-- in both human and RDFa formats.
Also I implemented get_absolute_url for flowcells & lanes, which
means "view on site" pops up on the flowcell admin page.
Also with modifying the templates for RDFa, many more elements
on the library, flowcell, and flowcell lane detail pages link to
each other.
I moved the table formatting css out of the library page
and into app.css.
I also switched experiments/views.py from using Context to RequestContext
which provides the default media url to the template.
There were a few changes to samples/views.py to get the more informative
object to the template instead of our on-the-fly created lists.
return u"Paired"
else:
return u"Single"
+
+ @models.permalink
+ def get_absolute_url(self):
+ return ('htsworkflow.frontend.experiments.views.flowcell_detail',
+ [str(self.flowcell_id)])
### -----------------------
class DataRun(models.Model):
cluster_estimate = models.IntegerField(blank=True, null=True)
status = models.IntegerField(choices=LANE_STATUS_CODES, null=True, blank=True)
comment = models.TextField(null=True, blank=True)
+
+ @models.permalink
+ def get_absolute_url(self):
+ return ('htsworkflow.frontend.experiments.views.flowcell_lane_detail',
+ [str(self.flowcell.flowcell_id), str(self.lane_number)])
from django.core.mail import EmailMessage, mail_managers
from django.http import HttpResponse
from django.shortcuts import render_to_response, get_object_or_404
-from django.template import Context
+from django.template import RequestContext
from django.template.loader import get_template
from htsworkflow.frontend.experiments.models import *
for user_email in email_lane.keys():
sending = ""
# build body
- context = Context({u'flowcell': fc,
- u'lanes': email_lane[user_email],
- u'runfolder': 'blank',
- u'finish_low': estimate_low,
- u'finish_high': estimate_high,
- u'now': datetime.now(),
- })
+ context = RequestContext(request,
+ {u'flowcell': fc,
+ u'lanes': email_lane[user_email],
+ u'runfolder': 'blank',
+ u'finish_low': estimate_low,
+ u'finish_high': estimate_high,
+ u'now': datetime.now(),
+ })
# build view
subject = "Flowcell %s" % ( fc.flowcell_id )
emails.append((user_email, subject, body, sending))
- verify_context = Context({
- 'emails': emails,
- 'flowcell': fc,
- 'from': sender,
- 'send': send,
- 'site_managers': settings.MANAGERS,
- 'title': fc.flowcell_id,
- 'warnings': warnings,
+ verify_context = RequestContext(
+ request,
+ { 'emails': emails,
+ 'flowcell': fc,
+ 'from': sender,
+ 'send': send,
+ 'site_managers': settings.MANAGERS,
+ 'title': fc.flowcell_id,
+ 'warnings': warnings,
})
return HttpResponse(email_verify.render(verify_context))
"""
"""
return HttpResponse("I've got nothing.")
+
+
+def flowcell_detail(request, flowcell_id):
+ fc = get_object_or_404(FlowCell, flowcell_id=flowcell_id)
+
+ print unicode(fc.get_absolute_url())
+ for lane in fc.lane_set.all():
+ print unicode(lane.get_absolute_url())
+
+ context = RequestContext(request,
+ {'flowcell': fc})
+
+ return render_to_response('experiments/flowcell_detail.html',
+ context)
+
+def flowcell_lane_detail(request, flowcell_id, lane_number):
+ fc = get_object_or_404(FlowCell, flowcell_id=flowcell_id)
+ lane = get_object_or_404(fc.lane_set, lane_number=lane_number)
+
+ context = RequestContext(request,
+ {'lib': lane.library,
+ 'lane': lane,
+ 'flowcell': fc})
+
+ return render_to_response('experiments/flowcell_lane_detail.html',
+ context)
class Meta:
verbose_name_plural = "species"
ordering = ["scientific_name"]
+
+ @models.permalink
+ def get_absolute_url(self):
+ return ('htsworkflow.frontend.samples.views.species', [str(self.id)])
class Affiliation(models.Model):
name = models.CharField(max_length=256, db_index=True, verbose_name='Name')
@models.permalink
def get_absolute_url(self):
return ('htsworkflow.frontend.samples.views.library_to_flowcells', [str(self.id)])
-
-
-
class HTSUser(User):
urlpatterns = patterns('',
(r"^library/(?P<library_id>\w+)/json", 'htsworkflow.frontend.samples.views.library_json'),
