--- /dev/null
+from rest_framework import serializers
+
+from .models import (
+ ClusterStation,
+ Lane,
+ FlowCell,
+ Sequencer,
+)
+
+
+class ClusterStationSerializer(serializers.HyperlinkedModelSerializer):
+ class Meta:
+ model = ClusterStation
+
+
+class LaneSerializer(serializers.HyperlinkedModelSerializer):
+ flowcell = serializers.HyperlinkedRelatedField(
+ lookup_field='flowcell_id',
+ view_name='flowcell-detail')
+
+ library = serializers.HyperlinkedRelatedField(
+ view_name='library-detail')
+
+ class Meta:
+ model = Lane
+ fields = (
+ 'url',
+ 'lane_number',
+ 'library',
+ 'pM',
+ 'cluster_estimate',
+ 'status',
+ 'comment')
+
+
+class FlowCellSerializer(serializers.HyperlinkedModelSerializer):
+ url = serializers.HyperlinkedIdentityField(
+ lookup_field='flowcell_id',
+ view_name='flowcell-detail')
+
+ class Meta:
+ model = FlowCell
+ depth = 2
+ fields = (
+ 'url',
+ 'flowcell_id',
+ 'run_date',
+ 'paired_end',
+# 'flowcell_type',
+ 'read_length',
+ 'control_lane',
+ 'cluster_station',
+ 'sequencer',
+ 'notes',
+ 'lane_set',
+ )
+
+class SequencerSerializer(serializers.HyperlinkedModelSerializer):
+ class Meta:
+ model = Sequencer
+ fields = ('url', 'name', 'instrument_name', 'serial_number', 'model')
</tr>
</thead>
<tbody>
- {% for lane in lanes %}
+ {% for lane in lane_set %}
<tr>
<td rel="libns:has_lane">
- <a href="{{lane.get_absolute_url}}" typeof="libns:IlluminaLane">
+ <a href="{{lane.url}}" typeof="libns:IlluminaLane">
<span property="libns:lane_number">{{lane.lane_number}}</span>
</a>
</td>
<div class="flowcell_identity" typeof="libns:IlluminaFlowcell" resource="{{flowcell.get_absolute_url}}">
<h2>About this Flowcell</h2>
<b>Flowcell</b>:
- <a href="{{
flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{flowcell.flowcell_id}}</span></a>{% if user.is_staff %}<a href="{{flowcell.get_admin_url}}"><img class="icon_button" src="{% static "admin/img/icon_changelink.gif" %}" alt="Edit"/></a>{% endif%}
+ <a href="{{
url}}"><span property="libns:flowcell_id">{{flowcell_id}}</span></a>{% if user.is_staff %}<a href="{{flowcell.get_admin_url}}"><img class="icon_button" src="{% static "admin/img/icon_changelink.gif" %}" alt="Edit"/></a>{% endif%}
<br/>
<div rel="libns:sequenced_by">
<div typeof="libns:Sequencer"
- about="{{flowcell.sequencer.get_absolute_url}}">
+ about="{{ sequencer.url }}">
<b>Instrument</b>:
- <span property="libns:sequencer_name">{{ flowcell.sequencer.name }}</span>
- {% if flowcell.sequencer.instrument_name %}
- (<span property="libns:sequencer_instrument">{{ flowcell.sequencer.instrument_name}}</span>)
+ <span property="libns:sequencer_name">{{ sequencer.name }}</span>
+ {% if sequencer.instrument_name %}
+ (<span property="libns:sequencer_instrument">{{ sequencer.instrument_name}}</span>)
{% endif %}
<br/>
<b>Instrument Model</b>:
- <span property="libns:sequencer_model">{{flowcell.sequencer.model}}</span>
+ <span property="libns:sequencer_model">{{sequencer.model}}</span>
<br/>
</div>
</div>
- {% for datarun in flowcell.datarun_set.all %}
+ {% for datarun in datarun_set.all %}
<b>Image Analysis</b>:
<span property="libns:image_software">{{datarun.image_software}}</span>
<span property="libns:image_version">{{datarun.image_version}}</span><br/>
<span property="libns:alignment_version">{{datarun.alignment_version}}</span><br/>
{% endfor %}
<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/>
+ <span property="libns:date" content="{{flowcell.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ run_date }}</span><br/>
<b>Type</b>:
- <span property="libns:flowcell_type">{{flowcell.flowcell_type}}</span><br/>
+ <span property="libns:flowcell_type">{{flowcell_type}}</span><br/>
<b>Read Length</b>:
- <span property="libns:read_length" datatype="xsd:integer">{{flowcell.read_length}}</span><br/>
+ <span property="libns:read_length" datatype="xsd:integer">{{read_length}}</span><br/>
<b>Control Lane</b>:
- <span property="libns:control_lane">{{flowcell.control_lane}}</span><br/>
+ <span property="libns:control_lane">{{control_lane}}</span><br/>
<b>Notes</b>:
