-{% extends "flowcell_libraries_app.html" %}
-{% load humanize %}
+{% extends "base_site.html" %}
+{% load adminmedia humanize i18n %}
+{% block extrahead %}
+ <!-- App Stuff -->
+ <link type="text/css" rel="stylesheet" href="/static/css/app.css" />
+ <script type="text/javascript" src="/static/js/jquery.min.js"></script>
+
+ {% block additional_javascript %}
+ {% endblock %}
-{% block additional_css %}
-<style type="text/css">
- /* <![CDATA[ */
- div#librarydetail table, div#librarydetail td {
- border-style: solid;
- }
- div#librarydetail table {
- border-width: 0 0 1px 1px;
- border-spacing: 0;
- border-collapse: collapse;
- }
- div#librarydetail td {
- margin: 0;
- padding: 4px;
- border-width: 1px 1px 0 0;
- }
- div#librarydetail thead {
- text-align: center;
- }
- div#librarydetail tbody {
- text-align: right;
- }
- /* ]]> */
-</style>
{% endblock %}
{% block content %}
-<div id="librarydetail">
+<div id="library_detail">
<h2>About this library</h2>
<b>Library ID</b>: {{ lib.id }}<br/>
- <b>Name</b>: {{ lib.library_name }}<br/>
- <b>Species</b>: {{ lib.library_species.scientific_name }}<br/>
+ <b>Name</b>:
+ <span property="libns:name">{{ lib.library_name }}</span>
+ <br/>
+ <b>Species</b>:
+ <a href="{{lib.library_species.get_absolute_url}}" rel="libns:species">
+ <span property="libns:species_name">{{ lib.library_species.scientific_name }}</span></a>
+ <br/>
+ <b>Concentration</b>:
+ <span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
+ <br/>
+ <b>Gel Cut Size</b>:
+ <span property="libns:gel_cut">{{ lib.gel_cut_size }}</span>
+ <br/>
+ <b>Insert Size</b>:
+ <span property="libns:insert_size">{{ lib.insert_size }}</span>
+ <br/>
+ <b>Background or Cell Line</b>:
+ <span property="libns:cell_line">{{ lib.cell_line }}</span>
+ <br/>
+ <b>Replicate</b>:
+ <span property="libns:replicate">{{ lib.replicate }}</span>
+ <br/>
+ <b>Library Type</b>:
+ <span property="libns:library_type">{{ lib.library_type }}</span>
+ <br/>
+ <b>Experiment Type</b>:
+ <span property="libns:experiment_type">{{ lib.experiment_type }}</span>
+ <br/>
+ <b>Made By</b>:
+ <span property="libns:made_by">{{ lib.made_by }}</span>
+ <br/>
+ <b>Creation Date</b>
+ <span property="libns:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ lib.creation_date }}</span>
+ <br/>
+ <b>Protocol Stopping Point</b>
+ <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
+ <br/>
<b>Affiliations</b>:
<ul>
{% for individual in lib.affiliations.all %}
- <li>{{ individual.name }} ( {{ individual.contact }} )</li>
+ <li property="libns:affliation" content="{{individual.name}}">
+ {{ individual.name }} ( {{ individual.contact }} )
+ </li>
{% endfor %}
</ul>
-
+ <div class="htswdetail">
<h2>Raw Result Files</h2>
<table>
<thead>
<tr>
+ <td>Run Start Date</td>
<td>Cycle</td>
<td>Flowcell</td>
<td>Lane</td>
<td>Bed</td>
<td>Archived</td>
</tr>
- {% for result in eland_results %}
- <tr>
- <td>{{ result.cycle }}</td>
- <td>{{ result.flowcell_id }}</td>
- <td>{{ result.lane }}</td>
- <td><a href="{{ result.summary_url }}">Summary</a></td>
- <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
- <td>
- {% if result.bed_url %}
- <a href="{{ result.bed_url }}">Bed</a>
- {% endif %}
- </td>
- <td>
- {% if result.storage_ids %}
- {{ result.storage_ids|safe }}
+ </thead>
+ <tbody>
+ {% for result in eland_results %}
+ <tr about="{{result.flowcell.get_absolute_url}}">
+ <td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ result.run_date|date}}</td>
+ <td>{{ result.cycle }}</td>
+ <td><a href="{{result.flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{ result.flowcell_id }}</span></a></td>
+ <td><a href="{{result.lane.get_absolute_url}}" rel="libns:has_lane"><span property="libns:lane_number" datatype="xsd:decimal">{{ result.lane.lane_number }}</span></a></td>
+ <td><a href="{{ result.summary_url }}">Summary</a></td>
+ <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
+ <td>
+ {% if result.bed_url %}
+ <a href="{{ result.bed_url }}">Bed</a>
{% endif %}
- </td>
- </tr>
- {% endfor %}
+ </td>
+ <td>
+ {% if result.storage_ids %}
+ {{ result.storage_ids|safe }}
+ {% endif %}
+ </td>
+ </tr>
+ {% endfor %}
+ </tbody>
</table>
<h2>Lane Summary Statistics</h2>
<tbody>
{% for lane in lane_summary_list %}
- <tr>
+ <tr about="/flowcell/{{lane.flowcell_id}}/{{lane.lane_id}}/{% if lane.end %}#end{{ lane.end }}{% endif %}">
<td>{{ lane.cycle_width }}</td>
<td>{{ lane.flowcell_id }}</td>
<td>{{ lane.lane_id }}</td>
<td>{{ lane.match_codes.U0|intcomma }}</td>
<td>{{ lane.match_codes.U1|intcomma }}</td>
<td>{{ lane.match_codes.U2|intcomma }}</td>
- <td>{{ lane.unique_reads|intcomma }}</td>
+ <td {% if lane.unique_reads %}property="libns:total_unique_locations" content="{{lane.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ lane.unique_reads|intcomma }}</td>
<td>{{ lane.match_codes.R0|intcomma }}</td>
<td>{{ lane.match_codes.R1|intcomma }}</td>
<td>{{ lane.match_codes.R2|intcomma }}</td>
{% endfor %}
</tbody>
</table>
- <br/>
- <hr/>
- <h2>Count of multi-reads</h2>
- {% for lane in lane_summary_list %}
- {% if lane.summarized_reads %}
- <h3>
- {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }}
- {% if lane.end %} end {{ lane.end }}{% endif %}
- </h3>
- <ul>
- {% for name, counts in lane.summarized_reads.items %}
- <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
- {% endfor %}
- </ul>
- {% endif %}
- {% endfor %}
+
+ <h2>Flowcell Notes</h2>
+ <table>
+ <thead>
+ <tr>
+ <td>Flowcell ID</td>
+ <td>Lane</td>
+ <td>Comment</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for lane in lib.lane_set.all %}
+ <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}">
+ <td><a href="{{lane.flowcell.get_absolute_url}}" rel="libns:flowcell">
+ <span property="libns:flowcell_id">{{ lane.flowcell.flowcell_id }}</span></a></td>
+ <td><a href="{{lane.get_absolute_url}}">
+ <span property="libns:lane_number" datatype="xsd:decimal"
+ >{{ lane.lane_number }}</span></a></td>
+ <td>{{ lane.comment }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
{% endblock %}
+ </div>
</div>
{% endblock %}
projects / htsworkflow.git / blobdiff