(r"^species/(?P<species_id>\w+)/json", 'htsworkflow.frontend.samples.views.species_json'),
+ (r"^species/(?P<species_id>\w+)", 'htsworkflow.frontend.samples.views.species'),
)
from htsworkflow.frontend.auth import require_api_key
from htsworkflow.frontend.experiments.models import FlowCell, Lane, LANE_STATUS_MAP
from htsworkflow.frontend.samples.changelist import ChangeList
-from htsworkflow.frontend.samples.models import Library, HTSUser
+from htsworkflow.frontend.samples.models import Library, Species, HTSUser
from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
from django.core.exceptions import ObjectDoesNotExist
from django.http import HttpResponse, HttpResponseRedirect, Http404
-from django.shortcuts import render_to_response
+from django.shortcuts import render_to_response, get_object_or_404
from django.template import RequestContext
from django.template.loader import get_template
from django.contrib.auth.decorators import login_required
#for lib in library_items.object_list:
for lib in cl.result_list:
summary = {}
+ summary['library'] = lib
summary['library_id'] = lib.id
summary['library_name'] = lib.library_name
summary['species_name' ] = lib.library_species.scientific_name
else:
return 'unknown'
-def _make_eland_results(flowcell_id, lane, interesting_flowcells):
+def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
fc_id, status = parse_flowcell_id(flowcell_id)
cur_fc = interesting_flowcells.get(fc_id, None)
if cur_fc is None:
return []
flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
+ lane = flowcell.lane_set.get(lane_number=lane_number)
# Loop throw storage devices if a result has been archived
storage_id_list = []
if cur_fc is not None:
result_path = cur_fc[cycle]['eland_results'].get(lane, None)
result_link = make_result_link(fc_id, cycle, lane, result_path)
results.append({'flowcell_id': fc_id,
+ 'flowcell': flowcell,
'run_date': flowcell.run_date,
'cycle': cycle,
'lane': lane,
require_api_key(request)
# what validation should we do on library_id?
- lib = library_dict(library_id)
- if lib is None:
- raise Http404
+ lib = get_object_or_404(Library, library_id=library_id)
lib_json = json.dumps(lib)
return HttpResponse(lib_json, mimetype='application/json')
"""
raise Http404
+def species(request, species_id):
+ species = get_object_or_404(Species, id=species_id)
+
+ context = RequestContext(request,
+ { 'species': species })
+
+ return render_to_response("samples/species_detail.html", context)
+
@login_required
def user_profile(request):
"""
color: white;
background: #880000;
}
+
+div.htswdetail {
+ margin: 0;
+ padding: 0;
+}
+div.htswdetail table, div.htswdetail td {
+ border-style: solid;
+}
+div.htswdetail table {
+ border-width: 0 0 1px 1px;
+ border-spacing: 0;
+ border-collapse: collapse;
+}
+div.htswdetail td {
+ margin: 0;
+ padding: 3px;
+ border-width: 1px 1px 0 0;
+}
+div.htswdetail thead {
+ text-align: center;
+}
+div.htswdetail tbody {
+ text-align: left;
+ }
+div.htswdetail h1,
+div.htswdetail h2
+{
+ font-size: 150%;
+}
+
+div.htswdetail h3 {
+ font-size: 125%;
+ margin: 0;
+}
+
+ div.htswdetail h4,
+ div.htswdetail h5,
+ div.htswdetail ul,
+ div.htswdetail ol,
+ div.htswdetail li
+ {
+ list-style: none;
+ margin: 0;
+ }
+
+ div.htswdetail ul,
+ div.htswdetail ol
+ {
+ margin-bottom: .5em;
+ }
+ /* ]]> */
+</style>
<div id="branding">
{% block branding %}{% endblock %}
</div>
- {% if user.is_authenticated and user.is_staff %}
- <div id="user-tools">{% trans 'Welcome,' %} <strong>{% firstof user.first_name user.username %}</strong>. {% block userlinks %}{% url django-admindocs-docroot as docsroot %}{% if docsroot %}<a href="{{ docsroot }}">{% trans 'Documentation' %}</a> / {% endif %}<a href="/admin/password_change/">{% trans 'Change password' %}</a> / <a href="/admin/logout/">{% trans 'Log out' %}</a>{% endblock %}
- </div>
+ <div id="user-tools">
+ {% if user.is_authenticated %}
