src="https://gist.github.com/dtitov/dfe73a792685e6b9be81228b234c886c.js"></script>
</div>
</div>
<div class="grid-row grid-row--center">
<div class="grid-column mt3 mb2 reveal-on-scroll is-revealing">
<img src="/img/assign.svg" alt="Metadata">
</div>
<div class="grid-column span-1"></div>
<div class="grid-column mt3 mb2">
<div class="border--bottom pb2 mb2">
<a id="metadata"></a><h2><a href="#metadata" class="link link--text">6. Submitting metadata</a></h2>
<p class="mt2">
After successful upload, the metadata about the submission must be entered into the <a class="link link--text" target="_blank" href="https://submission.norway.ega-archive.org">FEGA Norway Submitter Portal</a>.
</p>
<p class="mt2">
A detailed <a class="link link--text" target="_blank" href="https://ega-archive.org/submission/FAQ">FAQ</a> about the metadata submission is available at the EGA website.
</p>
</div>
<p class="italic text--gray mb1">
If you have any questions regarding metadata submission to Federated EGA, please contact us at <a href="mailto:[email protected]" class="text">[email protected]</a>
</p>
</div>
</div>
</div>
</main>
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