def get_schema(self):
basis_list = self.basis_list_to_precompute
nbins = self.nbins
bin_agg_function = self.bin_agg_function
result = SimpleData.schema(self.adata)
markers = result.get('markers', [])
if self.markers is not None: # add from file
markers += get_markers(self.markers)
markers = filter_markers(self.adata, markers)
for marker in markers:
if marker.get('id') is None:
marker['id'] = unique_id()
marker['readonly'] = True
result['markers'] = markers
result['format'] = self.output_format
if self.stats:
result['precomputed'] = True # has stats
if nbins is not None:
result['embeddings'] = []
for basis_name in basis_list:
result['embeddings'].append({
'precomputed': True,
'name': basis_name,
'nbins': nbins,
'agg': bin_agg_function,
'dimensions': 2
})
return result
def create_job(self, email, dataset_id, job_name, job_type, params):
job_id = unique_id()
self.job_id_to_job[job_id] = dict(id=job_id,
dataset_id=dataset_id,
name=job_name,
type=job_type,
params=params,
status=None,
submitted=str(
datetime.datetime.utcnow()))
return job_id
def __upsert_entity(self, dataset_id, entity_id, kind, entity_dict):
if entity_id is None:
entity_id = unique_id()
json_data = self.dataset_to_info[dataset_id]['json_data']
entity = json_data[kind].get(entity_id)
if entity is None:
entity = {}
json_data[kind][entity_id] = entity
entity.update(entity_dict)
write_json(json_data, self.dataset_to_info[dataset_id]['json_path'])
return entity_id
def get_schema(self):
result = dataset_schema(self.dataset, n_features=self.group_nfeatures)
markers = result.get('markers', [])
if self.markers is not None: # add results specified from file
markers += get_markers(self.markers)
markers = filter_markers(self.dataset, markers)
for marker in markers:
if marker.get('id') is None:
marker['id'] = unique_id()
marker['readonly'] = True
result['markers'] = markers
result['format'] = self.output_format
return result
def get_schema(self):
result = dataset_schema(self.dataset, n_features=self.group_nfeatures)
markers = result.get("markers", [])
if self.markers is not None: # add results specified from file
markers += get_markers(self.markers)
markers = filter_markers(self.dataset, markers)
for marker in markers:
if marker.get("id") is None:
marker["id"] = unique_id()
marker["readonly"] = True
result["markers"] = markers
result["format"] = self.output_format
return result
def upsert_feature_set(self, email, dataset_id, set_id, category, name,
features):
if set_id is None:
set_id = unique_id()
else:
self.delete_feature_set(email=email,
dataset_id=dataset_id,
set_id=set_id)
json_data = self.dataset_to_info[dataset_id]['json_data']
markers = json_data.get('markers')
if markers is None:
markers = []
json_data['markers'] = markers
markers.append(
dict(id=set_id, features=features, name=name, category=category))
write_json(json_data, self.dataset_to_info[dataset_id]['json_path'])
return set_id
def upsert_dataset_filter(self, email, dataset_id, filter_id, filter_name,
filter_notes, dataset_filter):
if filter_id is None:
filter_id = unique_id()
json_data = self.dataset_to_info[dataset_id]['json_data']
entity = json_data['filters'].get(filter_id)
if entity is None:
entity = {}
json_data['filters'][filter_id] = entity
if filter_name is not None:
entity['name'] = filter_name
if dataset_filter is not None:
entity['value'] = json.dumps(dataset_filter)
if email is not None:
entity['email'] = email
if dataset_id is not None:
entity['dataset_id'] = dataset_id
if filter_notes is not None:
entity['notes'] = filter_notes
write_json(json_data, self.dataset_to_info[dataset_id]['json_path'])
return filter_id