Mercurial > repos > tduigou > parameters_maystro_workflow_2

comparison maystro.py @ 0:f80ed73f9f9a draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:40:00 +0000
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-1:000000000000 0:f80ed73f9f9a
1 import argparse
2 import tempfile
3 import os
4 import json
5 import shutil
6
7
8 def parse_command_line_args():
9 parser = argparse.ArgumentParser(description="Maystro JSON Handler")
10
11 parser.add_argument("--distribute_json", required=True, help="true or false")
12 parser.add_argument("--json_from_workflow", required=False, nargs='+', help="JSON files from tools", default=[])
13 parser.add_argument("--json_from_user", required=False, help="User-provided JSON")
14 parser.add_argument("--json_name_mapping", required=True, help="map the real json name")
15 parser.add_argument("--output_workflow", required=True, help="JSON output for next workflow steps")
16 parser.add_argument("--output_user", required=True, help="Final JSON output to user")
17
18 return parser.parse_args()
19
20
21 def parse_file_name_mapping(mapping_str):
22 mapping = {}
23 if mapping_str:
24 for pair in mapping_str.split(','):
25 stored, original = pair.strip().split(':', 1)
26 # Strip .json from original
27 real_name = os.path.splitext(original)[0]
28 mapping[os.path.basename(stored)] = real_name
29 return mapping
30
31
32 def handle_distribute_json_false(args):
33 temp_dir = tempfile.mkdtemp(prefix="maystro_merge_")
34 print(f"[INFO] Watching temp dir for new JSONs: {temp_dir}")
35
36 try:
37 # Collect JSONs from json_from_workflow
38 initial_jsons = list(filter(os.path.isfile, args.json_from_workflow))
39 print(f"[INFO] Initial JSONs from workflow: {initial_jsons}")
40
41 # Parse filename mapping if provided
42 filename_mapping = parse_file_name_mapping(getattr(args, 'json_name_mapping', ''))
43
44 # Merge all together
45 merged = {}
46 for file_path in initial_jsons:
47 try:
48 with open(file_path, 'r') as f:
49 data = json.load(f)
50 basename = os.path.basename(file_path)
51 real_name = filename_mapping.get(basename, basename) # fallback if not in mapping
52 merged[real_name] = data
53 print(f"[INFO] Added data under key: {real_name}")
54 except json.JSONDecodeError as e:
55 print(f"[WARN] Skipping invalid JSON file {file_path}: {e}")
56
57 with open(args.output_user, "w") as f:
58 json.dump(merged, f, indent=2)
59 print(f"[INFO] Merged JSON written to: {args.output_user}")
60
61 finally:
62 print(f"[INFO] Cleaning up: {temp_dir}")
63 shutil.rmtree(temp_dir)
64
65
66 def merge_json_files(paths):
67 merged = {}
68 for path in paths:
69 try:
70 with open(path, "r") as f:
71 data = json.load(f)
72 merged.update(data)
73 except Exception as e:
74 print(f"[WARN] Skipping {path}: {e}")
75 return merged
76
77
78 def handle_distribute_json_true(args):
79 if not args.json_from_user:
80 raise ValueError("json_from_user is required when distribute_json is true")
81
82 with open(args.json_from_user, 'r') as in_f:
83 user_data = json.load(in_f)
84
85 with open(args.output_workflow, 'w') as out_f:
86 json.dump(user_data, out_f, indent=2)
87
88
89 def main():
90 args = parse_command_line_args()
91
92 if args.distribute_json.lower() == 'false':
93 handle_distribute_json_false(args)
94 else:
95 handle_distribute_json_true(args)
96
97 if __name__ == "__main__":
98 main()