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
  11 <style type="text/css">
  12   /* <![CDATA[ */
  13   div#librarydetail {
  14     margin: 0;
  15     padding: 0;
  16   }
  17   div#librarydetail table, div#librarydetail td {
  18     border-style: solid;
  19   }
  20   div#librarydetail table {
  21     border-width: 0 0 1px 1px;
  22     border-spacing: 0;
  23     border-collapse: collapse;
  24   }
  25   div#librarydetail td {
  26     margin: 0;
  27     padding: 3px;
  28     border-width: 1px 1px 0 0;
  29   }
  30   div#librarydetail thead {
  31     text-align: center;
  32     }
  33   div#librarydetail tbody {
  34     text-align: right;
  35   }
  36   div#librarydetail h1,
  37   div#librarydetail h2
  38   {
  39     font-size: 150%;
  40   }
  41
  42   div#librarydetail h3 {
  43      font-size: 125%;
  44      margin: 0;
  45   }
  46
  47   div#librarydetail h4,
  48   div#librarydetail h5,
  49   div#librarydetail ul,
  50   div#librarydetail ol,
  51   div#librarydetail li
  52   {
  53     list-style: none;
  54     margin: 0;
  55   }
  56
  57   div#librarydetail ul,
  58   div#librarydetail ol
  59   {
  60     margin-bottom: .5em;
  61   }
  62  /* ]]> */
  63 </style>
  64 {% endblock %}
  65
  66 {% block content %}
  67 <div id="librarydetail">
  68   <h2>About this library</h2>
  69   <b>Library ID</b>: {{ lib.id }}<br/>
  70   <b>Name</b>:
  71     <span property="libns:name">{{ lib.library_name }}</span>
  72   <br/>
  73   <b>Species</b>:
  74     <span property="libns:species">{{ lib.library_species.scientific_name }}</span>
  75   <br/>
  76   <b>Concentration</b>:
  77     <span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
  78   <br/>
  79   <b>Gel Cut Size</b>:
  80     <span property="libns:gel_cut">{{ lib.gel_cut_size }}</span>
  81   <br/>
  82   <b>Insert Size</b>:
  83     <span property="libns:insert_size">{{ lib.insert_size }}</span>
  84   <br/>
  85   <b>Background or Cell Line</b>:
  86      <span property="libns:cell_line">{{ lib.cell_line }}</span>
  87   <br/>
  88   <b>Replicate</b>:
  89      <span property="libns:replicate">{{ lib.replicate }}</span>
  90   <br/>
  91   <b>Library Type</b>:
  92      <span property="libns:library_type">{{ lib.library_type }}</span>
  93   <br/>
  94   <b>Experiment Type</b>:
  95      <span property="libns:experiment_type">{{ lib.experiment_type }}</span>
  96   <br/>
  97   <b>Made By</b>:
  98     <span property="libns:made_by">{{ lib.made_by }}</span>
  99   <br/>
 100   <b>Creation Date</b>
 101     <span property="libns:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ lib.creation_date }}</span>
 102   <br/>
 103   <b>Protocol Stopping Point</b>
 104     <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
 105   <br/>
 106   <b>Affiliations</b>:
 107   <ul>
 108     {% for individual in lib.affiliations.all %}
 109       <li property="libns:affliation" content="{{individual.name}}">
 110         {{ individual.name }} ( {{ individual.contact }} )
 111       </li>
 112     {% endfor %}
 113   </ul>
 114
 115   <h2>Raw Result Files</h2>
 116   <table>
 117   <thead>
 118     <tr>
 119       <td>Run Start Date</td>
 120       <td>Cycle</td>
 121       <td>Flowcell</td>
 122       <td>Lane</td>
 123       <td>Summary</td>
 124       <td>Eland</td>
 125       <td>Bed</td>
 126       <td>Archived</td>
 127     </tr>
 128   </thead>
 129   <tbody>
 130     {% for result in eland_results %}
 131     <tr about="/flowcell/{{result.flowcell_id}}/lane/{{result.lane}}">
 132       <td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ result.run_date|date}}</td>
 133       <td>{{ result.cycle }}</td>
 134       <td property="libns:flowcell_id">{{ result.flowcell_id }}</td>
 135       <td property="libns:lane">{{ result.lane }}</td>
 136       <td><a href="{{ result.summary_url }}">Summary</a></td>
