def setUpClass(cls, msg=""):
'''Set up FireCloud etc to run tests'''
print("\nStarting low-level api tests ...\n", file=sys.stderr)
fiss_verbosity = os.environ.get("FISS_TEST_VERBOSITY", None)
if fiss_verbosity == None:
fiss_verbosity = 0
fcconfig = fccore.config_parse()
cls.project = fcconfig.project
if not cls.project:
raise ValueError("Your configuration must define a FireCloud project")
fcconfig.set_verbosity(fiss_verbosity)
# Set up a temp workspace for duration of tests; and in case a previous
# test failed, attempt to unlock & delete before creating anew. Note
# that bc we execute space create/delete here, their tests are NO-OPs
cls.workspace = getuser() + '_FISS_TEST'
r = fapi.unlock_workspace(cls.project, cls.workspace)
r = fapi.delete_workspace(cls.project, cls.workspace)
r = fapi.create_workspace(cls.project, cls.workspace)
fapi._check_response_code(r, 201)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
Run before 04_v2_genotype_batch
"""
import argparse
import os
import firecloud.api as fapi
from firecloud import fccore
from google.cloud import storage
fcconfig = fccore.config_parse()
def get_bucket_name(namespace, workspace):
response = fapi.get_workspace(namespace, workspace)
fapi._check_response_code(response, 200)
return response.json()['workspace']['bucketName']
def get_sample_sets(namespace, workspace, batches):
response = fapi.get_entities(namespace, workspace, 'sample_set')
fapi._check_response_code(response, 200)
return [entity for entity in response.json() if entity['name'] in batches]
def make_vcfs_list(namespace, workspace, batches):
sample_sets = get_sample_sets(namespace, workspace, batches)