Merge pull request #18 from ELIXIR-Belgium/main

First user guide for DataHub production
ELIXIR-Belgium · Mar 27, 2024 · a2e88da · a2e88da
2 parents 3ef1f25 + 267b015
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diff --git a/.travis.yml b/.travis.yml
diff --git a/CNAME b/CNAME
@@ -1 +1 @@
-datahub.help.elixir-belgium.org
+help.datahub-test.elixir-belgium.org
diff --git a/Gemfile b/Gemfile
@@ -1,5 +1,5 @@
 source 'https://rubygems.org'
-ruby '2.7.1'
+ruby '2.7.7'
 
 gem 'github-pages'
 gem 'jekyll-sitemap'

diff --git a/Rakefile b/Rakefile
@@ -6,7 +6,7 @@ task :test do
   sh 'bundle exec jekyll build'
   options = {
     alt_ignore: [/.*/], # don't worry about images without an alt tag
-    url_ignore: [
+    ignore_urls: [
       /http(s)?:\/\/localhost.*/, # ignore links to localhost, which are shown when walking through the installation
       /https:\/\/www.nationalarchives.gov.uk.*/, 
       /https:\/\/bitbucket.org\/fairdom\/seek\/downloads\/seek*/,

diff --git a/_config.yml b/_config.yml
@@ -1,13 +1,13 @@
 #baseurl: /seek
 
-current_seek_version: "1.12.0"
-current_docker_tag: "1.12"
+current_seek_version: "1.14.2"
+current_docker_tag: "1.14"
 
 plugins:
   - jekyll-sitemap
   - jekyll-redirect-from
   - jekyll-feed
 
 name: FAIRDOM
-url: https://docs.seek4science.org
+url: https://help.datahub-test.elixir-belgium.org
 author: FAIRDOM
diff --git a/_includes/head.html b/_includes/head.html
@@ -1,6 +1,6 @@
 <head>
     <meta charset="UTF-8">
-    <title>Seek4Science Docs - {{ page.title }}</title>
+    <title>FAIRDOM-SEEK Docs - {{ page.title }}</title>
 
     <link href="/images/favicon.png" rel="shortcut icon" type="image/png" />
     <meta name="viewport" content="width=device-width, initial-scale=1">
@@ -10,15 +10,12 @@
     <link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/stylesheets/stylesheet.css" media="screen">
     <link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/stylesheets/github-light.css" media="screen">
     <link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/stylesheets/seek.css" media="screen">
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
-
-    <link rel="canonical" href="{{ site.url }}{{ page.url | replace:'index.html',''}}">
+<!--    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>-->
 
     <!-- jQuery (necessary for Bootstrap's JavaScript plugins) -->
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
+    <script src="{{ site.baseurl }}/js/jquery/1.11.2/jquery.min.js"></script>
     <!-- Include all compiled plugins (below), or include individual files as needed -->
     <script src="{{ site.baseurl }}/js/bootstrap.min.js"></script>
 
-    {% include analytics.html %}
-    {% include cookie-popup.html %}
+
 </head>
diff --git a/_includes/header.html b/_includes/header.html
@@ -10,24 +10,28 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" rel="home" href="{{ site.baseurl }}/">
+      <a class="navbar-brand" rel="home" href="https://datahub-test.elixir-belgium.org">
         <div>
-        <img style="max-width:50px; margin-top: -12px;"
-             src="{{ site.baseurl }}/images/seek-logo-header.png">
+        <img style="max-height: 50px; margin-top: -16px;" alt="Datahub logo"
+             src="{{ site.baseurl }}/images/datahub-logo.jpg">
         </div>
       </a>
     </div>
 
