htsworkflow/frontend/templates/samples/library_detail.html

   1 {% extends "base_site.html" %}
   2 {% load adminmedia humanize i18n %}
   3 {% block extrahead %}
   4     <!-- App Stuff -->
   5     <link type="text/css" rel="stylesheet" href="/static/css/app.css" />
   6     <script type="text/javascript" src="/static/js/jquery.min.js"></script>
   7
   8     {% block additional_javascript %}
   9     {% endblock %}
  10 {% endblock %}
  11
  12 {% block content %}
  13   {% include "sample_header.html" %}
  14   <hr/>
  15   <div class="library_statistics">
  16   <h2>Raw Result Files</h2>
  17   <table>
  18   <thead>
  19     <tr>
  20       <td>Run Start Date</td>
  21       <td>Cycle</td>
  22       <td>Flowcell</td>
  23       <td>Lane</td>
  24       <td>Summary</td>
  25       <td>Eland</td>
  26       <td>Bed</td>
  27       <td>Archived</td>
  28     </tr>
  29   </thead>
  30   <tbody>
  31     {% for result in eland_results %}
  32     <tr about="{{result.flowcell.get_absolute_url}}">
  33       <td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ result.run_date|date}}</td>
  34       <td>{{ result.cycle }}</td>
  35       <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="/media/img/admin/icon_changelink.gif" alt="Edit"/></a>{% endif%}</td>
  36       <td>{{ result.lane.lane_number }}</td>
  37       <td><a href="{{ result.summary_url }}">Summary</a></td>
  38       <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
  39       <td>
  40       {% if result.bed_url %}
  41         <a href="{{ result.bed_url }}">Bed</a>
  42       {% endif %}
  43       </td>
  44       <td>
  45         {% if result.storage_ids %}
  46           {{ result.storage_ids|safe }}
  47         {% endif %}
  48       </td>
  49     </tr>
  50     {% endfor %}
  51   </tbody>
  52   </table>
  53
  54   <h2>Lane Summary Statistics</h2>
  55   {% block summary_stats %}
  56   <table>
  57     <thead>
  58       <tr>
  59         <td colspan="7"></td>
  60         <td colspan="2">No Match</td>
  61         <td colspan="2">QC Failed</td>
  62         <td colspan="4">Unique</td>
  63         <td colspan="4">Repeat</td>
  64       </tr>
  65       <tr>
  66       <td>Cycles</td>
  67       <td>Flowcell</td>
  68       <td>Lane</td>
  69       <td>End</td>
  70       <td>Cluster / Tile</td>
  71       <td>pM</td>
  72       <td>Raw Reads</td>
  73       <td>total</td>
  74       <td>%</td>
  75       <td>total</td>
  76       <td>%</td>
  77       <td>0 mismatch</td>
  78       <td>1 mismatch</td>
  79       <td>2 mismatch</td>
  80       <td>Total</td>
  81       <td>0 mismatch</td>
  82       <td>1 mismatch</td>
  83       <td>2 mismatch</td>
  84       <td>Total</td>
  85       </tr>
  86     </thead>
  87     <tbody>
  88
  89       {# ls short for lane summary #}
  90       {% for ls in lane_summary_list %}
  91       <tr about="{{ls.lane.get_absolute_url}}">
  92         <td>{{ ls.cycle_width }}</td>
  93         <td><a href="{{ls.flowcell.get_absolute_url}}">{{ ls.flowcell_id }}</a>
  94         </td>
  95         <td><a href="{{ls.lane.get_absolute_url}}">{{ ls.lane_id }}</a></td>
  96         <td>{% if ls.end %}{{ ls.end }}{% endif %}</td>
  97         <td>{{ ls.clusters.0|intcomma }}</td>
  98         <td>{{ ls.successful_pm }}</td>
  99         <td>{{ ls.reads|intcomma }}</td>
 100         <td>{{ ls.no_match|intcomma }}</td>
 101         <td>{{ ls.no_match_percent|stringformat:".2f" }}</td>
 102         <td>{{ ls.qc_failed|intcomma }}</td>
 103         <td>{{ ls.qc_failed_percent|stringformat:".2f" }}</td>
 104         <td>{{ ls.match_codes.U0|intcomma }}</td>
 105         <td>{{ ls.match_codes.U1|intcomma }}</td>
 106         <td>{{ ls.match_codes.U2|intcomma }}</td>
 107         <td {% if ls.unique_reads %}property="libns:total_unique_locations" content="{{ls.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ ls.unique_reads|intcomma }}</td>
 108         <td>{{ ls.match_codes.R0|intcomma }}</td>
 109         <td>{{ ls.match_codes.R1|intcomma }}</td>
 110         <td>{{ ls.match_codes.R2|intcomma }}</td>
 111         <td>{{ ls.repeat_reads|intcomma }}</td>
 112       </tr>
 113       {% endfor %}
 114     </tbody>
 115   </table>
 116
 117   <h2>Flowcell Notes</h2>
 118   <table>
 119     <thead>
 120       <tr>
 121         <td>Flowcell ID</td>
 122         <td>Lane</td>
 123         <td>Comment</td>
 124       </tr>
 125     </thead>
 126     <tbody>
 127       {% for lane in lib.lane_set.all %}
 128       <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}">
 129         <td>
 130           <a typeof="libns:IlluminaFlowcell" href="{{lane.flowcell.get_absolute_url}}">
 131             <span property="libns:flowcell_id"
 132                   >{{lane.flowcell.flowcell_id}}</span></a>
 133           {% if user.is_staff %}
 134             <a href="{{lane.flowcell.get_admin_url}}">
 135                <img class="icon_button"
 136                     src="/media/img/admin/icon_changelink.gif" alt="Edit"/>
 137             </a>
 138           {% endif%}
 139         </td>
 140         <td typeof="libns:IlluminaLane" about="{{lane.get_absolute_url}}">
 141           <span rel="libns:flowcell" resource="{{lane.flowcell.get_absolute_url}}"></span>
 142           <a href="{{lane.get_absolute_url}}">
 143             <span property="libns:lane_number"  datatype="xsd:decimal"
 144                >{{ lane.lane_number }}</span>
 145             </a></td>
 146         <td>{{ lane.comment }}</td>
 147       </tr>
 148           {% endfor %}
 149     </tbody>
 150   </table>
 151   <br/>
 152   <hr/>
 153   <h2>Count of multi-reads</h2>
 154   {% for eland_lane in lane_summary_list %}
 155     {% if eland_lane.summarized_reads %}
 156     <h3>{{eland_lane.cycle_width}} {{ eland_lane.flowcell_id }} lane {{ eland_lane.lane_id }}
 157       {% if eland_lane.end %} end {{ eland_lane.end }}{% endif %}
 158     </h3>
 159     <ul about="{{eland_lane.lane.get_absolute_url}}">
 160       {% for name, counts in eland_lane.summarized_reads.items %}
 161       <li rel="libns:has_mappings">
 162          <b property="libns:mapped_to">{{ name }}</b>:
 163          <span property="libns:reads" content="{{counts}}" datatype="xsd:integer">{{ counts|intcomma }}</span></li>
 164       {% endfor %}
 165     </ul>
 166     {% endif %}
 167   {% endfor %}
 168   {% endblock %}
 169   </div>
 170 </div>
 171 {% endblock %}