def create_input_json(method, out, config):
"""
Create JSON method input for specified method and config.
"""
method_namespace, method_name, method_version = alto.fs_split(method)
if method_namespace is None:
raise ValueError(
'Method should be specified as namespace/name (e.g. regev/drop-seq)'
)
payload = alto.get_method(method_namespace, method_name)['payload']
tmp_wdl_file = tempfile.mkstemp(suffix='.wdl')[1]
with open(tmp_wdl_file, 'w') as w:
w.write(payload)
repo_config = None
if config is not None:
config_namespace, config_name, config_version = alto.fs_split(config)
if config_version is not None:
repo_config = fapi.get_repository_config(config_namespace,
config_name,
config_version).json()
else:
repo_configs = fapi.list_repository_configs().json()
for config in repo_configs:
if config['namespace'] == config_namespace and config[
'name'] == config_name and config['method'][
'name'] == method_name and config['method'][
'namespace'] == method_namespace:
repo_config = config
break
if repo_config is not None:
repo_config = fapi.get_repository_config(
repo_config['namespace'], repo_config['name'],
repo_config['snapshotId']).json()
jar = pkg_resources.resource_filename('alto', 'womtool-30.2.jar')
tmp_json_file = tempfile.mkstemp(suffix='.json')[1]
with open(tmp_json_file, 'w') as tmp_json_out:
subprocess.check_call(['java', '-jar', jar, 'inputs', tmp_wdl_file],
stdout=tmp_json_out)
with open(tmp_json_file, 'r') as tmp_json_in:
inputs = json.loads(tmp_json_in.read())
if repo_config is not None:
repo_config = json.loads(repo_config['payload'])['inputs']
for key in repo_config:
value = repo_config[key]
if inputs.get(key) is not None and value != '':
inputs[key] = value
if out is None:
out = method_name + '_inputs.json'
if not out.lower().endswith('.json'):
out = out + '.json'
with open(out, 'w') as json_out:
json.dump(inputs, json_out, indent=0)
os.remove(tmp_json_file)
os.remove(tmp_wdl_file)
def test_list_repository_configs(self):
"""Test list_repository_configs()."""
r = fapi.list_repository_configs()
print(r.status_code, r.content)
self.assertEqual(r.status_code, 200)
def do_fc_inputs(method, out, config):
method_namespace, method_name, method_version = kco.fs_split(method)
if method_namespace is None:
raise ValueError(
'Method should be specified as namespace/name (e.g. regev/drop-seq)'
)
if method_version is None:
version = -1
list_methods = fapi.list_repository_methods(method_name)
if list_methods.status_code != 200:
raise ValueError('Unable to list methods ' + ' - ' +
str(list_methods.json))
methods = list_methods.json()
for method in methods:
if method['namespace'] == method_namespace:
version = max(version, method['snapshotId'])
if version == -1:
raise ValueError(method_name + ' not found')
method_version = version
payload = fapi.get_repository_method(method_namespace, method_name,
method_version).json()['payload']
tmp_wdl_file = tempfile.mkstemp(suffix='.wdl')[1]
with open(tmp_wdl_file, 'w') as w:
w.write(payload)
repo_config = None
if config is not None:
config_namespace, config_name, config_version = kco.fs_split(
config)
if config_version is not None:
repo_config = fapi.get_repository_config(
config_namespace, config_name, config_version).json()
else:
repo_configs = fapi.list_repository_configs().json()
for config in repo_configs:
if config['namespace'] == config_namespace and config[
'name'] == config_name and config['method'][
'name'] == method_name and config['method'][
'namespace'] == method_namespace:
repo_config = config
break
if repo_config is not None:
repo_config = fapi.get_repository_config(
repo_config['namespace'], repo_config['name'],
repo_config['snapshotId']).json()
jar = pkg_resources.resource_filename('kco', 'womtool-33.1.jar')
tmp_json_file = tempfile.mkstemp(suffix='.json')[1]
with open(tmp_json_file, 'w') as tmp_json_out:
subprocess.check_call(
['java', '-jar', jar, 'inputs', tmp_wdl_file],
stdout=tmp_json_out)
with open(tmp_json_file, 'r') as tmp_json_in:
inputs = json.loads(tmp_json_in.read())
if repo_config is not None:
repo_config = json.loads(repo_config['payload'])['inputs']
for key in repo_config:
value = repo_config[key]
if inputs.get(key) is not None and value != '':
inputs[key] = value
if out is None:
out = method_name + '_inputs.json'
if not out.lower().endswith('.json'):
out = out + '.json'
with open(out, 'w') as json_out:
json.dump(inputs, json_out, indent=0)
os.remove(tmp_json_file)
os.remove(tmp_wdl_file)