{% extends "base_site.html" %}
{% load adminmedia humanize i18n %}
{% block extrahead %}
    <!-- App Stuff -->
    <link type="text/css" rel="stylesheet" href="/static/css/app.css" />
    <script type="text/javascript" src="/static/js/jquery.min.js"></script>
    
    {% block additional_javascript %}
    {% endblock %}

<style type="text/css">
  /* <![CDATA[ */
  div#librarydetail {
    margin: 0;
    padding: 0;
  }
  div#librarydetail table, div#librarydetail td {
    border-style: solid;
  }
  div#librarydetail table {
    border-width: 0 0 1px 1px;
    border-spacing: 0;
    border-collapse: collapse;
  }
  div#librarydetail td {
    margin: 0;
    padding: 3px;
    border-width: 1px 1px 0 0;
  }
  div#librarydetail thead {
    text-align: center;
    }
  div#librarydetail tbody {
    text-align: right;
  }
  div#librarydetail h1,
  div#librarydetail h2
  {
    font-size: 150%;
  }

  div#librarydetail h3 {
     font-size: 125%;
     margin: 0;
  }

  div#librarydetail h4,
  div#librarydetail h5,
  div#librarydetail ul,
  div#librarydetail ol,
  div#librarydetail li
  {
    list-style: none;
    margin: 0;   
  }

  div#librarydetail ul,
  div#librarydetail ol
  {
    margin-bottom: .5em;
  }
 /* ]]> */
</style>
{% endblock %}

{% block content %}
<div id="librarydetail">
  <h2>About this library</h2>
  <b>Library ID</b>: {{ lib.id }}<br/>
  <b>Name</b>: 
    <span property="libns:name">{{ lib.library_name }}</span>
  <br/>
  <b>Species</b>: 
    <span property="libns:species">{{ lib.library_species.scientific_name }}</span>
  <br/>
  <b>Concentration</b>: 
    <span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
  <br/>
  <b>Gel Cut Size</b>: 
    <span property="libns:gel_cut">{{ lib.gel_cut_size }}</span>
  <br/>
  <b>Insert Size</b>: 
    <span property="libns:insert_size">{{ lib.insert_size }}</span>
  <br/>
  <b>Background or Cell Line</b>:
     <span property="libns:cell_line">{{ lib.cell_line }}</span>
  <br/>
  <b>Replicate</b>: 
     <span property="libns:replicate">{{ lib.replicate }}</span>
  <br/>
  <b>Library Type</b>:
     <span property="libns:library_type">{{ lib.library_type }}</span>
  <br/>
  <b>Experiment Type</b>:
     <span property="libns:experiment_type">{{ lib.experiment_type }}</span>
  <br/>
  <b>Made By</b>: 
    <span property="libns:made_by">{{ lib.made_by }}</span>
  <br/>
  <b>Creation Date</b>
    <span property="libns:creation_date">{{ lib.creation_date }}</span>
  <br/> 
  <b>Protocol Stopping Point</b>
    <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
  <br/> 
  <b>Affiliations</b>:
  <ul>
    {% for individual in lib.affiliations.all %}
      <li property="libns:affliation" content="{{individual.name}}">
        {{ individual.name }} ( {{ individual.contact }} )
      </li>
    {% endfor %}
  </ul>
  
  <h2>Raw Result Files</h2>
  <table>
  <thead>
    <tr>
      <td>Run Start Date</td>
      <td>Cycle</td>
      <td>Flowcell</td>
      <td>Lane</td>
      <td>Summary</td>
      <td>Eland</td>
      <td>Bed</td>
      <td>Archived</td>
    </tr>
  </thead>
  <tbody>
    {% for result in eland_results %}
    <tr about="/flowcell/{{result.flowcell_id}}/lane/{{result.lane}}">
      <td property="libns:run_date" contents="{{result.run_date}}" datatype="xmls:datetime">{{ result.run_date|date}}</td>
      <td>{{ result.cycle }}</td>
      <td property="libns:flowcell_id">{{ result.flowcell_id }}</td>
      <td property="libns:lane">{{ result.lane }}</td>
      <td><a href="{{ result.summary_url }}">Summary</a></td>
      <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
      <td>
      {% if result.bed_url %}
        <a href="{{ result.bed_url }}">Bed</a>
      {% endif %}
      </td>
      <td>
        {% if result.storage_ids %}
          {{ result.storage_ids|safe }}
        {% endif %}
      </td>
    </tr>
    {% endfor %}
  </tbody>
  </table>
  
