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Adds verbose CLI mode option #85

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merged 5 commits into from
May 7, 2020
Merged

Adds verbose CLI mode option #85

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8088b3c
Adds changes for executing through cli with flow vars
May 5, 2020
41f2ed0
removes print statements
May 5, 2020
92a708a
Adds verbose mode to get details on which node is being executed at w…
May 5, 2020
bab5446
Adds instruction to run CLI using verbose option to README
May 5, 2020
6a454b0
Merge branch 'master' into dev/diego
diegostruk May 6, 2020
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11 changes: 7 additions & 4 deletions CLI/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,8 @@ def cli():

@cli.command()
@click.argument('filename', type=click.Path(exists=True), nargs=-1)
def execute(filename):
@click.option('--verbose', is_flag=True, help='Enables verbose mode.')
def execute(filename, verbose):

write_to_stdout = not click.get_text_stream('stdout').isatty()

Expand All @@ -45,15 +46,17 @@ def execute(filename):

stdin_files.append(file_name)



if workflow_file is None:
click.echo('Please specify a workflow to run')
return
try:
if not write_to_stdout:
click.echo('Loading workflow file from %s' % workflow_file)
Workflow.execute_workflow(workflow_file, stdin_files, write_to_stdout)

Workflow.execute_workflow(workflow_file, stdin_files, write_to_stdout, verbose)

if verbose:
click.echo('Completed workflow execution!')


except NodeException as ne:
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9 changes: 6 additions & 3 deletions pyworkflow/pyworkflow/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -590,8 +590,7 @@ def execute_write_csv(self, node_id):
try:
# Validate input data, and replace flow variables
node_to_execute.validate_input_data(len(preceding_data))
execution_options = node_to_execute.get_execution_options(flow_nodes)

execution_options = node_to_execute.get_execution_options(self, flow_nodes)
# Pass in data to current Node to use in execution
output = node_to_execute.execute(preceding_data, execution_options)

Expand All @@ -609,7 +608,7 @@ def execute_write_csv(self, node_id):
return node_to_execute

@staticmethod
def execute_workflow(workflow_location, stdin_files, write_to_stdout):
def execute_workflow(workflow_location, stdin_files, write_to_stdout, verbose_mode):
"""Execute entire workflow at a certain location.
Current use case: CLI.
"""
Expand All @@ -626,6 +625,10 @@ def execute_workflow(workflow_location, stdin_files, write_to_stdout):
#execute each node in the order returned by execution order method
#TODO exception handling: stop and provide details on which node failed to execute
for node in execution_order:

if verbose_mode:
print('Executing node of type ' + str(type(workflow_instance.get_node(node))))

if type(workflow_instance.get_node(node)) is ReadCsvNode and len(stdin_files) > 0:
csv_location = stdin_files[0]
executed_node = workflow_instance.execute_read_csv(node, csv_location)
Expand Down