Formatting changes

run_galaxy_workflow.py

@@ -16,16 +16,35 @@
 """
 
 import argparse
-from os import path, remove
+import logging
+from collections.abc import Mapping
 from sys import exit
-from bioblend.galaxy import GalaxyInstance
+
 from bioblend import ConnectionError
+from bioblend.galaxy import GalaxyInstance
+
+from wfexecutor import (
+    ExecutionState,
+    completion_state,
+    download_results,
+    export_results_to_data_library,
+    get_instance,
+    get_workflow_from_file,
+    get_workflow_id,
+    load_input_files,
+    process_allowed_errors,
+    produce_versions_file,
+    read_json_file,
+    read_yaml_file,
+    set_params,
+    validate_dataset_id_exists,
+    validate_file_exists,
+    validate_input_labels,
+    validate_labels,
+)
 
-from wfexecutor import *
 # Exit status:
 # 3 - history deletion problem
-#from wfexecutor import download_results, set_params, load_input_files, validate_labels, validate_input_labels, \
-#    validate_file_exists, validate_dataset_id_exists, completion_state, process_allowed_errors, produce_versions_file
 
 
 def get_args():
@@ -81,12 +100,16 @@ def get_args():
     arg_parser.add_argument('-l', '--library-name',
                             required=False,
                             default=None,
-                            help="Upload results to data library with the name specified. Results will not be downoaded locally."
+                            help=("Upload results to data library with the name specified. "
+                                  "Results will not be downloaded locally.")
                             )
     arg_parser.add_argument('--publish', action='store_true',
-                            default=False, help="Keep result history and make it public/accesible.")
+                            default=False, 
+                            help="Keep result history and make it public/accesible.")
     arg_parser.add_argument('--accessible', action='store_true',
-                            default=False, help="Keep result history and make it accessible via link only.")
+                            default=False, 
+                            help="Keep result history and make it accessible "
+                            "via link only.")
     args = arg_parser.parse_args()
     return args
 
@@ -106,14 +129,19 @@ def main():
         # Load workflows, inputs and parameters
         wf_from_json = read_json_file(args.workflow)
         if args.parameters:
-            param_data = read_yaml_file(args.parameters) if args.parameters_yaml else read_json_file(args.parameters)
+            param_data = (
+                read_yaml_file(args.parameters)
+                if args.parameters_yaml
+                else read_json_file(args.parameters)
+            )
         else:
             param_data = dict()
         inputs_data = read_yaml_file(args.yaml_inputs_path)
         allowed_error_states = {'tools': {}, 'datasets': set()}
         if args.allowed_errors is not None:
             allowed_error_states = \
-                process_allowed_errors(read_yaml_file(args.allowed_errors), wf_from_json)
+                process_allowed_errors(read_yaml_file(args.allowed_errors),
+                                       wf_from_json)
 
         # Move any simple parameters from parameters to inputs
         params_to_move = []
@@ -184,22 +212,28 @@ def main():
         if state.results is None:
             try:
                 logging.info('Running workflow {}...'.format(show_wf['name']))
-                results = gi.workflows.invoke_workflow(workflow_id=workflow_id,
-                                                       inputs=datamap,
-                                                       params=params,
-                                                       history_name=(args.history + '_results'))
+                results = gi.workflows.invoke_workflow(
+                    workflow_id=workflow_id,
+                    inputs=datamap,
+                    params=params,
+                    history_name=(args.history + '_results')
+                )
                 state.results = results
                 state.save_state()
             except Exception as ce:
-                logging.error("Failure when invoking invoke workflows: {}".format(str(ce)))
+                logging.error(
+                    "Failure when invoking invoke workflows: {}".format(str(ce))
+                )
                 raise ce
         else:
             logging.info("Invocation result present in state, resuming that invocation")
             results = state.results
 
         # Produce tool versions file
         produce_versions_file(gi=gi, workflow_from_json=wf_from_json,
-                              table_path="{}/software_versions_galaxy.txt".format(args.output_dir))
+                              table_path=(
+                                  "{}/software_versions_galaxy.txt".format(args.output_dir)
+                              ))
 
         # wait for a little while and check if the status is ok
         logging.info("Waiting for results to be available...")
@@ -265,7 +299,7 @@ def main():
             if lib_id:
                 export_results_to_data_library(gi=gi, history_id=results['history_id'], lib_id=lib_id, allowed_error_states=allowed_error_states)
             else:
-                logging.error('Library {} not found, results not uploaded to library'.args.library_name)
+                logging.error(f'Library {args.library_name} not found, results not uploaded to library')
 
         else:
         # If library name not specied then Download results
@@ -324,4 +358,3 @@ def main():
 
 if __name__ == '__main__':
     main()
-