  <h2>Lane Summary Statistics</h2>
  {% block summary_stats %}
  <table>
    <thead>
      <tr>
        <td colspan="7"></td>
        <td colspan="2">No Match</td>
        <td colspan="2">QC Failed</td>
        <td colspan="4">Unique</td>
        <td colspan="4">Repeat</td>
      </tr>
      <tr>
      <td>Cycles</td>
      <td>Flowcell</td>
      <td>Lane</td>
      <td>End</td>
      <td>Cluster / Tile</td>
      <td>pM</td>
      <td>Raw Reads</td>
      <td>total</td>
      <td>%</td>
      <td>total</td>
      <td>%</td>
      <td>0 mismatch</td>
      <td>1 mismatch</td>
      <td>2 mismatch</td>
      <td>Total</td>
      <td>0 mismatch</td>
      <td>1 mismatch</td>
      <td>2 mismatch</td>
      <td>Total</td>
      </tr>
    </thead>
    <tbody>
  
      {% for lane in lane_summary_list %}
      <tr about="/flowcell/{{lane.flowcell_id}}/lane/{{lane.lane_id}}/end/{% if lane.end %}{{ lane.end }}{% endif %}">
        <td>{{ lane.cycle_width }}</td>
        <td>{{ lane.flowcell_id }}</td>
        <td>{{ lane.lane_id }}</td>
        <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
        <td>{{ lane.clusters.0|intcomma }}</td>
        <td>{{ lane.successful_pm }}</td>
        <td>{{ lane.reads|intcomma }}</td>
        <td>{{ lane.no_match|intcomma }}</td>
        <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
        <td>{{ lane.qc_failed|intcomma }}</td>
        <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
        <td>{{ lane.match_codes.U0|intcomma }}</td>
        <td>{{ lane.match_codes.U1|intcomma }}</td>
        <td>{{ lane.match_codes.U2|intcomma }}</td>
        <td property="libns:sequence_unique_location" contents="{{lane.unique_reads}}" datatype="xmls:decimal">{{ lane.unique_reads|intcomma }}</td>
        <td>{{ lane.match_codes.R0|intcomma }}</td>
        <td>{{ lane.match_codes.R1|intcomma }}</td>
        <td>{{ lane.match_codes.R2|intcomma }}</td>
        <td>{{ lane.repeat_reads|intcomma }}</td>
      </tr>
      {% endfor %}
    </tbody>
  </table>

  <h2>Flowcell Notes</h2>
  <table>
    <thead>
      <tr>
    	<td>Flowcell ID</td>
    	<td>Lane</td>
    	<td>Comment</td>
      </tr>
    </thead>
    <tbody>
      {% for lane in lib.lane_set.all %}
      <tr>
        <td>{{ lane.flowcell.flowcell_id }}</td>
        <td>{{ lane.lane_number }}</td>
        <td>{{ lane.comment }}</td>
      </tr>
	  {% endfor %}
    </tbody>
  </table>
  <br/>
  <hr/>
  <h2>Count of multi-reads</h2>
  {% for lane in lane_summary_list %}
    {% if lane.summarized_reads %}
    <h3>
      {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }} 
      {% if lane.end %} end {{ lane.end }}{% endif %}
    </h3>
    <ul>
      {% for name, counts in lane.summarized_reads.items %}
      <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
      {% endfor %}
    </ul>
    {% endif %}
  {% endfor %}
  {% endblock %}
</div>
{% endblock %}