{% extends "base_site.html" %}
-{% load adminmedia humanize i18n %}
+{% load staticfiles %}
+{% load 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>
-
+ <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 %}
-
-<style type="text/css">
- /* <![CDATA[ */
- div#librarydetail {
- margin: 0;
- padding: 0;
- }
- 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: 3px;
- border-width: 1px 1px 0 0;
- }
- div#librarydetail thead {
- text-align: center;
- }
- div#librarydetail tbody {
- text-align: right;
- }
- div#librarydetail h1,
- div#librarydetail h2
- {
- font-size: 150%;
- }
-
- div#librarydetail h3 {
- font-size: 125%;
- margin: 0;
- }
-
- div#librarydetail h4,
- div#librarydetail h5,
- div#librarydetail ul,
- div#librarydetail ol,
- div#librarydetail li
- {
- list-style: none;
- margin: 0;
- }
-
- div#librarydetail ul,
- div#librarydetail ol
- {
- margin-bottom: .5em;
- }
- /* ]]> */
-</style>
{% endblock %}
{% block content %}
-<div id="librarydetail">
- <h2>About this library</h2>
- <b>Library ID</b>: {{ lib.id }}<br/>
- <b>Name</b>:
- <span property="libns:name">{{ lib.library_name }}</span>
- <br/>
- <b>Species</b>:
- <span property="libns:species">{{ lib.library_species.scientific_name }}</span>
- <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:creation_date">{{ 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 property="libns:affliation" content="{{individual.name}}">
- {{ individual.name }} ( {{ individual.contact }} )
- </li>
- {% endfor %}
- </ul>
-
+ {% include "sample_header.html" %}
+ <hr/>
+ <div class="library_statistics">
<h2>Raw Result Files</h2>
<table>
<thead>
</tr>
</thead>
<tbody>
+ {% if eland_results %}
{% for result in eland_results %}
- <tr about="/flowcell/{{result.flowcell_id}}/lane/{{result.lane}}">
- <td property="libns:run_date" contents="{{result.run_date}}" datatype="xmls:datetime">{{ result.run_date|date}}</td>
+ <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 property="libns:flowcell_id">{{ result.flowcell_id }}</td>
- <td property="libns:lane">{{ result.lane }}</td>
+ <td><a href="{{result.flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{ result.flowcell_id }}</span></a>{% if user.is_staff %}<a href="{{result.flowcell.get_admin_url}}"><img class="icon_button" src="{% static "admin/img/icon_changelink.gif" %}" alt="Edit"/></a>{% endif%}</td>
+ <td>{{ result.lane.lane_number }}</td>
<td><a href="{{ result.summary_url }}">Summary</a></td>
<td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
<td>
</td>
</tr>
{% endfor %}
+ {% else %}
+ <tr><td colspan="8">No data</td></tr>
+ {% endif %}
</tbody>
</table>
-
+
<h2>Lane Summary Statistics</h2>
{% block summary_stats %}
<table>
</tr>
</thead>
<tbody>
-
- {% for lane in lane_summary_list %}
- <tr about="/flowcell/{{lane.flowcell_id}}/lane/{{lane.lane_id}}/end/{% if lane.end %}{{ lane.end }}{% endif %}">
- <td>{{ lane.cycle_width }}</td>
- <td>{{ lane.flowcell_id }}</td>
- <td>{{ lane.lane_id }}</td>
- <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
- <td>{{ lane.clusters.0|intcomma }}</td>
- <td>{{ lane.successful_pm }}</td>
- <td>{{ lane.reads|intcomma }}</td>
- <td>{{ lane.no_match|intcomma }}</td>
- <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
- <td>{{ lane.qc_failed|intcomma }}</td>
- <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
- <td>{{ lane.match_codes.U0|intcomma }}</td>
- <td>{{ lane.match_codes.U1|intcomma }}</td>