+ {% trans 'Welcome,' %} <strong>{% firstof user.first_name user.username %}</strong>. {% block userlinks %}{% url django-admindocs-docroot as docsroot %}{% if docsroot %}<a href="{{ docsroot }}">{% trans 'Documentation' %}</a> / {% endif %}<a href="/admin/password_change/">{% trans 'Change password' %}</a> / <a href="/admin/logout/">{% trans 'Log out' %}</a>{% endblock %}
+ {% else %}
+ <a href="/admin/login/">{% trans 'Log in' %}</a>
{% endif %}
+ </div>
{% block nav-global %}{% endblock %}
</div>
{% endif %}
--- /dev/null
+{% 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 %}
+{% endblock %}
+
+{% block content %}
+<div id="flowcell_detail">
+ <h2>About this Flowcell</h2>
+ <b>Flowcell</b>:
+ <a href="{{flowcell.get_absolute_url}}" property="libns:flowcell_id">{{flowcell.flowcell_id}}</a><br/>
+ <b>Run Date</b>:
+ <span property="libns:date" content="{{flowcell.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ flowcell.run_date }}</span><br/>
+ <b>Type</b>:
+ <span property="libns:flowcell_type">{{flowcell.flowcell_type}}</span><br/>
+ <b>Read Length</b>:
+ <span property="libns:read_length">{{flowcell.read_length}}</span><br/>
+ <b>Control Lane</b>:
+ <span property="libns:control_lane">{{flowcell.control_lane}}</span><br/>
+
+ <b>Notes</b>:
+ <p property="libns:flowcell_notes">{{flowcell.notes}}</p>
+ <div class="htswdetail">
+ <h2>Lanes</h2>
+ <table>
+ <thead>
+ <tr>
+ <td>Lane</td>
+ <td>Library ID</td>
+ <td>Library Name</td>
+ <td>Species</td>
+ <td>Comment</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for lane in flowcell.lane_set.all %}
+ <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}" >
+ <td><a href="{{lane.get_absolute_url}}">
+ <span property="libns:lane_number">{{lane.lane_number}}</span></a></td>
+ <td><a href="{{lane.library.get_absolute_url}}"
+ rel="libns:library"><span property="libns:library_id"
+ >{{lane.library.id}}</span></a></td>
+ <td><a href="{{lane.library.get_absolute_url}}" rel="libns:library"><span property="libns:name">{{lane.library.library_name}}</span></a></td>
+ <td><a href="{{lane.library.library_species.get_absolute_url}}" rel="libns:species">
+ <span property="libns:species_name">{{ lane.library.library_species.scientific_name }}</span></a></td>
+ <td><span property="libns:comment">{{lane.comment}}</span></td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+</div>
+{% endblock %}
--- /dev/null
+{% 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 %}
+{% endblock %}
+
+{% block content %}
+<div id="lane_detail">
+ <h2>About this lane</h2>
+ <div rel="libns:flowcell" resource="{{flowcell.get_absolute_url}}">
+ <b>Flowcell</b>:
+ <a href="{{flowcell.get_absolute_url}}">{{flowcell.flowcell_id}}</a><br/>
+ <b>Run Date</b>:
+ <span property="libns:date" content="{{flowcell.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ flowcell.run_date }}</span><br/>
+ <b>Type</b>:
+ <span property="libns:flowcell_type">{{flowcell.flowcell_type}}</span><br/>
+ </div>
+ <b>Lane</b>:
+ <span property="libns:lane_number" datatype="xsd:decimal">{{lane.lane_number}}</span><br/>
+ <b>pM</b>
+ <span property="libns:pM" datatype="xsd:decimal">{{ lane.pM }}</span><br/>
+ <b>Cluster Estimate</b>
+ <span property="libns:cluster_estimate" datatype="xsd:decimal"
+ content="{{lane.cluster_estimate}}">{{ lane.cluster_estimate|intcomma }}</span><br/>
+ <b>Lane Status</b>:
+ <span property="libns:status">{{ lane.status }}</span><br/>
+ <b>Comment</b>:
+ <span property="libns:comment">{{ lane.comment }}</span><br/>
+
+
+ <div rel="libns:library" resource="{{lib.get_absolute_url}}">
+ <h2>About the library</h2>
+ <b>Library ID</b>:
+ <a href="{{lib.get_absolute_url}}" property="libns:library_id">{{ lib.id }}</a><br/>
+ <b>Name</b>:
+ <span property="libns:name">{{ lib.library_name }}</span>
+ <br/>
+ <b>Species</b>:
+ <a href="{{lib.library_species.get_absolute_url}}" rel="libns:species"><span property="libns:species_name">{{ lib.library_species.scientific_name }}</span></a>
+ <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:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ 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>
+ </div>
+</div>
+{% endblock %}
{% 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">
