def get(self, request):
query_list_types = ["job_groups", "jira_ids", "request_ids", "runs"]
fixed_query_params = fix_query_list(request.query_params,
query_list_types)
serializer = CWLJsonSerializer(data=fixed_query_params)
show_inputs = False
if serializer.is_valid():
job_groups = fixed_query_params.get("job_groups")
jira_ids = fixed_query_params.get("jira_ids")
request_ids = fixed_query_params.get("request_ids")
runs = fixed_query_params.get("runs")
cwl_inputs = fixed_query_params.get("cwl_inputs")
if not job_groups and not jira_ids and not request_ids and not runs:
return Response("Error: No runs specified",
status=status.HTTP_400_BAD_REQUEST)
queryset = Run.objects.all()
if job_groups:
queryset = queryset.filter(job_group__in=job_groups)
if jira_ids:
queryset = queryset.filter(
job_group_notifier__jira_id__in=jira_ids)
if request_ids:
queryset = queryset.filter(tags__requestId__in=request_ids)
if runs:
queryset = queryset.filter(id__in=runs)
if cwl_inputs:
show_inputs = bool(strtobool(cwl_inputs))
try:
page = self.paginate_queryset(
queryset.order_by("-created_date").all())
except ValidationError as e:
return Response(e, status=status.HTTP_400_BAD_REQUEST)
if page is not None:
if show_inputs:
serializer = RunSerializerCWLInput(page, many=True)
else:
serializer = RunSerializerCWLOutput(page, many=True)
return self.get_paginated_response(serializer.data)
else:
return Response([], status=status.HTTP_200_OK)
else:
return Response(serializer.errors,
status=status.HTTP_400_BAD_REQUEST)
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)
def list(self, request, *args, **kwargs):
query_list_types = [
'job_groups', 'request_ids', 'inputs', 'tags', 'jira_ids',
'run_ids', 'apps', 'run', 'values_run', 'ports'
]
fixed_query_params = fix_query_list(request.query_params,
query_list_types)
serializer = RunApiListSerializer(data=fixed_query_params)
if serializer.is_valid():
queryset = time_filter(Run, fixed_query_params)
queryset = time_filter(Run,
request.query_params,
time_modal='modified_date',
previous_queryset=queryset)
job_groups = fixed_query_params.get('job_groups')
jira_ids = fixed_query_params.get('jira_ids')
run_ids = fixed_query_params.get('run_ids')
status_param = fixed_query_params.get('status')
ports = fixed_query_params.get('ports')
tags = fixed_query_params.get('tags')
request_ids = fixed_query_params.get('request_ids')
apps = fixed_query_params.get('apps')
values_run = fixed_query_params.get('values_run')
run = fixed_query_params.get('run')
run_distribution = fixed_query_params.get('run_distribution')
count = fixed_query_params.get('count')
full = fixed_query_params.get('full')
if full:
full = bool(strtobool(full))
if job_groups:
queryset = queryset.filter(job_group__in=job_groups)
if jira_ids:
queryset = queryset.filter(job_group__jira_id__in=jira_ids)
if run_ids:
queryset = queryset.filter(id__in=run_ids)
if status_param:
queryset = queryset.filter(
status=RunStatus[status_param].value)
if ports:
queryset = self.query_from_dict("port__%s__exact", queryset,
ports)
if tags:
queryset = self.query_from_dict("tags__%s__contains", queryset,
tags)
if request_ids:
queryset = queryset.filter(tags__requestId__in=request_ids)
if apps:
queryset = queryset.filter(app__in=apps)
if run:
filter_query = dict()
for single_run in run:
key, value = single_run.split(':')
if value == 'True' or value == 'true':
value = True
if value == 'False' or value == 'false':
value = False
filter_query[key] = value
if filter_query:
queryset = queryset.filter(**filter_query)
if values_run:
if len(values_run) == 1:
ret_str = values_run[0]
queryset = queryset.values_list(
ret_str, flat=True).order_by(ret_str).distinct(ret_str)
else:
values_run_query_list = [
single_run for single_run in values_run
]
values_run_query_set = set(values_run_query_list)
sorted_query_list = sorted(values_run_query_set)
queryset = queryset.values_list(
*sorted_query_list).distinct()
if run_distribution:
distribution_dict = {}
run_query = run_distribution
run_ids = queryset.values_list('id', flat=True)
