Merge pull request #45 from ahornos/main

BioHackathon 2022 technical content addition

CONTRIBUTORS.yaml

@@ -42,3 +42,33 @@ silviabah:
     email: [email protected]
     orcid: 0000-0002-2734-0449
     elixir_node: embl
+
+ahornos:
+    name: Albert Hornos Vidal
+    email: [email protected]
+    orcid: 0000-0002-7330-668X
+    elixir_node: es
+
+blankdots:
+    name: Stefan Negru
+    email:
+    orcid:
+    elixir_node: fi
+
+alex-dem:
+    name: Alexandros Dimopoulos
+    email: [email protected]
+    orcid: 0000-0002-4602-2040
+    elixir_node: gr
+
+d-salgado:
+    name: David Salgado
+    email: [email protected]
+    orcid: 0000-0002-5905-3591
+    elixir_node: fr
+
+lilachic:
+    name: Liisa Lado-Villar
+    email: [email protected]
+    orcid:
+    elixir_node: fi

docs/search.html

@@ -0,0 +1,89 @@
+---
+layout: base
+title: Search
+nav_exclude: true
+search_exclude: true
+---
+
+  <h1 id="search">Search Results</h1>
+
+  <div id="search-results" class="search-results">
+    Enter a search query in the search box on the left.
+  </div>
+
+  <!-- We only need to load the search dependencies in this page. -->
+  <script src="https://unpkg.com/lunr/lunr.js"></script>
+  <script type="text/javascript">
+    "use strict";
+
+    // First we figure out if there is a search query and show a "searching..." animation
+    var getQueryVariable = function(variable) {
+      var query = window.location.search.substring(1);
+      var vars = query.split('&');
+      for (var i = 0; i < vars.length; i++) {
+        var pair = vars[i].split('=');
+        if (pair[0] === variable) {
+          return decodeURIComponent(pair[1].replace(/\+/g, '%20'));
+        }
+      }
+    };
+    var searchResults = document.getElementById('search-results');
+    var searchQuery = getQueryVariable('q');
+    var dotAnimation = null;
+    if (searchQuery) {
+      document.getElementById('search-query').setAttribute('value', searchQuery);
+      var dotsCount = 0;
+      dotAnimation = setInterval(function() {
+        dotsCount++;
+        var dots = new Array(dotsCount % 5).join('.');
+        searchResults.innerHTML = '<li>Searching' + dots + '</li>';
+      }, 500);
+    }
+
+    // Then we perform the search on page load
+    window.addEventListener('load', function() {
+      var displaySearchResults = function(results, store) {
+        clearInterval(dotAnimation);
+        if (results.length) {
+          var appendString = '';
+          for (var i = 0; i < results.length; i++) {
+            var item = store[results[i].ref];
+            appendString += '<li><a href="' + item.url + '"><h3>' + item.title + '</h3></a>';
+            appendString += '<p>' + item.content.substring(0, 150) + '...</p></li>';
+          }
+          searchResults.innerHTML = appendString;
+        } else {
+          searchResults.innerHTML = '<li>Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.</li>';
+        }
+      };
+
+      if (searchQuery) {
+        var idx = lunr(function() {
+          this.field('id');
+          this.field('title', { boost: 10 });
+          this.field('author');
+          this.field('content');
+        });
+        $.getJSON('/search_data.json').then(function(search_data) {
+          var idx = lunr(function() {
+            this.field('id');
+            this.field('title', { boost: 10 });
+            this.field('author');
+            this.field('content');
+
+            for (var key in search_data) {
+              this.add({
+                'id': key,
+                'title': search_data[key].title,
+                'author': search_data[key].author,
+                'content': search_data[key].content
+              });
+            }
+          });
+
+          var results = idx.search(searchQuery);
+          displaySearchResults(results, search_data);
+        });
+      }
+    });
+  </script>

docs/search_data.json

@@ -0,0 +1,32 @@
+---
+layout: null
+nav_exclude: true
+search_exclude: true
+---
+{
+{%- for site_page in site.pages %}
+{%- unless site_page.search_exclude == true %}
+    "{{ site_page.url | slugify }}": {
+        "title": "{{ site_page.title | xml_escape }}",
+        "content": {{site_page.content | markdownify | newline_to_br | replace: '<br />', ' ' | strip_html | normalize_whitespace | jsonify }},
+        "url": " {{ site_page.url | xml_escape }}",
+        "author": "{{ site_page.author | xml_escape }}"
+    },
+{%- endunless %}
+{%- endfor %}
+{%- for site_post in site.posts %}
+{%- unless site_page.search_exclude == true %}
+    "{{ site_post.url | slugify }}": {
+        "title": "{{ site_post.title | xml_escape }}",
+        "content": {{site_post.content | markdownify | newline_to_br | replace: '<br />', ' ' | strip_html | normalize_whitespace | jsonify }},
+        "url": " {{ site_post.url | xml_escape }}",
+        "author": "{{ site_post.author | xml_escape }}"
+    }{%- unless forloop.last %},{%- endunless %}
+{%- endunless %}
+{%- else %}
+    {%- comment %} Dirty trick: There is a comma at the end of the sites loop, so we need at least one entry after {% endcomment %}
+    ".": {
+        ".": "."
+    }
+{%- endfor %}
+}

docs/topics/technical-operational/countries_tech_stack/component_description.html