- <td>{{ lane.match_codes.U2|intcomma }}</td>
- <td property="libns:sequence_unique_location" contents="{{lane.unique_reads}}" datatype="xmls:decimal">{{ 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>
- <td>{{ lane.repeat_reads|intcomma }}</td>
+ {% if lane_summary_list %}
+ {# ls short for lane summary #}
+ {% for ls in lane_summary_list %}
+ <tr about="{{ls.lane.get_absolute_url}}">
+ <td>{{ ls.cycle_width }}</td>
+ <td><a href="{{ls.flowcell.get_absolute_url}}">{{ ls.flowcell_id }}</a>
+ </td>
+ <td><a href="{{ls.lane.get_absolute_url}}">{{ ls.lane_id }}</a></td>
+ <td>{% if ls.end %}{{ ls.end }}{% endif %}</td>
+ <td>{{ ls.clusters.0|intcomma }}</td>
+ <td>{{ ls.successful_pm }}</td>
+ <td>{{ ls.reads|intcomma }}</td>
+ <td>{{ ls.no_match|intcomma }}</td>
+ <td>{{ ls.no_match_percent|stringformat:".2f" }}</td>
+ <td>{{ ls.qc_failed|intcomma }}</td>
+ <td>{{ ls.qc_failed_percent|stringformat:".2f" }}</td>
+ <td>{{ ls.match_codes.U0|intcomma }}</td>
+ <td>{{ ls.match_codes.U1|intcomma }}</td>
+ <td>{{ ls.match_codes.U2|intcomma }}</td>
+ <td {% if ls.unique_reads %}property="libns:total_unique_locations" content="{{ls.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ ls.unique_reads|intcomma }}</td>
+ <td>{{ ls.match_codes.R0|intcomma }}</td>
+ <td>{{ ls.match_codes.R1|intcomma }}</td>
+ <td>{{ ls.match_codes.R2|intcomma }}</td>
+ <td>{{ ls.repeat_reads|intcomma }}</td>
</tr>
{% endfor %}
- </tbody>
- </table>
+ {% else %}
+ <tr><td colspan="20">No data</td></tr>
+ {% endif %}
+ </tbody>
+ </table>
<h2>Flowcell Notes</h2>
<table>
<td>Comment</td>
</tr>
</thead>
+ {% if lib.lane_set.all %}
<tbody>
{% for lane in lib.lane_set.all %}
- <tr>
- <td>{{ lane.flowcell.flowcell_id }}</td>
- <td>{{ lane.lane_number }}</td>
+ <tr rel="libns:has_lane"
+ about="{{lib.get_absolute_url}}"
+ resource="{{lane.get_absolute_url}}">
+ <td>
+ <a typeof="libns:IlluminaFlowcell" href="{{lane.flowcell.get_absolute_url}}">
+ <span property="libns:flowcell_id"
+ >{{lane.flowcell.flowcell_id}}</span></a>
+ {% if user.is_staff %}
+ <a href="{{lane.flowcell.get_admin_url}}">
+ <img class="icon_button"
+ src="{% static "admin/img/icon_changelink.gif" %}" alt="Edit"/>
+ </a>
+ {% endif%}
+ </td>
+ <td typeof="libns:IlluminaLane" about="{{lane.get_absolute_url}}">
+ <span rel="libns:flowcell" resource="{{lane.flowcell.get_absolute_url}}"></span>
+ <a href="{{lane.get_absolute_url}}">
+ <span property="libns:lane_number"
+ >{{ lane.lane_number }}</span>
+ </a></td>
<td>{{ lane.comment }}</td>
</tr>
{% endfor %}
</tbody>
+ {% endif %}
</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 %}
+ {% for eland_lane in lane_summary_list %}
+ {% if eland_lane.summarized_reads %}
+ <h3>{{eland_lane.cycle_width}} {{ eland_lane.flowcell_id }} lane {{ eland_lane.lane_id }}
+ {% if eland_lane.end %} end {{ eland_lane.end }}{% endif %}
</h3>
- <ul>
- {% for name, counts in lane.summarized_reads.items %}
- <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
+ <ul about="{{eland_lane.lane.get_absolute_url}}">
+ {% for name, counts in eland_lane.summarized_reads.items %}
+ <li rel="libns:has_mappings">
+ <b property="libns:mapped_to">{{ name }}</b>:
+ <span property="libns:reads" content="{{counts}}" datatype="xsd:integer">{{ counts|intcomma }}</span></li>
{% endfor %}
</ul>
{% endif %}
{% endfor %}
{% endblock %}
-</div>
+ </div>
{% endblock %}
projects / htsworkflow.git / blobdiff