Mercurial > repos > tduigou > parameters_maystro_workflow_1
view maystro.py @ 0:c4f98010d9ac draft default tip
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author | tduigou |
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date | Wed, 23 Jul 2025 09:40:14 +0000 |
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import argparse import tempfile import os import json import shutil def parse_command_line_args(): parser = argparse.ArgumentParser(description="Maystro JSON Handler") parser.add_argument("--distribute_json", required=True, help="true or false") parser.add_argument("--json_from_workflow", required=False, nargs='+', help="JSON files from tools", default=[]) parser.add_argument("--json_from_user", required=False, help="User-provided JSON") parser.add_argument("--json_name_mapping", required=True, help="map the real json name") parser.add_argument("--output_workflow", required=True, help="JSON output for next workflow steps") parser.add_argument("--output_user", required=True, help="Final JSON output to user") return parser.parse_args() def parse_file_name_mapping(mapping_str): mapping = {} if mapping_str: for pair in mapping_str.split(','): stored, original = pair.strip().split(':', 1) # Strip .json from original real_name = os.path.splitext(original)[0] mapping[os.path.basename(stored)] = real_name return mapping def handle_distribute_json_false(args): temp_dir = tempfile.mkdtemp(prefix="maystro_merge_") print(f"[INFO] Watching temp dir for new JSONs: {temp_dir}") try: # Collect JSONs from json_from_workflow initial_jsons = list(filter(os.path.isfile, args.json_from_workflow)) print(f"[INFO] Initial JSONs from workflow: {initial_jsons}") # Parse filename mapping if provided filename_mapping = parse_file_name_mapping(getattr(args, 'json_name_mapping', '')) # Merge all together merged = {} for file_path in initial_jsons: try: with open(file_path, 'r') as f: data = json.load(f) basename = os.path.basename(file_path) real_name = filename_mapping.get(basename, basename) # fallback if not in mapping merged[real_name] = data print(f"[INFO] Added data under key: {real_name}") except json.JSONDecodeError as e: print(f"[WARN] Skipping invalid JSON file {file_path}: {e}") with open(args.output_user, "w") as f: json.dump(merged, f, indent=2) print(f"[INFO] Merged JSON written to: {args.output_user}") finally: print(f"[INFO] Cleaning up: {temp_dir}") shutil.rmtree(temp_dir) def merge_json_files(paths): merged = {} for path in paths: try: with open(path, "r") as f: data = json.load(f) merged.update(data) except Exception as e: print(f"[WARN] Skipping {path}: {e}") return merged def handle_distribute_json_true(args): if not args.json_from_user: raise ValueError("json_from_user is required when distribute_json is true") with open(args.json_from_user, 'r') as in_f: user_data = json.load(in_f) with open(args.output_workflow, 'w') as out_f: json.dump(user_data, out_f, indent=2) def main(): args = parse_command_line_args() if args.distribute_json.lower() == 'false': handle_distribute_json_false(args) else: handle_distribute_json_true(args) if __name__ == "__main__": main()