     <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
       <ul class="nav navbar-nav">
-        <li><a href="{{ site.baseurl }}/">Home</a></li>
-        <li><a href="{{ site.baseurl }}/tech/roadmap.html">Roadmap</a></li>
-        <li><a href="{{ site.baseurl }}/get-seek.html">Getting FAIRDOM-SEEK</a></li>
-        <li><a href="{{ site.baseurl }}/contacting-us.html">Contacting Us</a></li>
-        <li><a href="{{ site.baseurl }}/contributing.html">Contributing</a></li>
-        <li><a href="{{ site.baseurl }}/help/user-guide/index.html">User Guide</a></li>
+        <li><a href="{{ site.baseurl }}/index.html">Get Started</a></li>
+<!--        <li><a href="{{ site.baseurl }}/tech/roadmap.html">Roadmap</a></li> --> 
+<!--        <li><a href="{{ site.baseurl }}/get-seek.html">Getting FAIRDOM-SEEK</a></li> -->
+        <li><a href="{{ site.baseurl }}/dh-for-users.html">For Users</a></li>
+        <li><a href="{{ site.baseurl }}/dh-for-system-admin.html">For System Admin</a></li>
         <li><a href="{{ site.baseurl }}/help/user-guide/api.html">API</a></li>
-        <li><a href="{{ site.baseurl }}/tech/useful-links.html">Useful Links</a></li>
+        <li><a href="{{ site.baseurl }}/contacting-us.html">Contacting Us</a></li>
+<!--        <li><a href="{{ site.baseurl }}/contributing.html">Contributing</a></li> -->
+        <li><a href="{{ site.baseurl }}/dh-contributing-to-pages.html">Contribute</a></li>
+<!--        <li><a href="{{ site.baseurl }}/help/user-guide/index.html">User Guide</a></li> -->
+        <li><a href="{{ site.baseurl }}/dh-about.html">About</a></li>
+<!--       <li><a href="{{ site.baseurl }}/tech/useful-links.html">Useful Links</a></li> --> 
       </ul>
     </div>
 

diff --git a/_includes/search.html b/_includes/search.html
@@ -1,16 +1,5 @@
-<script>
-    (function() {
-        var cx = '000557171303025515437:vrcbow5ltbc';
-        var gcse = document.createElement('script');
-        gcse.type = 'text/javascript';
-        gcse.async = true;
-        gcse.src = (document.location.protocol == 'https:' ? 'https:' : 'http:') +
-        '//cse.google.com/cse.js?cx=' + cx;
-        var s = document.getElementsByTagName('script')[0];
-        s.parentNode.insertBefore(gcse, s);
-    })();
+<script async src="https://cse.google.com/cse.js?cx=873655217ca584cfa">
 </script>
-
-<div id='google-search'>
-    <gcse:search></gcse:search>
+<div class="gcse-search" id='google-search'>
+    <gcse:search enablehistory="false"></gcse:search>
 </div>
diff --git a/contacting-us.md b/contacting-us.md
@@ -6,34 +6,29 @@ redirect_from: "/contacting_us.html"
 
 # Contacting us
 
-We have a number of ways you can contact us:
+<!--We have a number of ways you can contact us:
 
 
-## Mailing lists
+## Contact FAIRDOM
 
-We have 2 Google Groups. These groups are open to anonymous queries, you don't have to be a group member to submit a query.
-
-* For technical or development related queries please use [SEEK Developers Group](http://groups.google.com/group/seek-developers)
-* For general queries, or queries about using SEEK please us [Seek4Science Group](http://groups.google.com/group/seek4science)
-
-
-## Contact form
+You can contact us through [FAIRDOM](https://fair-dom.org) using [various channels](https://fair-dom.org/get_involved).
 
-You can also contact us through [FAIRDOM](http://fair-dom.org) using our [Contact form](http://fair-dom.org/contact).
-
-This should be used if your query or feedback is of a more confidential nature. Remember to provide your email address.
+This should be used if your query or feedback is of a more confidential nature. Remember to provide your email address.-->
 
 ## Email
 
-For general support you can contact us through [support@fair-dom.org](mailto:support@fair-dom.org).
-
-For community related questions, you can use [community@fair-dom.org](mailto:community@fair-dom.org)
+For general support you can contact us through [datahub@elixir-belgium.org](mailto:datahub@elixir-belgium.org).
 
 ## Reporting bugs and feature requests
 
 Bugs and feature requests can be reported through [Github Issues](https://fair-dom.org/issues).
 
 For more details and guidelines please visit [Reporting Bugs and raising Feature Requests](/tech/reporting-bugs-and-features.html)
 
+## Google groups
+
+We have 2 Google Groups. These groups are open to anonymous queries, you don't have to be a group member to submit a query.
 
