{% 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 %}
-
{% endblock %}
{% block content %}
-<div id="library_detail">
- <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>:
- <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 property="libns:affliation" content="{{individual.name}}">
- {{ individual.name }} ( {{ individual.contact }} )
- </li>
- {% endfor %}
- </ul>
- <div class="htswdetail">
+ {% 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="{{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.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_id}}/{% if lane.end %}#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 {% 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>
- <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 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>
+ <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 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 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