htsworkflow/frontend/templates/samples/library_detail.html

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