+* For technical or development related queries please use [SEEK Developers Group](https://groups.google.com/group/seek-developers)
+* For general queries, or queries about using SEEK please us [Seek4Science Group](https://groups.google.com/group/seek4science)
 
diff --git a/contributing-to-pages.md b/contributing-to-pages.md
@@ -29,3 +29,56 @@ If you want to view your changes as you edit them, with Ruby installed you can i
 and then goto [localhost:4000/seek/](http://localhost:4000/seek/). For more information please see [Using Jekyll with Pages](https://help.github.com/articles/using-jekyll-with-pages/)
 
 You can make a change by forking and issuing a pull request. If contributing through GitHub is unfamiliar to you, please read [Contributing to Open Source on GitHub](https://guides.github.com/activities/contributing-to-open-source/)
+
+# Working with DataHub documentation
+
+## FAIRDOM-SEEK documentation
+
+FAIRDOM-SEEK documentation is in branches of the GitHub repository seek4science/seek
+* gh-pages:
+* gh-pages-1.13:
+* gh-pages-master:
+* gh-pages-sample-update: temporary branch to record features agreed upon during sample working group
+
+## DataHub documentation
+
+FAIRDOM-SEEK documentation (gh-pages branches) has been cloned in GitHub
+* ELIXIR-Belgium/DataHub-help: to deploy documentation of the production instance (https://datahub.elixir-belgium.org)
+* ELIXIR-Belgium/DataHub-help-test: to deploy documentation (https://help.datahub-test.elixir-belgium.org) of the test instance (https://datahub-test.elixir-belgium.org). Forked from ELIXIR-Belgium/DataHub-help.
+* ELIXIR-Belgium/DataHub-help-usecase: to deploy documentation (https://help.datahub-usecase.elixir-belgium.org) of the usecase instance (https://datahub-usecase.elixir-belgium.org). Forked from ELIXIR-Belgium/DataHub-help.
+
+## How to contribute to DataHub documentation
+
+### General way of working
+1. Use [ELIXIR-Belgium/DataHub-help-test](https://github.com/ELIXIR-Belgium/DataHub-help-test) to propose changes to the DataHub documentation pages.
+2. DataHub team will review and approve/reject your changes.
+3. DataHub team will push the changes towards ELIXIR-Belgium/DataHub-help.
+
+### via GitHub GUI
+1. Go to [ELIXIR-Belgium/DataHub-help-test](https://github.com/ELIXIR-Belgium/DataHub-help-test).
+2. Make the changes you want to propose.
+3. Open a pull request from your fork (that is created by GitHub by default) towards ELIXIR-Belgium/DataHub-help-test. 
+
+   *IMPORTANT: please check that your pull request is against **DataHub-help-test main**  and not DataHub-help.*
+
+4. Follow up via GitHub for comments from the DataHub team.
+
+### via code editor of your choice (e.g. VSCode)
+
+This is a general workflow in how to work on your own fork (copy) of the repository and request changes through a pull request.
+1. In GitHub, make a fork of [ELIXIR-Belgium/DataHub-help-test](https://github.com/ELIXIR-Belgium/DataHub-help-test) using the fork button. Then go to `Code --> SSH --> copy`
+2. Open a terminal and choose a directory. Then clone your fork there using:
+    ```
+    git clone git@github.com:USERNAME/DataHub-help-test.git
+    cd DataHub-help-test
+    ```
+    NOTE: Make sure you clone the fork and not the original ELIXIR-Belgium/DataHub-help-test one.
+3. Set your fork of DataHub-Help (e.g. username/DataHub-help) as your **remote**
+4. Set ELIXIR-Belgium/DataHub-help-test as your **origin**
+5. When making changes
+* Keep your fork up to date by pulling from **origin** (ELIXIR-Belgium/DataHub-help-test).
+* Create a new branch named after your feature/edit and make the changes you want to make.
+* Commit and push to **remote** (e.g. username/DataHub-help).
+6. In GitHub, open a pull request and make sure to set ELIXIR-Belgium/DataHub-help-test main as base repository.
+
+   *IMPORTANT: please check that your pull request is against **DataHub-help-test main**  and not DataHub-help.*
diff --git a/contributing.md b/contributing.md
@@ -5,11 +5,11 @@ layout: page
 
 # Contributing
 
-We welcome many contributions to our [SEEK software](http://seek4science.org), these Documentation pages and our [FAIRDOM](http://fair-dom.org) project in general.
+We welcome many contributions to our [SEEK software](https://seek4science.org), these Documentation pages and our [FAIRDOM](https://fair-dom.org) project in general.
 
