def cloud_storage_file_paths(self, request):
"""
Takes a sample barcode as a required parameter and
returns cloud storage paths to files associated with that sample.
"""
cursor = None
db = None
sample_barcode = request.get_assigned_value('sample_barcode')
platform = request.get_assigned_value('platform')
pipeline = request.get_assigned_value('pipeline')
if are_there_bad_keys(request):
err_msg = construct_parameter_error_message(request, False)
raise endpoints.BadRequestException(err_msg)
query_str, query_tuple = CohortsSamplesFilesQueryBuilder().build_query(
platform=platform, pipeline=pipeline, sample_barcode=sample_barcode)
try:
db = sql_connection()
cursor = db.cursor(MySQLdb.cursors.DictCursor)
cursor.execute(query_str, query_tuple)
cursor_rows = cursor.fetchall()
# add 'cloud_storage_path' to cursor_rows
bad_repo_count, bad_repo_set = CohortsSamplesFilesMessageBuilder().get_GCS_file_paths_and_bad_repos(cursor_rows)
cloud_storage_path_list = [row['cloud_storage_path'] for row in cursor_rows]
if bad_repo_count > 0:
logger.warn("not returning {count} row(s) in sample_details due to repositories: {bad_repo_list}"
.format(count=bad_repo_count, bad_repo_list=list(bad_repo_set)))
return GCSFilePathList(cloud_storage_file_paths=cloud_storage_path_list, count=len(cloud_storage_path_list))
except (IndexError, TypeError), e:
logger.warn(e)
raise endpoints.NotFoundException("File paths for sample {} not found.".format(sample_barcode))
def preview(self, request):
"""
Takes a JSON object of filters in the request body and returns a "preview" of the cohort that would
result from passing a similar request to the cohort **save** endpoint. This preview consists of
two lists: the lists of participant (aka patient) barcodes, and the list of sample barcodes.
Authentication is not required.
"""
patient_cursor = None
sample_cursor = None
if are_there_bad_keys(request) or are_there_no_acceptable_keys(request):
err_msg = construct_parameter_error_message(request, True)
raise endpoints.BadRequestException(err_msg)
query_dict, gte_query_dict, lte_query_dict = CohortsCreatePreviewQueryBuilder().build_query_dictionaries(
request
)
patient_query_str, sample_query_str, value_tuple = CohortsCreatePreviewQueryBuilder().build_query(
query_dict, gte_query_dict, lte_query_dict
)
patient_barcodes = []
sample_barcodes = []
try:
db = sql_connection()
patient_cursor = db.cursor(MySQLdb.cursors.DictCursor)
patient_cursor.execute(patient_query_str, value_tuple)
for row in patient_cursor.fetchall():
patient_barcodes.append(row["case_barcode"])
sample_cursor = db.cursor(MySQLdb.cursors.DictCursor)
sample_cursor.execute(sample_query_str, value_tuple)
for row in sample_cursor.fetchall():
sample_barcodes.append(row["sample_barcode"])
except (IndexError, TypeError), e:
logger.warn(e)
raise endpoints.NotFoundException("Error retrieving samples or patients: {}".format(e))
