def get(self, request, pk):
mapping = get_mapping(pk)
authenticated = False
if request.user and request.user.is_authenticated:
authenticated = True
email_recipients_list = {
recipient_id: recipient_details.get('name')
for (recipient_id,
recipient_details) in settings.EMAIL_RECIPIENT_LIST.items()
}
data = {
'taxonomy':
build_taxonomy_data(mapping),
'mapping':
MappingsSerializer.build_mapping(mapping,
fetch_sequence=True,
authenticated=authenticated),
'relatedEntries': {
'mapped': build_related_mappings_data(mapping),
'unmapped': build_related_unmapped_entries_data(mapping)
},
'emailRecipientsList':
email_recipients_list
}
serializer = MappingSerializer(data)
return Response(serializer.data)
def build_related_mappings_data(mapping):
"""
Return the list of mappings sharing the same ENST or Uniprot accession of
the given mapping.
Parameters
----------
mapping : Mapping object
Returns
-------
list
List of objects that are related to the same mapping group
"""
# related mappings share the same group_id and tax id
mapping_mh = mapping.mapping_history.latest(
'release_mapping_history__time_mapped')
mapping_mh_rmh = mapping_mh.release_mapping_history
mapping_grouping_id = mapping_mh.grouping_id
related_mappings_mh = MappingHistory.objects.filter(
release_mapping_history=mapping_mh_rmh,
grouping_id=mapping_grouping_id)
related_mappings = []
for mh in related_mappings_mh:
m = mh.mapping
if m.mapping_id != mapping.mapping_id:
related_mappings.append(
MappingsSerializer.build_mapping(m, fetch_sequence=False))
return related_mappings
def post(self, request, pk, difference):
mapping = get_mapping(pk)
mapping.alignment_difference = difference
mapping.save()
serializer = EnsemblUniprotMappingSerializer(
MappingsSerializer.build_mapping(mapping))
return Response(serializer.data)
def build_related_mappings_data(mapping):
"""
Return the list of mappings sharing the same ENST or Uniprot accession of the given mapping.
"""
# related mapping share the same group_id and tax id
mappings = Mapping.objects.filter(
unique_grouping_id=mapping.unique_grouping_id,
uniprot__uniprot_tax_id=mapping.uniprot.uniprot_tax_id).exclude(
pk=mapping.mapping_id)
return list(
map(
lambda m: MappingsSerializer.build_mapping(m, fetch_sequence=False
), mappings))
def get(self, request, pk):
mapping = get_mapping(pk)
data = {
'taxonomy':
build_taxonomy_data(mapping),
'mapping':
MappingsSerializer.build_mapping(
mapping,
fetch_sequence=True,
authenticated=request.user.is_authenticated),
'relatedMappings':
build_related_mappings_data(mapping)
}
serializer = MappingSerializer(data)
return Response(serializer.data)
def get(self, request, pk):
mapping = get_mapping(pk)
data = {
'taxonomy':
build_taxonomy_data(mapping),
'mapping':
MappingsSerializer.build_mapping(
mapping,
fetch_sequence=True,
authenticated=True
if request.user and request.user.is_authenticated else False),
'relatedEntries': {
'mapped': build_related_mappings_data(mapping),
'unmapped': build_related_unmapped_entries_data(mapping)
}
}
serializer = MappingSerializer(data)
return Response(serializer.data)
def build_related_mappings_data(mapping):
"""
Return the list of mappings sharing the same ENST or Uniprot accession of the given mapping.
"""
# related mappings share the same group_id and tax id
mapping_mh = mapping.mapping_history.latest(
'release_mapping_history__time_mapped')
mapping_mh_rmh = mapping_mh.release_mapping_history
mapping_grouping_id = mapping_mh.grouping_id
related_mappings_mh = MappingHistory.objects.filter(
release_mapping_history=mapping_mh_rmh,
grouping_id=mapping_grouping_id)
related_mappings = filter(lambda m: m.mapping_id != mapping.mapping_id,
(mh.mapping for mh in related_mappings_mh))
# mappings = Mapping.objects.filter(mapping_history__grouping_id=mapping.mapping_history.latest('release_mapping_history__time_mapped').grouping_id, uniprot__uniprot_tax_id=mapping.uniprot.uniprot_tax_id).exclude(pk=mapping.mapping_id)
return list(
map(
lambda m: MappingsSerializer.build_mapping(m, fetch_sequence=False
), related_mappings))
def paginate_queryset(self, queryset, request, view=None):
self.count = queryset.grouped_count
self.limit = self.get_limit(request)
if self.limit is None:
return None
self.offset = self.get_offset(request)
self.request = request
if self.count > self.limit and self.template is not None:
self.display_page_controls = True
if self.count == 0 or self.offset > self.count:
return []
mapping_groups = []
self.facets = self.create_facets(queryset)
for _, group in queryset.grouped_slice(self.offset,
self.limit).items():
mapping_groups.append(
MappingsSerializer.build_mapping_group(group))
return mapping_groups