 Below are some guides for how you contribute to the software or these pages.
 
-However, if there other ways you feel you can contribute, such as running a workshop or providing training material, then please contact us at <community@fair-dom.org>.
+<!--However, if there other ways you feel you can contribute, such as running a workshop or providing training material, then please contact us at <community@fair-dom.org>.-->
 
 ## Contributing to SEEK
 
@@ -19,4 +19,4 @@ Please read [contributing to SEEK](tech/contributing-to-seek.html)
 ## Contributing to these pages
 
 You can also contribute to these pages.
-Please read [contributing to these pages](contributing-to-pages.html)
+Please read <!--[contributing to these pages](contributing-to-pages.html) TO BE MADE--> 
diff --git a/cookies.md b/cookies.md
@@ -11,4 +11,4 @@ Google Analytics records the pages you visited on the site, and information abou
 
 The information we gather from Google Analytics helps us measure which parts of the site are useful and popular, and which parts do not work so well. This allows us to tailor and improve the site for our visitors.
 
-You can learn more about [Google Analytics](http://www.google.com/analytics/learn/privacy.html), or if you wish to you can [Opt Out](https://tools.google.com/dlpage/gaoptout)
+You can learn more about [Google Analytics](https://www.google.com/analytics/learn/privacy.html), or if you wish to you can [Opt Out](https://tools.google.com/dlpage/gaoptout)
diff --git a/credits.md b/credits.md
@@ -9,29 +9,29 @@ layout: page
 
 * [WorkflowHub](https://about.workflowhub.eu/)
   - <https://workflowhub.eu/> is based on SEEK
-* [OpenBIS](http://fair-dom.org/platform/openbis/)
-* [BioVel](http://web.archive.org/web/20180202071633/http://www.biovel.eu/) (archived 2018-02-02)
-  - [BioVel portal](http://web.archive.org/web/20171112080623/https://portal.biovel.eu/) (archived 2017-11-12) was based on SEEK
+* [OpenBIS](https://openbis.ch/)
+* [BioVel](https://web.archive.org/web/20180202071633/http://www.biovel.eu/) (archived 2018-02-02)
+  - [BioVel portal](https://web.archive.org/web/20171112080623/https://portal.biovel.eu/) (archived 2017-11-12) was based on SEEK
 * [BiVeS](https://sems.uni-rostock.de/projects/bives/)
-* [SynBioChem](http://synbiochem.co.uk/)
+* [SynBioChem](https://synbiochem.co.uk/)
 * [Virtual Liver Network](http://www.virtual-liver.de/)
-* [myExperiment](http://www.myexperiment.org/)
-* [BioCatalogue](http://www.biocatalogue.org/)
+* [myExperiment](https://www.myexperiment.org/)
+* [BioCatalogue](https://esciencelab.org.uk/products/biocatalogue/)
 * [MethodBox](http://www.esciencelab.org.uk/products/methodbox/)
 
 ## External Services we use
 
-* [Sabio-RK](http://sabio.villa-bosch.de)
-* [CytoScape](http://cytoscapeweb.cytoscape.org)
-* [BioPortal](http://bioportal.bioontology.org)
-* [BioModels](http://www.ebi.ac.uk/biomodels-main/)
-* [JWS Online](http://jjj.biochem.sun.ac.za/)
-* [Pubmed](http://www.ncbi.nlm.nih.gov/pubmed)
-* [CrossRef](http://www.crossref.org/)
+* [Sabio-RK](http://sabio.h-its.org/)
+* [CytoScape](https://github.com/cytoscape/cytoscapeweb)
+* [BioPortal](https://bioportal.bioontology.org)
+* [BioModels](https://www.ebi.ac.uk/biomodels/)
+* [JWS Online](https://jjj.biochem.sun.ac.za/)
+* [Pubmed](https://pubmed.ncbi.nlm.nih.gov/)
+* [CrossRef](https://www.crossref.org/)
 
