def get_features(self, request, **kwargs):
""" Returns a DAS GFF xml.
Calls ''obj_get'' to fetch only the objects requested. This method
only responds to HTTP GET.
Similar to obj_get_list in ModelResource with modifications. Need to
make this a factory so that specific fields and be mapped to the
segment and start end.
"""
if hasattr(request, 'GET'):
reference, start, stop = parse_das_segment(request)
query_seg = {'id': reference, 'start':start, 'stop':stop}
query_method = getattr(self, "%s_query" % self._meta.filetype, None)
if query_method:
hits = query_method(**query_seg)
else:
raise NotImplementedError("No query function implemented for\
filetype %s" % self._meta.filetyp)
#:TODO implement json return as well.
try:
content = feature_serializer(request, hits, format_json = getattr(self._meta , 'json'), **query_seg)
except:
content = feature_serializer(request, hits, **query_seg)
response = HttpResponse(content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
def get_features(self, request, **kwargs):
""" Returns a DAS GFF xml.
Calls ''obj_get'' to fetch only the objects requested. This method
only responds to HTTP GET.
Similar to obj_get_list in ModelResource with modifications. Need to
make this a factory so that specific fields and be mapped to the
segment and start end.
"""
if hasattr(request, 'GET'):
reference, start, stop = parse_das_segment(request)
query_seg = {'id': reference, 'start':start, 'stop':stop}
# Attempts to be smart about field mapping
# :TODO implement this
if 'chrom' in self.fields:
pass
# :TODO Need to implement type, category, feature_id and maxbins
# :TODO Check if model has a Kent bin. Also benchmark using this overa
# standard index.
# :TODO make reference more general
try:
reference = int(reference)
except ValueError:
# For when the query is 'chr1'
reference = reference
self.is_authenticated(request)
# Check if there is a binning scheme. Assume it follows the
# UCSC binning scheme.
try:
if start:
base_object_list = self.get_object_list(request).filter(
Q(start__range=(start,stop)) |\
Q(end__range=(start,stop)),
chrom__exact = reference)
else:
base_object_list = self.get_object_list(request).filter(
chrom__exact = reference)
# :TODO authorization check
except ValueError:
raise ValueError('Invalid Request')
# Do I need to convert to a bundle, or too much.
'''
bundles = [self.build_bundle(obj=obj, request=request) for obj in\
base_object_list]
to_be_serialized = [self.full_dehydrate(bundle) for bundle in bundles]
'''
try:
content = feature_serializer(request, base_object_list, format_json = getattr(self._meta , 'json'), **query_seg)
except:
content = feature_serializer(request, base_object_list, **query_seg)
response = HttpResponse(content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