 137       <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
 138       <td>
 139       {% if result.bed_url %}
 140         <a href="{{ result.bed_url }}">Bed</a>
 141       {% endif %}
 142       </td>
 143       <td>
 144         {% if result.storage_ids %}
 145           {{ result.storage_ids|safe }}
 146         {% endif %}
 147       </td>
 148     </tr>
 149     {% endfor %}
 150   </tbody>
 151   </table>
 152
 153   <h2>Lane Summary Statistics</h2>
 154   {% block summary_stats %}
 155   <table>
 156     <thead>
 157       <tr>
 158         <td colspan="7"></td>
 159         <td colspan="2">No Match</td>
 160         <td colspan="2">QC Failed</td>
 161         <td colspan="4">Unique</td>
 162         <td colspan="4">Repeat</td>
 163       </tr>
 164       <tr>
 165       <td>Cycles</td>
 166       <td>Flowcell</td>
 167       <td>Lane</td>
 168       <td>End</td>
 169       <td>Cluster / Tile</td>
 170       <td>pM</td>
 171       <td>Raw Reads</td>
 172       <td>total</td>
 173       <td>%</td>
 174       <td>total</td>
 175       <td>%</td>
 176       <td>0 mismatch</td>
 177       <td>1 mismatch</td>
 178       <td>2 mismatch</td>
 179       <td>Total</td>
 180       <td>0 mismatch</td>
 181       <td>1 mismatch</td>
 182       <td>2 mismatch</td>
 183       <td>Total</td>
 184       </tr>
 185     </thead>
 186     <tbody>
 187
 188       {% for lane in lane_summary_list %}
 189       <tr about="/flowcell/{{lane.flowcell_id}}/lane/{{lane.lane_id}}/end/{% if lane.end %}{{ lane.end }}{% endif %}">
 190         <td>{{ lane.cycle_width }}</td>
 191         <td>{{ lane.flowcell_id }}</td>
 192         <td>{{ lane.lane_id }}</td>
 193         <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
 194         <td>{{ lane.clusters.0|intcomma }}</td>
 195         <td>{{ lane.successful_pm }}</td>
 196         <td>{{ lane.reads|intcomma }}</td>
 197         <td>{{ lane.no_match|intcomma }}</td>
 198         <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
 199         <td>{{ lane.qc_failed|intcomma }}</td>
 200         <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
 201         <td>{{ lane.match_codes.U0|intcomma }}</td>
 202         <td>{{ lane.match_codes.U1|intcomma }}</td>
 203         <td>{{ lane.match_codes.U2|intcomma }}</td>
 204         <td {% if lane.unique_reads %}property="libns:total_unique_locations" content="{{lane.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ lane.unique_reads|intcomma }}</td>
 205         <td>{{ lane.match_codes.R0|intcomma }}</td>
 206         <td>{{ lane.match_codes.R1|intcomma }}</td>
 207         <td>{{ lane.match_codes.R2|intcomma }}</td>
 208         <td>{{ lane.repeat_reads|intcomma }}</td>
 209       </tr>
 210       {% endfor %}
 211     </tbody>
 212   </table>
 213
 214   <h2>Flowcell Notes</h2>
 215   <table>
 216     <thead>
 217       <tr>
 218         <td>Flowcell ID</td>
 219         <td>Lane</td>
 220         <td>Comment</td>
 221       </tr>
 222     </thead>
 223     <tbody>
 224       {% for lane in lib.lane_set.all %}
 225       <tr>
 226         <td>{{ lane.flowcell.flowcell_id }}</td>
 227         <td>{{ lane.lane_number }}</td>
 228         <td>{{ lane.comment }}</td>
 229       </tr>
 230           {% endfor %}
 231     </tbody>
 232   </table>
 233   <br/>
 234   <hr/>
 235   <h2>Count of multi-reads</h2>
 236   {% for lane in lane_summary_list %}
 237     {% if lane.summarized_reads %}
 238     <h3>
 239       {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }}
 240       {% if lane.end %} end {{ lane.end }}{% endif %}
 241     </h3>
 242     <ul>
 243       {% for name, counts in lane.summarized_reads.items %}
 244       <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
 245       {% endfor %}
 246     </ul>
 247     {% endif %}
 248   {% endfor %}
 249   {% endblock %}
 250 </div>
 251 {% endblock %}