 ## Javascript tools
 
-* [FLOT plotting library](http://code.google.com/p/flot/)
+* [FLOT plotting library](https://code.google.com/p/flot/)
 * [Curved Lines plugin for FLOT](https://github.com/MichaelZinsmaier/CurvedLines)
 * [Pdf rendering library](https://github.com/mozilla/pdf.js)
 * [jScrollPane](http://jscrollpane.kelvinluck.com/)
@@ -46,18 +46,18 @@ HITS gGmbH.
 ## Icons and themes
 
 * Fairdom Logo: [Autumn Firefly Design](http://autumn-firefly.co.uk/)
-* [FamFamFam icon set (flags and silk)](http://www.famfamfam.com/lab/icons/silk/)
-* Institution icon: from [Icon Eden](http://web.archive.org/web/20150206235106/http://www.iconeden.com/) (archived 2015-02-06)
-* [Test Tube & Flask icons](http://www.clker.com/clipart-test-tube-icon.html) by OCAL on clker
-* [Crystal Clear Icon Set](http://www.iconarchive.com/show/crystal-clear-icons-by-everaldo.html) (LGPL)
-* [Organism Icon from IconIcon](http://iconicon.net/?page_id=79)
-* Zoom images from [Lightbox by Lokesh Dhakar](http://www.lokeshdhakar.com/projects/lightbox2/)
-* [Presentation icon](http://web.archive.org/web/20110508124549/http://www.mricons.com/icon/785/128/presentation-slides-icon) (archived 2011-05-08) by David Vignoni at Mr. Icons (LGPL)
-* [Strain image](http://en.wikipedia.org/wiki/File:Enterococcus_faecalis20023-300.jpg#file) from Wikimedia Commons
-* [expand plus icon](http://findicons.com/icon/439241/toggle_expand?id=439541) by Jack Cai, Creative Commons Attribution (by) 
-* [collapse minus icon](http://findicons.com/icon/439180/toggle_collapse?id=439440) by Jack Cai, Creative Commons Attribution (by)
+* [FamFamFam icon set (flags and silk)](https://github.com/legacy-icons/famfamfam-silk)
+* Institution icon: from [Icon Eden](https://web.archive.org/web/20150206235106/http://www.iconeden.com/) (archived 2015-02-06)
+* [Test Tube & Flask icons](https://www.clker.com/clipart-test-tube-icon.html) by OCAL on clker
+* [Crystal Clear Icon Set](https://www.iconarchive.com/show/crystal-clear-icons-by-everaldo.html) (LGPL)
+* [Organism Icon from IconIcon](https://iconicon.net/?page_id=79)
+* Zoom images from [Lightbox by Lokesh Dhakar](https://www.lokeshdhakar.com/projects/lightbox2/)
+* [Presentation icon](https://web.archive.org/web/20110508124549/http://www.mricons.com/icon/785/128/presentation-slides-icon) (archived 2011-05-08) by David Vignoni at Mr. Icons (LGPL)
+* [Strain image](https://en.wikipedia.org/wiki/File:Enterococcus_faecalis20023-300.jpg#file) from Wikimedia Commons
+* [expand plus icon](https://findicons.com/icon/439241/toggle_expand?id=439541) by Jack Cai, Creative Commons Attribution (by) 
+* [collapse minus icon](https://findicons.com/icon/439180/toggle_collapse?id=439440) by Jack Cai, Creative Commons Attribution (by)
 * Waiting icon from [FatCow Web Hosting](http://www.fatcow.com/)
-* [Font awesome](http://fortawesome.github.io/Font-Awesome/)
+* [Font awesome](https://github.com/FortAwesome/Font-Awesome)
 * [Fatcow icons set](http://www.fatcow.com/free-icons) (Creative Commons Attribution)
 
 ## scale images (To BE UPDATED)