@@ -0,0 +1,153 @@
+<table class="tg">
+  <colgroup>
+  <col style="width: 34px">
+  <col style="width: 133px">
+  <col style="width: 304px">
+  <col style="width: 122px">
+  <col style="width: 56px">
+  </colgroup>
+  <thead>
+    <tr>
+      <th class="tg-center-bold"><b>#</b></th>
+      <th class="tg-left" ><b>Component</b></th>
+      <th class="tg-left"><b>Description</b></th>
+      <th class="tg-center"><b>Required</b></th>
+      <th class="tg-center" nowrap><b>Link to</b></th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td class="tg-center">1</td>
+      <td class="tg-left"><b>URL</b></td>
+      <td class="tg-left">Official website for documentation</td>
+      <td class="tg-center">-</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">2</td>
+      <td class="tg-left"><b>Credentials</b></td>
+      <td class="tg-left">For connecting to Central EGA there are 2 types of credentials required: <br>User API for identifying and validating in Submitter Inbox the cEGA accounts<br>cEGA MQ credentials for connecting FEGA Node MQ</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">3</td>
+      <td class="tg-left"><b>FEGA Node Encryption key pair</b></td>
+      <td class="tg-left">A Crypt4GH key pair generated by the FEGA Node, and the public is shared with the Submitter so that files are sent encrypted for the FEGA Node</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">4</td>
+      <td class="tg-left"><b>FEGA Node MQ</b></td>
+      <td class="tg-left">RabbitMQ which is connected in shovel and federation mechanism with the cEGA MQ</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">2</td>
+    </tr>
+    <tr>
+      <td class="tg-center">5</td>
+      <td class="tg-left"><b>Submitter Inbox</b></td>
+      <td class="tg-left">An Inbox solution for the Researcher to submit files to a specific Node (e.g. SFTP, REST API).<br>The Inbox needs to be accessible by a Researcher via an URL.</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">2, 3</td>
+    </tr>
+    <tr>
+      <td class="tg-center">6</td>
+      <td class="tg-left"><b>Ingest Pipeline</b></td>
+      <td class="tg-left">Means of interfacing with the cEGA so that the required messages are being sent at relevant steps of the submission process. https://localega.readthedocs.io/en/latest/amqp.html </td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">4, 7, 8, 9</td>
+    </tr>
+    <tr>
+      <td class="tg-center">7</td>
+      <td class="tg-left"><b>Archive storage</b></td>
+      <td class="tg-left">Storage solution for storing archived files.  e.g. S3, POSIX etc.</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">6</td>
+    </tr>
+    <tr>
+      <td class="tg-center">8</td>
+      <td class="tg-left"><b>Archive File Database</b></td>
+      <td class="tg-left">Means of storing information about the archived files and their AccessionIDs and dataset IDs mapping to AccessionIDs (file to dataset mapping).<br>Note: other details can be stored in the database e.g. checksums, timestamps, headers of crypt4gh file etc.</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">6</td>
+    </tr>
+    <tr>
+      <td class="tg-center">9</td>
+      <td class="tg-left"><b>Backup Storage</b></td>
+      <td class="tg-left">Storage solution for storing a backup of the archived files.  e.g. S3, POSIX etc.<br>Note: A file needs to be backed up in a different location than the Archive</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">6</td>
+    </tr>
+    <tr>
+      <td class="tg-center">10</td>
+      <td class="tg-left"><b>Main Source Code Repository</b></td>
+      <td class="tg-left">Where the source code can be found</td>
+      <td class="tg-center">N</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">11</td>
+      <td class="tg-left"><b>Main Programming Language</b></td>
+      <td class="tg-left">Main programming language for the technical stack pipeline</td>
+      <td class="tg-center">-</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">12</td>
+      <td class="tg-left"><b>Deployment Method</b></td>
+      <td class="tg-left">Means which technology is used to put in production different components</td>
+      <td class="tg-center">-</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">13</td>
+      <td class="tg-left"><b>Helpdesk Management System</b></td>
+      <td class="tg-left">Main tool for user/helpdesk communication</td>
+      <td class="tg-center">N</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">14</td>
+      <td class="tg-left"><b>Helpdesk Portal Technology</b></td>
+      <td class="tg-left">Federated EGA node helpedesk will provide means of interacting with submitter, registering DPA, establisng DACs and monitoring submissions.</td>
+      <td class="tg-center">N</td>
+      <td class="tg-center">15</td>
+    </tr>
+    <tr>
+      <td class="tg-center">15</td>
+      <td class="tg-left"><b>Monitoring Tool</b></td>
+      <td class="tg-left">Means of providing an overview of the status of submissions.<br>Good also for auditing purposes.</td>
+      <td class="tg-center">N</td>
+      <td class="tg-center">14</td>
+    </tr>
+    <tr>
+      <td class="tg-center">16</td>
+      <td class="tg-left"><b>Metadata Submission Method</b></td>
+      <td class="tg-left">Means how the researchers will send the metadata to Central EGA through a cEGA submitter portal, node portal or another solution</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">17</td>
+      <td class="tg-left"><b>Download Solution</b></td>
+      <td class="tg-left">Means for a Requester to access the data once approval has been granted.</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center">7, 8, 18</td>
+    </tr>
+    <tr>
+      <td class="tg-center">18</td>
+      <td class="tg-left"><b>Data Access Tool</b></td>
+      <td class="tg-left">Means of enabling Requesters to Download the archived data.<br>tool for facilitating DACs</td>
+      <td class="tg-center">N</td>
+      <td class="tg-center"></td>
+    </tr>
+    <tr>
+      <td class="tg-center">19</td>
+      <td class="tg-left"><b>General Contact</b></td>
+      <td class="tg-left">Email or website to contact the team deploying the solution</td>
+      <td class="tg-center">Y</td>
+      <td class="tg-center"></td>
+    </tr>
+  </tbody>
+</table>