Mercurial > repos > tduigou > parameters_maystro_workflow_2

annotate maystro.py @ 1:813aec57e9fd draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
author tduigou
date Thu, 31 Jul 2025 08:58:02 +0000
parents 4e2ae28020f7
children
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1 import argparse
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2 import tempfile
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3 import os
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4 import json
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5 import shutil
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8 def parse_command_line_args():
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9 parser = argparse.ArgumentParser(description="Maystro JSON Handler")
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11 parser.add_argument("--distribute_json", required=True, help="true or false")
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12 parser.add_argument("--json_from_workflow", required=False, nargs='+', help="JSON files from tools", default=[])
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13 parser.add_argument("--json_from_user", required=False, help="User-provided JSON")
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14 parser.add_argument("--json_name_mapping", required=True, help="map the real json name")
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15 parser.add_argument("--output_workflow", required=True, help="JSON output for next workflow steps")
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16 parser.add_argument("--output_user", required=True, help="Final JSON output to user")
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18 return parser.parse_args()
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21 def parse_file_name_mapping(mapping_str):
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22 mapping = {}
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23 if mapping_str:
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24 for pair in mapping_str.split(','):
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25 stored, original = pair.strip().split(':', 1)
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26 # Strip .json from original
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27 real_name = os.path.splitext(original)[0]
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28 mapping[os.path.basename(stored)] = real_name
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29 return mapping
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32 def handle_distribute_json_false(args):
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33 temp_dir = tempfile.mkdtemp(prefix="maystro_merge_")
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34 print(f"[INFO] Watching temp dir for new JSONs: {temp_dir}")
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35
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36 try:
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37 # Collect JSONs from json_from_workflow
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38 initial_jsons = list(filter(os.path.isfile, args.json_from_workflow))
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39 print(f"[INFO] Initial JSONs from workflow: {initial_jsons}")
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41 # Parse filename mapping if provided
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42 filename_mapping = parse_file_name_mapping(getattr(args, 'json_name_mapping', ''))
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43
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44 # Merge all together
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45 merged = {}
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46 for file_path in initial_jsons:
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47 try:
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48 with open(file_path, 'r') as f:
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49 data = json.load(f)
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50 basename = os.path.basename(file_path)
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51 real_name = filename_mapping.get(basename, basename) # fallback if not in mapping
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52 merged[real_name] = data
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53 print(f"[INFO] Added data under key: {real_name}")
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54 except json.JSONDecodeError as e:
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55 print(f"[WARN] Skipping invalid JSON file {file_path}: {e}")
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56
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57 with open(args.output_user, "w") as f:
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58 json.dump(merged, f, indent=2)
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59 print(f"[INFO] Merged JSON written to: {args.output_user}")
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60
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61 finally:
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62 print(f"[INFO] Cleaning up: {temp_dir}")
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63 shutil.rmtree(temp_dir)
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64
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65
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66 def merge_json_files(paths):
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67 merged = {}
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68 for path in paths:
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69 try:
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70 with open(path, "r") as f:
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71 data = json.load(f)
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72 merged.update(data)
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73 except Exception as e:
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74 print(f"[WARN] Skipping {path}: {e}")
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75 return merged
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76
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77
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78 def handle_distribute_json_true(args):
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79 if not args.json_from_user:
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80 raise ValueError("json_from_user is required when distribute_json is true")
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81
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82 with open(args.json_from_user, 'r') as in_f:
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83 user_data = json.load(in_f)
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84
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85 with open(args.output_workflow, 'w') as out_f:
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86 json.dump(user_data, out_f, indent=2)
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87
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88
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89 def main():
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90 args = parse_command_line_args()
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91
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92 if args.distribute_json.lower() == 'false':
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93 handle_distribute_json_false(args)
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94 else:
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95 handle_distribute_json_true(args)
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96
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97 if __name__ == "__main__":
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98 main()