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 {% endblock %}
  12
  13 {% block content %}
  14 <div id="library_detail">
  15   <h2>About this library</h2>
  16   <b>Library ID</b>: {{ lib.id }}<br/>
  17   <b>Name</b>:
  18     <span property="libns:name">{{ lib.library_name }}</span>
  19   <br/>
  20   <b>Species</b>:
  21     <a href="{{lib.library_species.get_absolute_url}}" rel="libns:species">
  22     <span property="libns:species_name">{{ lib.library_species.scientific_name }}</span></a>
  23   <br/>
  24   <b>Concentration</b>:
  25     <span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
  26   <br/>
  27   <b>Gel Cut Size</b>:
  28     <span property="libns:gel_cut">{{ lib.gel_cut_size }}</span>
  29   <br/>
  30   <b>Insert Size</b>:
  31     <span property="libns:insert_size">{{ lib.insert_size }}</span>
  32   <br/>
  33   <b>Background or Cell Line</b>:
  34      <span property="libns:cell_line">{{ lib.cell_line }}</span>
  35   <br/>
  36   <b>Replicate</b>:
  37      <span property="libns:replicate">{{ lib.replicate }}</span>
  38   <br/>
  39   <b>Library Type</b>:
  40      <span property="libns:library_type">{{ lib.library_type }}</span>
  41   <br/>
  42   <b>Experiment Type</b>:
  43      <span property="libns:experiment_type">{{ lib.experiment_type }}</span>
  44   <br/>
  45   <b>Made By</b>:
  46     <span property="libns:made_by">{{ lib.made_by }}</span>
  47   <br/>
  48   <b>Creation Date</b>
  49     <span property="libns:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ lib.creation_date }}</span>
  50   <br/>
  51   <b>Protocol Stopping Point</b>
  52     <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
  53   <br/>
  54   <b>Affiliations</b>:
  55   <ul>
  56     {% for individual in lib.affiliations.all %}
  57       <li property="libns:affliation" content="{{individual.name}}">
  58         {{ individual.name }} ( {{ individual.contact }} )
  59       </li>
  60     {% endfor %}
  61   </ul>
  62   <div class="htswdetail">
  63   <h2>Raw Result Files</h2>
  64   <table>
  65   <thead>
  66     <tr>
  67       <td>Run Start Date</td>
  68       <td>Cycle</td>
  69       <td>Flowcell</td>
  70       <td>Lane</td>
  71       <td>Summary</td>
  72       <td>Eland</td>
  73       <td>Bed</td>
  74       <td>Archived</td>
  75     </tr>
  76   </thead>
  77   <tbody>
  78     {% for result in eland_results %}
  79     <tr about="{{result.flowcell.get_absolute_url}}">
  80       <td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ result.run_date|date}}</td>
  81       <td>{{ result.cycle }}</td>
  82       <td><a href="{{result.flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{ result.flowcell_id }}</span></a></td>
  83       <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>
  84       <td><a href="{{ result.summary_url }}">Summary</a></td>
  85       <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
  86       <td>
  87       {% if result.bed_url %}
  88         <a href="{{ result.bed_url }}">Bed</a>
  89       {% endif %}
  90       </td>
  91       <td>
  92         {% if result.storage_ids %}
  93           {{ result.storage_ids|safe }}
  94         {% endif %}
  95       </td>
  96     </tr>
  97     {% endfor %}
  98   </tbody>
  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 about="/flowcell/{{lane.flowcell_id}}/{{lane.lane_id}}/{% if lane.end %}#end{{ lane.end }}{% endif %}">
 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 {% if lane.unique_reads %}property="libns:total_unique_locations" content="{{lane.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ 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       </tr>
 170     </thead>
 171     <tbody>
 172       {% for lane in lib.lane_set.all %}
 173       <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}">
 174         <td><a href="{{lane.flowcell.get_absolute_url}}" rel="libns:flowcell">
 175             <span property="libns:flowcell_id">{{ lane.flowcell.flowcell_id }}</span></a></td>
 176         <td><a href="{{lane.get_absolute_url}}">
 177             <span property="libns:lane_number"  datatype="xsd:decimal"
 178                >{{ lane.lane_number }}</span></a></td>
 179         <td>{{ lane.comment }}</td>
 180       </tr>
 181           {% endfor %}
 182     </tbody>
 183   </table>
 184   {% endblock %}
 185   </div>
 186 </div>
 187 {% endblock %}