queryset = Run.objects.all()
queryset = queryset.filter(
id__in=run_ids).values(run_query).order_by().annotate(
Count(run_query))
for single_arg in queryset:
single_arg_name = None
single_arg_count = 0
for single_key, single_value in single_arg.items():
if 'count' in single_key:
single_arg_count = single_value
else:
single_arg_name = single_value
if single_arg_name is not None:
distribution_dict[single_arg_name] = single_arg_count
return Response(distribution_dict, status=status.HTTP_200_OK)
if count:
count = bool(strtobool(count))
if count:
return Response(queryset.count(),
status=status.HTTP_200_OK)
try:
page = self.paginate_queryset(queryset.all())
except ValidationError as e:
return Response(e, status=status.HTTP_400_BAD_REQUEST)
if page is not None:
if values_run:
return self.get_paginated_response(page)
if full:
serializer = RunSerializerFull(page, many=True)
else:
serializer = RunSerializerPartial(page, many=True)
return self.get_paginated_response(serializer.data)
return Response([], status=status.HTTP_200_OK)
else:
return Response(serializer.errors,
status=status.HTTP_400_BAD_REQUEST)
def list(self, request, *args, **kwargs):
query_list_types = ['job_group','values_args','args']
fixed_query_params = fix_query_list(request.query_params, query_list_types)
serializer = JobQuerySerializer(data=fixed_query_params)
if serializer.is_valid():
queryset = time_filter(Job, request.query_params)
queryset = time_filter(Job, request.query_params,time_modal='modified_date', previous_queryset=queryset)
job_group = fixed_query_params.get('job_group')
job_type = fixed_query_params.get('type')
sample_id = fixed_query_params.get('sample_id')
request_id = fixed_query_params.get('request_id')
st = fixed_query_params.get('status')
values_args = fixed_query_params.get('values_args')
args = fixed_query_params.get('args')
args_distribution = fixed_query_params.get('args_distribution')
count = fixed_query_params.get('count')
if job_group:
queryset = queryset.filter(job_group__in=job_group)
if job_type:
queryset = queryset.filter(run=TYPES[job_type])
if sample_id:
queryset = queryset.filter(args__sample_id=sample_id)
if request_id:
queryset = queryset.filter(args__request_id=request_id)
if st:
queryset = queryset.filter(status=JobStatus[st].value)
if args:
filter_query = dict()
for single_arg in args:
key, value = single_arg.split(':')
key = 'args__%s' % key
if value == 'True' or value == 'true':
value = True
if value == 'False' or value == 'false':
value = False
filter_query[key] = value
if filter_query:
queryset = queryset.filter(**filter_query)
if values_args:
if len(values_args) == 1:
ret_str = 'args__%s' % values_args[0]
queryset = queryset.values_list(ret_str, flat=True).order_by(ret_str).distinct(ret_str)
else:
values_args_query_list = ['args__%s' % single_arg for single_arg in values_args ]
values_args_query_set = set(values_args_query_list)
queryset = queryset.values_list(*values_args_query_set).order_by(values_args_query_list[0]).distinct()
if args_distribution:
distribution_dict = {}
args_query = 'args__%s' % args_distribution
job_ids = queryset.values_list('id',flat=True)
queryset = Job.objects.all()
queryset = queryset.filter(id__in=job_ids).values(args_query).order_by().annotate(Count(args_query))
for single_arg in queryset:
single_arg_name = None
single_arg_count = 0
for single_key, single_value in single_arg.items():
if 'count' in single_key:
single_arg_count = single_value
else:
single_arg_name = single_value
if single_arg_name is not None:
distribution_dict[single_arg_name] = single_arg_count
return Response(distribution_dict, status=status.HTTP_200_OK)
if count:
count = bool(strtobool(count))
if count:
return Response(queryset.count(), status=status.HTTP_200_OK)
page = self.paginate_queryset(queryset.all())
if page is not None:
if values_args:
return self.get_paginated_response(page)
else:
serializer = JobSerializer(page, many=True)
return self.get_paginated_response(serializer.data)
else:
return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)
