Mercurial > repos > greg > queue_genotype_workflow

changeset 4:163ecfba5961 draft

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Uploaded
author greg
date Tue, 19 Nov 2019 09:34:57 -0500
parents 36f8098ff528
children 934acc64b30c
files queue_genotype_workflow.py
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/queue_genotype_workflow.py	Mon Nov 18 11:27:29 2019 -0500
+++ b/queue_genotype_workflow.py	Tue Nov 19 09:34:57 2019 -0500
@@ -107,7 +107,7 @@
     # from the current history.
     outputfh.write("\nSearching for history dataset named %s.\n" % str(dataset_name))
     history_dataset_dicts = get_history_datasets(gi, history_id)
-    for name, hd_dict in history_dataset_dicts.items():
+    for name, hd_dict in list(history_dataset_dicts.items()):
         name = name.lower()
         if name.startswith(dataset_name.lower()):
             outputfh.write("Found dataset named %s.\n" % str(dataset_name))
@@ -171,7 +171,7 @@
     outputfh.write("\nMapping datasets from history to workflow %s.\n" % workflow_name)
     steps_dict = workflow_dict.get('steps', None)
     if steps_dict is not None:
-        for step_index, step_dict in steps_dict.items():
+        for step_index, step_dict in list(steps_dict.items()):
             # Dicts that define dataset inputs for a workflow
             # look like this.
             # "0": {
@@ -211,7 +211,7 @@
                 annotation_check = annotation.lower()
                 # inputs is a list and workflow input datasets
                 # have no inputs.
-                for input_hda_name, input_hda_dict in history_datasets.items():
+                for input_hda_name, input_hda_dict in list(history_datasets.items()):
                     input_hda_name_check = input_hda_name.lower()
                     if input_hda_name_check.find(annotation_check) >= 0:
                         workflow_inputs[step_index] = {'src': 'hda', 'id': input_hda_dict['id']}
@@ -238,7 +238,7 @@
     name = workflow_dict['name']
     outputfh.write("\nChecking for tool parameter updates for workflow %s using dbkey %s.\n" % (name, dbkey))
     step_dicts = workflow_dict.get('steps', None)
-    for step_id, step_dict in step_dicts.items():
+    for step_id, step_dict in list(step_dicts.items()):
         tool_id = step_dict['tool_id']
         if tool_id is None:
             continue