def test_zero_samples_igocomplete_false(self, mock_get_sample):
mock_get_sample.return_value = MockResponse(
json_data=self.data_0_fastq, status_code=200)
with self.assertRaises(MissingDataException):
fetch_sample_metadata('igoId_000', False, 'sampleName_000', {})
count_files = FileRepository.all().count()
self.assertEqual(count_files, 0)
def list(self, request, *args, **kwargs):
query_list_types = [
"file_group",
"path",
"metadata",
"metadata_regex",
"filename",
"file_type",
"values_metadata",
"exclude_null_metadata",
]
fixed_query_params = fix_query_list(request.query_params,
query_list_types)
serializer = FileQuerySerializer(data=fixed_query_params)
if serializer.is_valid():
queryset = FileRepository.all()
queryset = time_filter(FileMetadata,
request.query_params,
time_modal="modified_date",
previous_queryset=queryset)
file_group = fixed_query_params.get("file_group")
path = fixed_query_params.get("path")
metadata = fixed_query_params.get("metadata")
metadata_regex = fixed_query_params.get("metadata_regex")
path_regex = fixed_query_params.get("path_regex")
filename = fixed_query_params.get("filename")
filename_regex = fixed_query_params.get("filename_regex")
file_type = fixed_query_params.get("file_type")
values_metadata = fixed_query_params.get("values_metadata")
exclude_null_metadata = fixed_query_params.get(
"exclude_null_metadata")
order_by = fixed_query_params.get("order_by")
distinct_metadata = fixed_query_params.get("distinct_metadata")
kwargs = {"queryset": queryset}
if file_group:
if len(file_group) == 1:
kwargs["file_group"] = file_group[0]
else:
kwargs["file_group_in"] = file_group
if path:
if len(path) == 1:
kwargs["path"] = path[0]
else:
kwargs["path_in"] = path
if metadata:
filter_query = dict()
for val in metadata:
k, v = val.split(":")
metadata_field = k.strip()
if metadata_field not in filter_query:
filter_query[metadata_field] = [v.strip()]
else:
filter_query[metadata_field].append(v.strip())
if filter_query:
kwargs["metadata"] = filter_query
if metadata_regex:
filter_query = []
for single_reqex_query in metadata_regex:
single_value = single_reqex_query.split("|")
single_reqex_filters = []
for val in single_value:
k, v = val.split(":")
single_reqex_filters.append((k.strip(), v.strip()))
filter_query.append(single_reqex_filters)
if filter_query:
kwargs["metadata_regex"] = filter_query
if path_regex:
kwargs["path_regex"] = path_regex
if filename:
if len(filename) == 1:
kwargs["file_name"] = filename[0]
else:
kwargs["file_name_in"] = filename
if filename_regex:
kwargs["file_name_regex"] = filename_regex
if file_type:
if len(file_type) == 1:
kwargs["file_type"] = file_type[0]
else:
kwargs["file_type_in"] = file_type
if exclude_null_metadata:
kwargs["exclude"] = exclude_null_metadata
if order_by:
kwargs["order_by"] = order_by
if distinct_metadata:
kwargs["distinct"] = distinct_metadata
if values_metadata:
if len(values_metadata) == 1:
kwargs["values_metadata"] = values_metadata[0]
else:
kwargs["values_metadata_list"] = values_metadata
try:
queryset = FileRepository.filter(**kwargs)
except Exception as e:
return Response({"details": str(e)},
status=status.HTTP_400_BAD_REQUEST)
page = self.paginate_queryset(queryset)
if page is not None:
if values_metadata:
return self.get_paginated_response(page)
else:
serializer = FileSerializer(page,
many=True,
context={"request": request})
return self.get_paginated_response(serializer.data)
else:
return Response(serializer.errors,
status=status.HTTP_400_BAD_REQUEST)