def get_queryset(self):
invalid_filters = check_filters(self)
if invalid_filters:
raise InvalidFilters(invalid_filters=invalid_filters)
return self.queryset
def get_queryset(self):
invalid_filters = check_filters(
self, special_filters=["organism__name", "result_id", "length"]
)
if invalid_filters:
raise InvalidFilters(invalid_filters=invalid_filters)
queryset = OrganismIndex.public_objects.all()
organism_name = self.request.query_params.get("organism__name", None)
if organism_name is not None:
queryset = queryset.filter(organism__name=organism_name.upper())
# https://github.com/AlexsLemonade/refinebio/issues/2459
# It looks like when we set `result_id` as a filterset field,
# django_forms goes nuts and tries to call __str__ on every single
# computational result in our database trying to find all of the
# different possible computational_results. So let's just take care of
# this one ourselves.
result_id = self.request.query_params.get("result_id", None)
if result_id is not None:
queryset = queryset.filter(result_id=result_id)
length = self.request.query_params.get("length", None)
if length is not None:
index_type = "TRANSCRIPTOME_{}".format(length.upper())
queryset = queryset.filter(index_type=index_type)
return queryset
def add_to_params(self, key, value):
"""Add to query params, converting to string if necessary"""
if type(value) == str:
self.query_params.appendlist(key, value)
elif type(value) == int or type(value) == bool:
self.query_params.appendlist(key, str(value))
else:
# We shouldn't be filtering on Null, lists, or dicts
raise InvalidFilters(
message="Invalid type {} for filter value {}".format(
type(value), str(value)))
def get_queryset(self):
"""
ref https://www.django-rest-framework.org/api-guide/filtering/#filtering-against-query-parameters
"""
invalid_filters = check_filters(
self,
special_filters=[
"ids",
"organism__name",
"dataset_id",
"experiment_accession_code",
"accession_codes",
"filter_by",
],
)
if invalid_filters:
raise InvalidFilters(invalid_filters=invalid_filters)
queryset = (Sample.public_objects.select_related(
"organism").prefetch_related("experiments").prefetch_related(
Prefetch(
"results",
queryset=ComputationalResult.objects.select_related(
"processor").select_related("organism_index").order_by(
"time_start"),
)).prefetch_related("sampleannotation_set").prefetch_related(
"original_files").prefetch_related("computed_files").
filter(**self.get_query_params_filters()))
# case insensitive search https://docs.djangoproject.com/en/2.1/ref/models/querysets/#icontains
filter_by = self.request.query_params.get("filter_by", None)
if filter_by:
queryset = queryset.filter(
Q(accession_code__icontains=filter_by)
| Q(title__icontains=filter_by)
| Q(sex__icontains=filter_by)
| Q(age__icontains=filter_by)
| Q(specimen_part__icontains=filter_by)
| Q(genotype__icontains=filter_by)
| Q(disease__icontains=filter_by)
| Q(disease_stage__icontains=filter_by)
| Q(cell_line__icontains=filter_by)
| Q(treatment__icontains=filter_by)
| Q(race__icontains=filter_by)
| Q(subject__icontains=filter_by)
| Q(compound__icontains=filter_by)
| Q(time__icontains=filter_by))
return queryset
def get_queryset(self):
invalid_filters = check_filters(self, ["sample_accession_code"])
if invalid_filters:
raise InvalidFilters(invalid_filters=invalid_filters)
queryset = DownloaderJob.objects.all()
sample_accession_code = self.request.query_params.get(
"sample_accession_code", None)
if sample_accession_code:
queryset = queryset.filter(
original_files__samples__accession_code=sample_accession_code
).distinct()
return queryset
def get_queryset(self):
invalid_filters = check_filters(self, ["latest_version"])
if invalid_filters:
raise InvalidFilters(invalid_filters)
public_result_queryset = CompendiumResult.objects.filter(
result__is_public=True)
latest_version = self.request.query_params.get("latest_version", False)
if latest_version:
version_filter = Q(
primary_organism=OuterRef("primary_organism"),
quant_sf_only=OuterRef("quant_sf_only"),
)
latest_version = (
public_result_queryset.filter(version_filter).order_by(
"-compendium_version").values("compendium_version"))
return public_result_queryset.annotate(
latest_version=Subquery(latest_version[:1])).filter(
compendium_version=F("latest_version"))
return public_result_queryset