+<div id="library_detail">
<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>
+ <a href="{{lib.library_species.get_absolute_url}}" rel="libns:species">
+ <span property="libns:species_name">{{ lib.library_species.scientific_name }}</span></a>
<br/>
<b>Concentration</b>:
<span property="libns:concentration">{{ lib.undiluted_concentration }} ng/µl</span>
</li>
{% endfor %}
</ul>
-
+ <div class="htswdetail">
<h2>Raw Result Files</h2>
<table>
<thead>
</thead>
<tbody>
{% for result in eland_results %}
- <tr about="/flowcell/{{result.flowcell_id}}/lane/{{result.lane}}">
+ <tr about="{{result.flowcell.get_absolute_url}}">
<td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd: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.flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{ result.flowcell_id }}</span></a></td>
+ <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>
<td><a href="{{ result.summary_url }}">Summary</a></td>
<td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
<td>
<tbody>
{% for lane in lane_summary_list %}
- <tr about="/flowcell/{{lane.flowcell_id}}/lane/{{lane.lane_id}}/end/{% if lane.end %}{{ lane.end }}{% endif %}">
+ <tr about="/flowcell/{{lane.flowcell_id}}/{{lane.lane_id}}/{% if lane.end %}#end{{ lane.end }}{% endif %}">
<td>{{ lane.cycle_width }}</td>
<td>{{ lane.flowcell_id }}</td>
<td>{{ lane.lane_id }}</td>
</thead>
<tbody>
{% for lane in lib.lane_set.all %}
- <tr>
- <td>{{ lane.flowcell.flowcell_id }}</td>
- <td>{{ lane.lane_number }}</td>
+ <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}">
+ <td><a href="{{lane.flowcell.get_absolute_url}}" rel="libns:flowcell">
+ <span property="libns:flowcell_id">{{ lane.flowcell.flowcell_id }}</span></a></td>
+ <td><a href="{{lane.get_absolute_url}}">
+ <span property="libns:lane_number" datatype="xsd:decimal"
+ >{{ lane.lane_number }}</span></a></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>
</div>
{% endblock %}
</thead>
<tbody >
{% for lib in library_list %}
- <tr about="/library/{{lib.library_id}}">
- <td ><a href="/library/{{ lib.library_id }}">{{ lib.amplified_from }}</a></td>
- <td ><a href="/library/{{ lib.library_id }}" property="libns:library_id">{{ lib.library_id }}</a></td>
- <td ><a href="/library/{{ lib.library_id }}" property="libns:species_name">{{ lib.species_name }}</a></td>
- <td ><a href="/library/{{ lib.library_id }}" property="libns:library_name">{{ lib.library_name }}</a></td>
+ <tr about="{{lib.library.get_absolute_url}}">
+ <td ><a href="{{lib.library.get_absolute_url}}">{{ lib.amplified_from }}</a></td>
+ <td ><a href="{{lib.library.get_absolute_url}}"><span property="libns:library_id">{{ lib.library_id }}</span></a></td>
+ <td ><a href="{{lib.library.library_species.get_absolute_url}}" rel="libns:species"><span property="libns:species_name">{{ lib.species_name }}</span></a></td>
+ <td ><a href="{{ lib.library.get_absolute_url }}"><span property="libns:library_name">{{ lib.library_name }}</span></a></td>
<td bgcolor="#00BFFF">{{ lib.lanes_run.0.0 }}</td>
<td bgcolor="#00BFFF">{{ lib.lanes_run.0.1 }}</td>
<td bgcolor="#00BFFF">{{ lib.lanes_run.0.2 }}</td>
--- /dev/null
+{% 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 %}
+{% endblock %}
+
+{% block content %}
+<div id="genome_detail">
+ <h2>About this Genome</h2>
+ <b>Common Name</b>:
+ <span property="libns:species">{{ species.common_name}}</span><br/>
+ <b>Scientific Name</b>:
+ <span property="libns:species">{{ species.scientific_name}}</span><br/>
+</div>
+{% endblock %}
#(r'^admin/(.*)', admin.site.root),
# Experiments:
(r'^experiments/', include('htsworkflow.frontend.experiments.urls')),
+ # Flowcell:
+ (r'^flowcell/(?P<flowcell_id>\w+)/(?P<lane_number>\w+)/',
+ 'htsworkflow.frontend.experiments.views.flowcell_lane_detail'),
+ (r'^flowcell/(?P<flowcell_id>\w+)/',
+ 'htsworkflow.frontend.experiments.views.flowcell_detail'),
# AnalysTrack:
#(r'^analysis/', include('htsworkflow.frontend.analysis.urls')),
# Inventory urls
projects / htsworkflow.git / commitdiff