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   div.library_identity {
  64     float: left; margin: 5px; }
  65   div.library_sample_detail { float: left; margin: 5px; }
  66   div.library_library_detail { float: left; margin: 5px; }
  67   div.library_statistics { clear: both; border: 1px; }
  68  /* ]]> */
  69 </style>
  70 {% endblock %}
  71
  72 {% block content %}
  73 <div id="librarydetail">
  74   <div class="library_identity">
  75     <h2>Library Name</h2>
  76     <b>Library ID</b>: {{ lib.id }}<br/>
  77     <b>Name</b>:
  78       <span property="libns:name">{{ lib.library_name }}</span>
  79     <br/>
  80     <b>Affiliations</b>:
  81     <ul>
  82       {% for individual in lib.affiliations.all %}
  83         <li property="libns:affliation" content="{{individual.name}}">
  84           {{ individual.name }} ( {{ individual.contact }} )
  85         </li>
  86       {% endfor %}
  87     </ul>
  88   </div>
  89   <div class="library_sample_detail">
  90     <h2>Sample Details</h2>
  91     <b>Species</b>:
  92       <span property="libns:species">{{ lib.library_species.scientific_name }}</span>
  93     <br/>
  94     <b>Experiment Type</b>:
  95        <span property="libns:experiment_type">{{ lib.experiment_type }}</span>
  96     <br/>
  97     {% if lib.antibody %}
  98     <b>Antibody</b>:
  99        <span property="libns:antibody">{{ lib.antibody.antibodies }}</span>
 100        {% if lib.antibody.antibodies.nuckname %}
 101        (<span property="libns:antibody_term">{{ lib.antibody.nickname }}</span>)
 102        {% endif %}
 103     <br/>
 104     {% endif %}
 105     {% if lib.cell_line %}
 106     <b>Background or Cell Line</b>:
 107        <span property="libns:cell_line">{{ lib.cell_line }}</span>
 108     <br/>
 109     {% endif %}
 110     {% if lib.condition %}
 111     <b>Condition</b>:
 112        <span property="libns:condition">{{ lib.condition.condition_name }}</span>
 113        {% if lib.condition.nickname %}
 114        (<span property="libns:condition_term">{{ lib.condition.nickname }}</span>)
 115        {% endif %}
 116     <br/>
 117     {% endif %}
 118     {% if lib.replicate %}
 119     <b>Replicate</b>:
 120        <span property="libns:replicate">{{ lib.replicate }}</span>
 121     <br/>
 122     {% endif %}
 123   </div>
 124   <div class="library_library_detail">
 125     <h2>Library Details</h2>
 126     <b>Library Type</b>:
 127        <span property="libns:library_type">{{ lib.library_type }}</span>
 128     <br/>
 129     <b>Creation Date</b>
 130       <span property="libns:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ lib.creation_date }}</span>
 131     <br/>
 132     <b>Made By</b>:
 133       <span property="libns:made_by">{{ lib.made_by }}</span>
 134     <br/>
 135     {% if lib.gel_cut_size %}
 136     <b>Gel Cut Size</b>:
 137       <span property="libns:gel_cut">{{ lib.gel_cut_size }}</span>
 138     <br/>
 139     {% endif %}
 140     {% if lib.insert_size %}
 141     <b>Insert Size</b>:
 142       <span property="libns:insert_size">{{ lib.insert_size }}</span>
 143     <br/>
 144     {% endif %}
 145     {% if lib.undiluted_concentration %}
 146     <b>Concentration</b>:
 147       <span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
 148     <br/>
 149     {% endif %}
 150     {% if lib.stopping_point_name %}
 151     <b>Protocol Stopping Point</b>
 152       <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
 153     <br/>
 154     {% endif %}
 155   </div>
 156   <div class="library_statistics">
 157   <h2>Raw Result Files</h2>
 158   <table>
 159   <thead>
 160     <tr>
 161       <td>Run Start Date</td>
 162       <td>Cycle</td>
 163       <td>Flowcell</td>
 164       <td>Lane</td>
 165       <td>Summary</td>
 166       <td>Eland</td>
 167       <td>Bed</td>
 168       <td>Archived</td>
 169     </tr>
 170   </thead>
 171   <tbody>
 172     {% for result in eland_results %}
 173     <tr about="{{result.flowcell.get_absolute_url}}">
 174       <td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ result.run_date|date}}</td>
