Merge branch 'dev/diego'

back-end/CLI/cli.py

@@ -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()
 
@@ -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:

back-end/pyworkflow/pyworkflow/workflow.py

@@ -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)
 
@@ -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.
         """
@@ -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)