- <pre property="libns:flowcell_notes">{{flowcell.notes}}</pre>
+ <pre property="libns:flowcell_notes">{{notes}}</pre>
</div>
from django.conf.urls import patterns
-urlpatterns = patterns('',
- (r'^$', 'experiments.views.index'),
- #(r'^liblist$', 'htsworkflow.frontend.experiments.views.test_Libs'),
- #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.experiments.views.detail'),
- (r'^config/(?P<fc_id>.+)/json$', 'experiments.experiments.flowcell_json'),
- (r'^lanes_for/(?P<username>.+)/json$', 'experiments.experiments.lanes_for_json'),
- (r'^file/(?P<key>.+)/?$', 'experiments.views.read_result_file'),
- (r'^started/(?P<pk>.+)/$', 'experiments.views.startedEmail'),
- (r'^finished/(?P<pk>.+)/$', 'experiments.views.finishedEmail'),
-)
+from rest_framework import routers
+
+from .views import (
+ ClusterStationViewSet,
+ LaneViewSet,
+ FlowCellViewSet,
+ SequencerViewSet,
+ )
+
+#urlpatterns = patterns('',
+# (r'^$', 'experiments.views.index'),
+# #(r'^liblist$', 'htsworkflow.frontend.experiments.views.test_Libs'),
+# #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.experiments.views.detail'),
+# (r'^config/(?P<fc_id>.+)/json$', 'experiments.experiments.flowcell_json'),
+# (r'^lanes_for/(?P<username>.+)/json$', 'experiments.experiments.lanes_for_json'),
+# (r'^file/(?P<key>.+)/?$', 'experiments.views.read_result_file'),
+# (r'^started/(?P<pk>.+)/$', 'experiments.views.startedEmail'),
+# (r'^finished/(?P<pk>.+)/$', 'experiments.views.finishedEmail'),
+#)
+
+router = routers.DefaultRouter()
+router.register(r'cluster_station', ClusterStationViewSet)
+router.register(r'lane', LaneViewSet)
+router.register(r'flowcell', FlowCellViewSet)
+router.register(r'sequencer', SequencerViewSet)
+urlpatterns = router.urls
from django.template.loader import get_template
from .models import DataRun, DataFile, FlowCell, Lane, Sequencer
+from rest_framework import viewsets
+from rest_framework.response import Response
+from rest_framework.renderers import (TemplateHTMLRenderer,
+ JSONRenderer,
+ BrowsableAPIRenderer)
+
from .admin import LaneOptions
from .experiments import estimateFlowcellDuration, estimateFlowcellTimeRemaining, roundToDays, \
getUsersForFlowcell, \
makeEmailLaneMap
+from .serializers import (
+ ClusterStationSerializer,
+ SequencerSerializer,
+ LaneSerializer,
+ FlowCellSerializer)
from samples.changelist import HTSChangeList
from samples.models import HTSUser
return HttpResponse("I've got nothing.")
+
+class ClusterStationViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (TemplateHTMLRenderer,
+ BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = ClusterStation.objects.all()
+ serializer_class = ClusterStationSerializer
+ # template_name = 'experiments/cluster_station.html'
+
+from pprint import pprint
+class FlowCellViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (TemplateHTMLRenderer,
+ BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = FlowCell.objects.all()
+ lookup_field = 'flowcell_id'
+ serializer_class = FlowCellSerializer
+ template_name = 'experiments/flowcell_detail.html'
+
+ def retrieve(self, request, *args, **kwargs):
+ fc = get_object_or_404(self.queryset, flowcell_id = kwargs['flowcell_id'])
+ context = kwargs.copy()
+ context['request'] = request
+ serializer = FlowCellSerializer(
+ fc,
+ context=context,
+ )
+ pprint(serializer.data)
+ return Response(serializer.data)
+
+ #def retrieve(self, request, flowcell_id=None, format=None):
+ # queryset = FlowCell.objects.all()
+ # fc = get_object_or_404(queryset, flowcell_id=flowcell_id)
+ # serializer = FlowCellSerializer(
+ # fc,
+ # context={
+ # 'request': request,
+ # 'format': format,
+ # }
+ # )
+ # return Response(
+ # serializer.data,
+ # )
+
+ #def list(self, *args, **kwargs):
+ # template_name = 'experiments/flowcell_index.html'
+ # return super(FlowCellViewSet, self).list(*args, **kwargs)
+
+class LaneViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (TemplateHTMLRenderer,
+ BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = Lane.objects.all()
+ serializer_class = LaneSerializer