 175       <td>{{ result.cycle }}</td>
 176       <td><a href="{{result.flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{ result.flowcell_id }}</span></a></td>
 177       <td><a href="{{result.lane.get_absolute_url}}" rel="libns:has_lane"><span property="libns:lane_number" datatype="xsd:decimal">{{ result.lane.lane_number }}</span></a></td>
 178       <td><a href="{{ result.summary_url }}">Summary</a></td>
 179       <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
 180       <td>
 181       {% if result.bed_url %}
 182         <a href="{{ result.bed_url }}">Bed</a>
 183       {% endif %}
 184       </td>
 185       <td>
 186         {% if result.storage_ids %}
 187           {{ result.storage_ids|safe }}
 188         {% endif %}
 189       </td>
 190     </tr>
 191     {% endfor %}
 192   </tbody>
 193   </table>
 194
 195   <h2>Lane Summary Statistics</h2>
 196   {% block summary_stats %}
 197   <table>
 198     <thead>
 199       <tr>
 200         <td colspan="7"></td>
 201         <td colspan="2">No Match</td>
 202         <td colspan="2">QC Failed</td>
 203         <td colspan="4">Unique</td>
 204         <td colspan="4">Repeat</td>
 205       </tr>
 206       <tr>
 207       <td>Cycles</td>
 208       <td>Flowcell</td>
 209       <td>Lane</td>
 210       <td>End</td>
 211       <td>Cluster / Tile</td>
 212       <td>pM</td>
 213       <td>Raw Reads</td>
 214       <td>total</td>
 215       <td>%</td>
 216       <td>total</td>
 217       <td>%</td>
 218       <td>0 mismatch</td>
 219       <td>1 mismatch</td>
 220       <td>2 mismatch</td>
 221       <td>Total</td>
 222       <td>0 mismatch</td>
 223       <td>1 mismatch</td>
 224       <td>2 mismatch</td>
 225       <td>Total</td>
 226       </tr>
 227     </thead>
 228     <tbody>
 229
 230       {% for lane in lane_summary_list %}
 231       <tr about="/flowcell/{{lane.flowcell_id}}/{{lane.lane_id}}/{% if lane.end %}#end{{ lane.end }}{% endif %}">
 232         <td>{{ lane.cycle_width }}</td>
 233         <td>{{ lane.flowcell_id }}</td>
 234         <td>{{ lane.lane_id }}</td>
 235         <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
 236         <td>{{ lane.clusters.0|intcomma }}</td>
 237         <td>{{ lane.successful_pm }}</td>
 238         <td>{{ lane.reads|intcomma }}</td>
 239         <td>{{ lane.no_match|intcomma }}</td>
 240         <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
 241         <td>{{ lane.qc_failed|intcomma }}</td>
 242         <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
 243         <td>{{ lane.match_codes.U0|intcomma }}</td>
 244         <td>{{ lane.match_codes.U1|intcomma }}</td>
 245         <td>{{ lane.match_codes.U2|intcomma }}</td>
 246         <td {% if lane.unique_reads %}property="libns:total_unique_locations" content="{{lane.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ lane.unique_reads|intcomma }}</td>
 247         <td>{{ lane.match_codes.R0|intcomma }}</td>
 248         <td>{{ lane.match_codes.R1|intcomma }}</td>
 249         <td>{{ lane.match_codes.R2|intcomma }}</td>
 250         <td>{{ lane.repeat_reads|intcomma }}</td>
 251       </tr>
 252       {% endfor %}
 253     </tbody>
 254   </table>
 255
 256   <h2>Flowcell Notes</h2>
 257   <table>
 258     <thead>
 259       <tr>
 260         <td>Flowcell ID</td>
 261         <td>Lane</td>
 262         <td>Comment</td>
 263       </tr>
 264     </thead>
 265     <tbody>
 266       {% for lane in lib.lane_set.all %}
 267       <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}">
 268         <td><a href="{{lane.flowcell.get_absolute_url}}" rel="libns:flowcell">
 269             <span property="libns:flowcell_id">{{ lane.flowcell.flowcell_id }}</span></a></td>
 270         <td><a href="{{lane.get_absolute_url}}">
 271             <span property="libns:lane_number"  datatype="xsd:decimal"
 272                >{{ lane.lane_number }}</span></a></td>
 273         <td>{{ lane.comment }}</td>
 274       </tr>
 275           {% endfor %}
 276     </tbody>
 277   </table>
 278   {% endblock %}
 279   </div>
 280 </div>
 281 {% endblock %}