def get_variable_value(variable_name):
Logger.log_task_event(GENERATE_INPUTS_TASK, "Getting value of: {}".format(variable_name))
if not os.environ.get(variable_name):
return
variable_value = os.environ.get(env_key)
if VARIABLE_DELIMITER in variable_value:
variable_value = [x for x in variable_value.split(VARIABLE_DELIMITER) if x]
Logger.log_task_event(GENERATE_INPUTS_TASK, "Value of {}:\n{}".format(variable_name, variable_value))
return variable_value
def pipe_log(message, status=TaskStatus.RUNNING):
global api_token
global api_url
global script_path
global current_run_id
if api_url and api_token:
Logger.log_task_event(NODEUP_TASK,
'[{}] {}'.format(current_run_id, message),
run_id=current_run_id,
instance=str(current_run_id),
log_dir=script_path,
api_url=api_url,
status=status,
omit_console=True)
else:
# Log as always
logging.info(message)
# Copyright 2017-2019 EPAM Systems, Inc. (https://www.epam.com/)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from pipeline import Logger, TaskStatus
Logger.log_task_event("Task1",
"Running python pipeline",
status=TaskStatus.SUCCESS)
inputs_json_file = None
if len(sys.argv) == 1:
raise Exception('WDL file path shall be specified')
wdl_file = sys.argv[1]
if len(sys.argv) > 2:
inputs_json_file = sys.argv[2]
if not os.path.isfile(wdl_file):
raise Exception('WDL file not found: {}'.format(wdl_file))
if inputs_json_file:
Logger.log_task_event(GENERATE_INPUTS_TASK, "inputs.json file is specified explicitly {}".format(inputs_json_file))
try:
input_json_content = None
with open(inputs_json_file, 'r') as input_json:
input_json_content = input_json.read()
Logger.log_task_event(GENERATE_INPUTS_TASK, '{} file contents"\n{}'.format(inputs_json_file, input_json_content), status=TaskStatus.SUCCESS)
except Exception as e:
Logger.log_task_event(GENERATE_INPUTS_TASK, str(e), status=TaskStatus.FAILURE)
exit(1)
else:
Logger.log_task_event(GENERATE_INPUTS_TASK, "Generating WDL inputs.json from {}".format(wdl_file))
try:
subprocess.check_output('java -jar /wdltool_bin/wdltool.jar inputs {} > inputs.json'.format(wdl_file), shell=True)
