htsworkflow/frontend/templates/samples/library_detail.html

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