Mercurial > repos > bgruening > create_tool_recommendation_model
diff extract_workflow_connections.py @ 4:f0da532be419 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
| author | bgruening |
|---|---|
| date | Fri, 06 May 2022 09:04:44 +0000 |
| parents | 50753817983a |
| children | 9ec705bd11cb |
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--- a/extract_workflow_connections.py Tue Jul 07 07:24:21 2020 +0000 +++ b/extract_workflow_connections.py Fri May 06 09:04:44 2022 +0000 @@ -10,7 +10,6 @@ class ExtractWorkflowConnections: - def __init__(self): """ Init method. """ @@ -33,12 +32,12 @@ workflow_paths = list() unique_paths = dict() standard_connections = dict() - with open(raw_file_path, 'rt') as workflow_connections_file: - workflow_connections = csv.reader(workflow_connections_file, delimiter='\t') + with open(raw_file_path, "rt") as workflow_connections_file: + workflow_connections = csv.reader(workflow_connections_file, delimiter="\t") for index, row in enumerate(workflow_connections): wf_id = str(row[0]) - in_tool = row[3] - out_tool = row[6] + in_tool = row[3].strip() + out_tool = row[6].strip() if wf_id not in workflows: workflows[wf_id] = list() if out_tool and in_tool and out_tool != in_tool: @@ -144,7 +143,9 @@ if end in graph: for node in graph[end]: if node not in path: - new_tools_paths = self.find_tool_paths_workflow(graph, start, node, path) + new_tools_paths = self.find_tool_paths_workflow( + graph, start, node, path + ) for tool_path in new_tools_paths: path_list.append(tool_path) return path_list