Revert "Revert "Partial support for subworkflows (#24)""

This reverts commit 554d585.

generate_params_from_workflow.py

@@ -82,6 +82,12 @@ def main():
             if str(value['label']) != 'None':
                 step_id = key
                 step_name = value['label']
+                # check for nested workflows
+                # don't need to extract anything as all parameters in nested wfs
+                # are set explicitly from the outer workflow
+                # TODO in the future, deal with parameters for steps of inner workflows to be able to set them.
+                if show_wf['steps'][step_id]['type'] == 'subworkflow':
+                    continue
                 content = show_wf['steps'][step_id]['tool_inputs']
                 if 'parameter_type' in content:
                     # treat simple input parameters differently

run_galaxy_workflow.py

@@ -16,7 +16,7 @@
 """
 
 import argparse
-import os.path
+from os import path, remove
 from sys import exit
 from bioblend.galaxy import GalaxyInstance
 from bioblend import ConnectionError
@@ -194,8 +194,8 @@ def main():
 
         # Produce tool versions file
         produce_versions_file(gi=gi, workflow_from_json=wf_from_json,
-                              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...")
         logging.info("...in the mean time, you can check {}/histories/view?id={} for progress."
@@ -302,5 +302,3 @@ def main():
 if __name__ == '__main__':
     main()
 
-
-

wfexecutor/__init__.py

@@ -402,22 +402,32 @@ def process_allowed_errors(allowed_errors_dict, wf_from_json):
 
     return allowed_errors_state
 
-def produce_versions_file(gi, workflow_from_json, path):
+def produce_versions_file(gi, workflow_from_json, table_path, tools_dict=[]):
     """
     Produces a tool versions file for the workflow run.
 
     :param gi:
     :param workflow_from_json:
-    :param path: path where to save the versions file
+    :param table_path: path where to save the versions file
+    :param tools_dict: list of tools used in the workflow
     :return:
     """
+    # remove file if exists already; but not in recursive case
+    if os.path.exists(table_path) and not tools_dict:
+        os.remove(table_path)
 
-    tools_dict = []
-
-    with open(file=path, mode="w") as f:
-        f.write("\t".join(["Analysis", "Software", "Version", "Citation"])+"\n")
+    with open(file=table_path, mode="a") as f:
+        # write header only if file is empty
+        if os.stat(table_path).st_size == 0:
+            f.write("\t".join(["Analysis", "Software", "Version", "Citation"])+"\n")
 
         for key, step in sorted(workflow_from_json['steps'].items(), reverse=True):
+            # parse sub-workflows recursively
+            if "subworkflow" in step.keys():
+                subworkflow = step['subworkflow']
+                produce_versions_file(gi, subworkflow, table_path, tools_dict)
+                # subworkflows don't have meaningful tool ids
+                continue
             # Input steps won't have tool ids, and we only need each tool once.
             if step['tool_id'] is not None and step['tool_id'] not in tools_dict:
                 tool = gi.tools.show_tool(step['tool_id'])