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.gel_cut_size }}<br/>
  58   <b>Insert Size</b>: {{ lib.insert_size }}<br/>
  59   <b>Made By</b>: {{ lib.made_by }} <br/>
  60   <b>Affiliations</b>:
  61   <ul>
  62     {% for individual in lib.affiliations.all %}
  63       <li>{{ individual.name }} ( {{ individual.contact }} )</li>
  64     {% endfor %}
  65   </ul>
  66
  67   <h2>Raw Result Files</h2>
  68   <table>
  69   <thead>
  70     <tr>
  71       <td>Run Start Date</td>
  72       <td>Cycle</td>
  73       <td>Flowcell</td>
  74       <td>Lane</td>
  75       <td>Summary</td>
  76       <td>Eland</td>
  77       <td>Bed</td>
  78       <td>Archived</td>
  79     </tr>
  80   {% for result in eland_results %}
  81   <tr>
  82     <td>{{ result.run_date|date }}</td>
  83     <td>{{ result.cycle }}</td>
  84     <td>{{ result.flowcell_id }}</td>
  85     <td>{{ result.lane }}</td>
  86     <td><a href="{{ result.summary_url }}">Summary</a></td>
  87     <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
  88     <td>
  89     {% if result.bed_url %}
  90       <a href="{{ result.bed_url }}">Bed</a>
  91     {% endif %}
  92     </td>
  93     <td>
  94       {% if result.storage_ids %}
  95         {{ result.storage_ids|safe }}
  96       {% endif %}
  97     </td>
  98   </tr>
  99   {% endfor %}
 100   </table>
 101
 102   <h2>Lane Summary Statistics</h2>
 103   {% block summary_stats %}
 104   <table>
 105     <thead>
 106       <tr>
 107         <td colspan="7"></td>
 108         <td colspan="2">No Match</td>
 109         <td colspan="2">QC Failed</td>
 110         <td colspan="4">Unique</td>
 111         <td colspan="4">Repeat</td>
 112       </tr>
 113       <tr>
 114       <td>Cycles</td>
 115       <td>Flowcell</td>
 116       <td>Lane</td>
 117       <td>End</td>
 118       <td>Cluster / Tile</td>
 119       <td>pM</td>
 120       <td>Raw Reads</td>
 121       <td>total</td>
 122       <td>%</td>
 123       <td>total</td>
 124       <td>%</td>
 125       <td>0 mismatch</td>
 126       <td>1 mismatch</td>
 127       <td>2 mismatch</td>
 128       <td>Total</td>
 129       <td>0 mismatch</td>
 130       <td>1 mismatch</td>
 131       <td>2 mismatch</td>
 132       <td>Total</td>
 133       </tr>
 134     </thead>
 135     <tbody>
 136
 137       {% for lane in lane_summary_list %}
 138       <tr>
 139         <td>{{ lane.cycle_width }}</td>
 140         <td>{{ lane.flowcell_id }}</td>
 141         <td>{{ lane.lane_id }}</td>
 142         <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
 143         <td>{{ lane.clusters.0|intcomma }}</td>
 144         <td>{{ lane.successful_pm }}</td>
 145         <td>{{ lane.reads|intcomma }}</td>
 146         <td>{{ lane.no_match|intcomma }}</td>
 147         <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
 148         <td>{{ lane.qc_failed|intcomma }}</td>
 149         <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
 150         <td>{{ lane.match_codes.U0|intcomma }}</td>
 151         <td>{{ lane.match_codes.U1|intcomma }}</td>
 152         <td>{{ lane.match_codes.U2|intcomma }}</td>
 153         <td>{{ lane.unique_reads|intcomma }}</td>
 154         <td>{{ lane.match_codes.R0|intcomma }}</td>
 155         <td>{{ lane.match_codes.R1|intcomma }}</td>
 156         <td>{{ lane.match_codes.R2|intcomma }}</td>
 157         <td>{{ lane.repeat_reads|intcomma }}</td>
 158       </tr>
 159       {% endfor %}
 160     </tbody>
 161   </table>
 162
 163   <h2>Flowcell Notes</h2>
 164   <table>
 165     <thead>
 166       <tr>
 167         <td>Flowcell ID</td>
 168         <td>Lane</td>
 169         <td>Comment</td>
 170     </thead>
 171     <tbody>
 172       {% for lane in lib.lane_set.all %}
 173       <tr>
 174         <td>{{ lane.flowcell.flowcell_id }}</td>
 175         <td>{{ lane.lane_number }}</td>
 176         <td>{{ lane.comment }}</td>
 177         {% endfor %}
 178     </tbody>
 179   </table>
 180   <br/>
 181   <hr/>
 182   <h2>Count of multi-reads</h2>
 183   {% for lane in lane_summary_list %}
 184     {% if lane.summarized_reads %}
 185     <h3>
 186       {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }}
 187       {% if lane.end %} end {{ lane.end }}{% endif %}
 188     </h3>
 189     <ul>
 190       {% for name, counts in lane.summarized_reads.items %}
 191       <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
 192       {% endfor %}
 193     </ul>
 194     {% endif %}
 195   {% endfor %}
 196   {% endblock %}
 197 </div>
 198 {% endblock %}