+ template_name = 'experiments/flowcell_lane_detail.html'
+
+
+
+class SequencerViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (TemplateHTMLRenderer,
+ BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = Sequencer.objects.all()
+ serializer_class = SequencerSerializer
+ template_name = 'experiments/sequencer.html'
+
def flowcell_detail(request, flowcell_id, lane_number=None):
fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
fc.update_data_runs()
raise Http404
-def sequencer(request, sequencer_id):
- sequencer = get_object_or_404(Sequencer, id=sequencer_id)
- context = RequestContext(request,
- {'sequencer': sequencer})
- return render_to_response('experiments/sequencer.html', context)
-
-
def lanes_for(request, username=None):
"""
Generate a report of recent activity for a user
'django.contrib.messages',
'django.contrib.staticfiles',
'django.contrib.humanize',
+ 'rest_framework',
'eland_config',
'samples',
# Update this in settings_local to point to your flowcell result directory
RESULT_HOME_DIR = join(PROJECT_ROOT, 'test', 'result', 'flowcells')
+
+
+REST_FRAMEWORK = {
+ 'DEFAULT_PAGINATION_SERIALIZER_CLASS': 'rest_framework.pagination.PaginationSerializer',
+ 'PAGINATE_BY' : 25,
+}
--- /dev/null
+{% extends "base_site.html" %}
+{% load admin_list i18n %}
+{% load staticfiles %}
+{% block bodyclass %}change-list{% endblock %}
+{% block coltype %}flex{% endblock %}
+
+{% block content %}
+<div id="species-index-div" >
+ <div class="module{% if cl.has_filters %} filtered{% endif %}" id="changelist">
+ {% block summary_stats %}
+ <table class="{% if cl.has_filters %} filtered{% endif %}">
+ <thead >
+ <tr >
+ <td >Species</td>
+ <td >Common Name</td>
+ </tr>
+ </thead>
+ <tbody >
+ {% for s in species %}
+ <tr>
+ <td><a href="{{s.url}}">{{ s.scientific_name }}</a></td>
+ <td>{{ s.common_name }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ {% endblock %}
+</div>
+{% endblock %}
import django
admin.autodiscover()
-from django.conf import settings
+from experiments.urls import urlpatterns as experiment_urls
-urlpatterns = patterns('',
+urlpatterns = experiment_urls
+
+urlpatterns += patterns(
+ '',
url('^accounts/', include('django.contrib.auth.urls')),
# Base:
url(r'^eland_config/', include('eland_config.urls')),
# Experiments:
- url(r'^experiments/', include('experiments.urls')),
- url(r'^lane/(?P<lane_pk>\w+)',
- 'experiments.views.flowcell_lane_detail'),
- url(r'^flowcell/(?P<flowcell_id>\w+)/((?P<lane_number>\w+)/)?$',
- 'experiments.views.flowcell_detail'),
+ # url(r'^experiments/', include('experiments.urls')),
+ # url(r'^lane/(?P<lane_pk>\w+)',
+ # 'experiments.views.flowcell_lane_detail'),
+ # url(r'^flowcell/(?P<flowcell_id>\w+)/((?P<lane_number>\w+)/)?$',
+ # 'experiments.views.flowcell_detail'),
url(r'^inventory/', include('inventory.urls')),
url(r'^library/', include('samples.urls')),
- url(r'^lanes_for/$', 'experiments.views.lanes_for'),
- url(r'^lanes_for/(?P<username>[-_ \w]+)', 'experiments.views.lanes_for'),
- ### library id to admin url
- url(r'^library_id_to_admin_url/(?P<lib_id>\w+)/$',
- 'samples.views.library_id_to_admin_url'),
- ### sample / library information
+ # url(r'^lanes_for/$', 'experiments.views.lanes_for'),
+ # url(r'^lanes_for/(?P<username>[-_ \w]+)', 'experiments.views.lanes_for'),
+ # library id to admin url
+ # url(r'^library_id_to_admin_url/(?P<lib_id>\w+)/$',
+ # 'samples.views.library_id_to_admin_url'),
+ # sample / library information
url(r'^samples/', include('samples.urls')),
- url(r'^sequencer/(?P<sequencer_id>\w+)',
- 'experiments.views.sequencer'),
+ # url(r'^sequencer/(?P<sequencer_id>\w+)',
+ # 'experiments.views.sequencer'),
url(r'^admin/', include(admin.site.urls)),
)
--- /dev/null
+from rest_framework import serializers
+
+from .models import (Antibody,
+ Cellline,
+ ExperimentType,
+ Species,
+ Affiliation,
+ Library,
+ HTSUser)
+
+
+class ExperimentTypeSerializer(serializers.HyperlinkedModelSerializer):
+ class Meta:
+ model = ExperimentType
+ fields = ('url', 'name')
+
+
+class SpeciesSerializer(serializers.HyperlinkedModelSerializer):
+ class Meta:
+ model = Species
+ fields = ('url', 'common_name', 'scientific_name')
+
+
+class LibrarySerializer(serializers.HyperlinkedModelSerializer):
+ class Meta:
+ model = Library
+ fields = ('url', 'library_name', 'library_species', 'replicate',
+ 'experiment_type',
+ 'made_for', 'made_by', 'stopping_point',
+ 'undiluted_concentration', 'gel_cut_size', 'notes')
from django.conf.urls import patterns, url
-urlpatterns = patterns('samples.views',
- # View livrary list
- url(r'^$', 'library'),
- url(r'^not_run/$', 'library_not_run'),
- url(r'^(?P<lib_id>\w+)/$',
- 'library_to_flowcells'),
+from rest_framework import routers
- url(r"^library/(?P<library_id>\w+)/json$", 'library_json'),
- url(r"^species/(?P<species_id>\w+)/json$", 'species_json'),
- url(r"^species/(?P<species_id>\w+)$", 'species'),
- url(r"^antibody/$", 'antibodies'),
+from .views import ExperimentTypeViewSet, LibraryViewSet, SpeciesViewSet
+
+urlpatterns = patterns(
+ 'samples.views',
+ # View library list
+ # url(r'^$', 'library'),
+ # url(r'^not_run/$', 'library_not_run'),
+ # url(r'^(?P<lib_id>\w+)/$',
+ # 'library_to_flowcells'),
+
+ # url(r"^library/(?P<library_id>\w+)/json$", 'library_json'),
+ # url(r"^species/(?P<species_id>\w+)/json$", 'species_json'),
+ # url(r"^species/(?P<species_id>\w+)$", 'species'),
+ # url(r"^antibody/$", 'antibodies'),
)
+
+router = routers.DefaultRouter()
+router.register(r'species', SpeciesViewSet)
+router.register(r'libraries', LibraryViewSet)
+router.register(r'experiment_type', ExperimentTypeViewSet)
+urlpatterns += router.urls
from django.template.loader import get_template
from django.contrib.auth.decorators import login_required
+from rest_framework import viewsets
+from rest_framework.response import Response
+from rest_framework.renderers import (TemplateHTMLRenderer,
+ JSONRenderer,
+ BrowsableAPIRenderer)
+
from htsworkflow.auth import require_api_key
from experiments.models import FlowCell, LANE_STATUS_MAP
from .changelist import HTSChangeList
from .models import Antibody, Library, Species
from .admin import LibraryOptions
from .results import get_flowcell_result_dict
+from .serializers import (ExperimentTypeSerializer,
+ LibrarySerializer,
+ SpeciesSerializer)
+
from bcmagic.forms import BarcodeMagicForm
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.samplekey import SampleKey
return HttpResponse(lib_json, content_type='application/json')
-@csrf_exempt
-def species_json(request, species_id):
- """
- Return information about a species.
- """
- 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)
+class LibraryViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (TemplateHTMLRenderer,
+ BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = Library.objects.all()
+ serializer_class = LibrarySerializer
+ pagination_class = 'rest_framework.pagination.LimitOffsetPagination'
+ default_limit = 50
+ template_name = 'samples/library_detail.html'
+
+
+class ExperimentTypeViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = ExperimentType.objects.all()
+ serializer_class = ExperimentTypeSerializer
+
+#@csrf_exempt
+#def species_json(request, species_id):
+# """
+# Return information about a species.
+# """
+# 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)
+#
+
+class SpeciesViewSet(viewsets.ReadOnlyModelViewSet):
+ renderer_classes = (TemplateHTMLRenderer,
+ BrowsableAPIRenderer,
+ JSONRenderer)
+ queryset = Species.objects.all()
+ serializer_class = SpeciesSerializer
+ template_name = 'samples/species_detail.html'
+
+ def list(self, request, format=format):
+ queryset = Species.objects.all()
+ serializer = self.serializer_class(
+ queryset,
+ many=True,
+ context={'request': request})
+ return Response({'species': serializer.data},
+ template_name='samples/species_list.html')
def antibodies(request):
- context = RequestContext(request,
- {'antibodies': Antibody.objects.order_by('antigene')})
+ context = RequestContext(
+ request,
+ {'antibodies': Antibody.objects.order_by('antigene')})
return render_to_response("samples/antibody_index.html", context)
projects / htsworkflow.git / commitdiff