1 {% extends "base_site.html" %}
2 {% load adminmedia humanize i18n %}
5 <link type="text/css" rel="stylesheet" href="/static/css/app.css" />
6 <script type="text/javascript" src="/static/js/jquery.min.js"></script>
8 {% block additional_javascript %}
11 <style type="text/css">
17 div#librarydetail table, div#librarydetail td {
20 div#librarydetail table {
21 border-width: 0 0 1px 1px;
23 border-collapse: collapse;
25 div#librarydetail td {
28 border-width: 1px 1px 0 0;
30 div#librarydetail thead {
33 div#librarydetail tbody {
42 div#librarydetail h3 {
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; }
73 <div id="librarydetail">
74 <div class="library_identity">
76 <b>Library ID</b>: {{ lib.id }}<br/>
78 <span property="libns:name">{{ lib.library_name }}</span>
82 {% for individual in lib.affiliations.all %}
83 <li property="libns:affiliation" content="{{individual.name}}">
84 {{ individual.name }} ( {{ individual.contact }} )
89 <div class="library_sample_detail">
90 <h2>Sample Details</h2>
92 <span property="libns:species">{{ lib.library_species.scientific_name }}</span>
94 <b>Experiment Type</b>:
95 <span property="libns:experiment_type">{{ lib.experiment_type }}</span>
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>)
105 {% if lib.cell_line %}
106 <b>Background or Cell Line</b>:
107 <span property="libns:cell_line">{{ lib.cell_line }}</span>
110 {% if lib.condition %}
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>)
118 {% if lib.replicate %}
120 <span property="libns:replicate">{{ lib.replicate }}</span>
124 <div class="library_library_detail">
125 <h2>Library Details</h2>
127 <span property="libns:library_type">{{ lib.library_type }}</span>
130 <span property="libns:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ lib.creation_date }}</span>
133 <span property="libns:made_by">{{ lib.made_by }}</span>
135 {% if lib.gel_cut_size %}
137 <span property="libns:gel_cut">{{ lib.gel_cut_size }}</span>
140 {% if lib.insert_size %}
142 <span property="libns:insert_size">{{ lib.insert_size }}</span>
145 {% if lib.undiluted_concentration %}
146 <b>Concentration</b>:
147 <span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
150 {% if lib.stopping_point_name %}
151 <b>Protocol Stopping Point</b>
152 <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
156 <div class="library_statistics">
157 <h2>Raw Result Files</h2>
161 <td>Run Start Date</td>
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>
181 {% if result.bed_url %}
182 <a href="{{ result.bed_url }}">Bed</a>
186 {% if result.storage_ids %}
187 {{ result.storage_ids|safe }}
195 <h2>Lane Summary Statistics</h2>
196 {% block summary_stats %}
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>
211 <td>Cluster / Tile</td>
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>
256 <h2>Flowcell Notes</h2>
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>