htsworkflow/frontend/templates/samples/library_detail.html

   1 {% extends "flowcell_libraries_app.html" %}
   2 {% load humanize %}
   3
   4 {% block additional_css %}
   5 <style type="text/css">
   6   /* <![CDATA[ */
   7   div#librarydetail table, div#librarydetail td {
   8     border-style: solid;
   9   }
  10   div#librarydetail table {
  11     border-width: 0 0 1px 1px;
  12     border-spacing: 0;
  13     border-collapse: collapse;
  14   }
  15   div#librarydetail td {
  16     margin: 0;
  17     padding: 4px;
  18     border-width: 1px 1px 0 0;
  19   }
  20   div#librarydetail thead {
  21     text-align: center;
  22     }
  23   div#librarydetail tbody {
  24     text-align: right;
  25   }
  26   div#librarydetail h1,
  27   div#librarydetail h2
  28   {
  29     font-size: 150%;
  30     padding: 0.5em 0 0.5em 0;
  31   }
  32
  33   div#librarydetail h3 {
  34      font-size: 125%;
  35      padding: 0 0 0.25em 2em;
  36   }
  37
  38   div#librarydetail h4,
  39   div#librarydetail h5,
  40   div#librarydetail ul,
  41   div#librarydetail ol,
  42   div#librarydetail li
  43   {
  44     padding-left: 2em;
  45   }
  46  /* ]]> */
  47 </style>
  48 {% endblock %}
  49
  50 {% block content %}
  51 <div id="librarydetail">
  52   <h2>About this library</h2>
  53   <b>Library ID</b>: {{ lib.id }}<br/>
  54   <b>Name</b>: {{ lib.library_name }}<br/>
  55   <b>Species</b>: {{ lib.library_species.scientific_name }}<br/>
  56   <b>Concentration</b>: {{ lib.undiluted_concentration }} ng/µl<br/>
  57   <b>Gel Cut Size</b>: {{ lib.avg_lib_size }}<br/>
  58   <b>Made By</b>: {{ lib.made_by }} <br/>
  59   <b>Affiliations</b>:
  60   <ul>
  61     {% for individual in lib.affiliations.all %}
  62       <li>{{ individual.name }} ( {{ individual.contact }} )</li>
  63     {% endfor %}
  64   </ul>
  65
  66   <h2>Raw Result Files</h2>
  67   <table>
  68   <thead>
  69     <tr>
  70       <td>Run Start Date</td>
  71       <td>Cycle</td>
  72       <td>Flowcell</td>
  73       <td>Lane</td>
  74       <td>Summary</td>
  75       <td>Eland</td>
  76       <td>Bed</td>
  77       <td>Archived</td>
  78     </tr>
  79   {% for result in eland_results %}
  80   <tr>
  81     <td>{{ result.run_date|date }}</td>
  82     <td>{{ result.cycle }}</td>
  83     <td>{{ result.flowcell_id }}</td>
  84     <td>{{ result.lane }}</td>
  85     <td><a href="{{ result.summary_url }}">Summary</a></td>
  86     <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
  87     <td>
  88     {% if result.bed_url %}
  89       <a href="{{ result.bed_url }}">Bed</a>
  90     {% endif %}
  91     </td>
  92     <td>
  93       {% if result.storage_ids %}
  94         {{ result.storage_ids|safe }}
  95       {% endif %}
  96     </td>
  97   </tr>
  98   {% endfor %}
  99   </table>
 100
 101   <h2>Lane Summary Statistics</h2>
 102   {% block summary_stats %}
 103   <table>
 104     <thead>
 105       <tr>
 106         <td colspan="7"></td>
 107         <td colspan="2">No Match</td>
 108         <td colspan="2">QC Failed</td>
 109         <td colspan="4">Unique</td>
 110         <td colspan="4">Repeat</td>
 111       </tr>
 112       <tr>
 113       <td>Cycles</td>
 114       <td>Flowcell</td>
 115       <td>Lane</td>
 116       <td>End</td>
 117       <td>Cluster / Tile</td>
 118       <td>pM</td>
 119       <td>Raw Reads</td>
 120       <td>total</td>
 121       <td>%</td>
 122       <td>total</td>
 123       <td>%</td>
 124       <td>0 mismatch</td>
 125       <td>1 mismatch</td>
 126       <td>2 mismatch</td>
 127       <td>Total</td>
 128       <td>0 mismatch</td>
 129       <td>1 mismatch</td>
 130       <td>2 mismatch</td>
 131       <td>Total</td>
 132       </tr>
 133     </thead>
 134     <tbody>
 135
 136       {% for lane in lane_summary_list %}
 137       <tr>
 138         <td>{{ lane.cycle_width }}</td>
 139         <td>{{ lane.flowcell_id }}</td>
 140         <td>{{ lane.lane_id }}</td>
 141         <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
 142         <td>{{ lane.clusters.0|intcomma }}</td>
 143         <td>{{ lane.successful_pm }}</td>
 144         <td>{{ lane.reads|intcomma }}</td>
 145         <td>{{ lane.no_match|intcomma }}</td>
 146         <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
 147         <td>{{ lane.qc_failed|intcomma }}</td>
 148         <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
 149         <td>{{ lane.match_codes.U0|intcomma }}</td>
 150         <td>{{ lane.match_codes.U1|intcomma }}</td>
 151         <td>{{ lane.match_codes.U2|intcomma }}</td>
 152         <td>{{ lane.unique_reads|intcomma }}</td>
 153         <td>{{ lane.match_codes.R0|intcomma }}</td>
 154         <td>{{ lane.match_codes.R1|intcomma }}</td>
 155         <td>{{ lane.match_codes.R2|intcomma }}</td>
 156         <td>{{ lane.repeat_reads|intcomma }}</td>
 157       </tr>
 158       {% endfor %}
 159     </tbody>
 160   </table>
 161
 162   <h2>Flowcell Notes</h2>
 163   <table>
 164     <thead>
 165       <tr>
 166         <td>Flowcell ID</td>
 167         <td>Lane</td>
 168         <td>Comment</td>
 169     </thead>
 170     <tbody>
 171       {% for lane in lib.lane_set.all %}
 172       <tr>
 173         <td>{{ lane.flowcell.flowcell_id }}</td>
 174         <td>{{ lane.lane_number }}</td>
 175         <td>{{ lane.comment }}</td>
 176         {% endfor %}
 177     </tbody>
 178   </table>
 179   <br/>
 180   <hr/>
 181   <h2>Count of multi-reads</h2>
 182   {% for lane in lane_summary_list %}
 183     {% if lane.summarized_reads %}
 184     <h3>
 185       {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }}
 186       {% if lane.end %} end {{ lane.end }}{% endif %}
 187     </h3>
 188     <ul>
 189       {% for name, counts in lane.summarized_reads.items %}
 190       <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
 191       {% endfor %}
 192     </ul>
 193     {% endif %}
 194   {% endfor %}
 195   {% endblock %}
 196 </div>
 197 {% endblock %}