From 0bc028d53027d1146e74b8f1dbc2ccd92498e7dd Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Fri, 21 May 2021 15:38:22 +0200
Subject: [PATCH] uncomment invoke_wf
---
run_workflow_phaeoexplorer.py | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 661ea13..9ac3f23 100755
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -987,12 +987,13 @@ if __name__ == "__main__":
args = parser.parse_args()
+ bioblend_logger = logging.getLogger("bioblend")
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
+ bioblend_logger.setLevel(logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
- logging.getLogger("urllib3").setLevel(logging.INFO)
- logging.getLogger("bioblend").setLevel(logging.INFO)
+ bioblend_logger.setLevel(logging.INFO)
# Parsing the config file if provided, using the default config otherwise
if not args.config:
@@ -1000,6 +1001,12 @@ if __name__ == "__main__":
else:
args.config = os.path.abspath(args.config)
+ if args.config:
+ config_file = os.path.abspath(args.config)
+ else:
+ config_file = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])), constants.DEFAULT_CONFIG)
+ config = utilities.parse_config(config_file)
+
if not args.main_directory:
args.main_directory = os.getcwd()
else:
@@ -1190,7 +1197,7 @@ if __name__ == "__main__":
logging.warning("Error finding workflow %s" % workflow_name)
# Finally, invoke the workflow alogn with its datamap, parameters and the history in which to invoke it
- # instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
+ instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
logging.info("Successfully imported and invoked workflow {0}, check the galaxy instance ({1}) for the jobs state".format(workflow_name, instance_url))
@@ -1426,7 +1433,7 @@ if __name__ == "__main__":
logging.warning("Error finding workflow %s" % workflow_name)
# Finally, invoke the workflow alogn with its datamap, parameters and the history in which to invoke it
- # instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
+ instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
logging.info("Successfully imported and invoked workflow {0}, check the galaxy instance ({1}) for the jobs state".format(workflow_name, instance_url))
@@ -1541,7 +1548,7 @@ if __name__ == "__main__":
logging.warning("Error finding workflow %s" % workflow_name)
# Finally, invoke the workflow alogn with its datamap, parameters and the history in which to invoke it
- # instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
+ instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
logging.info("Successfully imported and invoked workflow {0}, check the galaxy instance ({1}) for the jobs state".format(workflow_name, instance_url))
@@ -1695,7 +1702,7 @@ if __name__ == "__main__":
logging.warning("Error finding workflow %s" % workflow_name)
# Finally, invoke the workflow alogn with its datamap, parameters and the history in which to invoke it
- # instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
+ instance.workflows.invoke_workflow(workflow_id=workflow_id, history_id=history_id, params=workflow_parameters, inputs=datamap, allow_tool_state_corrections=True)
logging.info("Successfully imported and invoked workflow {0}, check the galaxy instance ({1}) for the jobs state".format(workflow_name, instance_url))
--
GitLab