diff maystro.py @ 1:c6708a220f23 draft default tip

planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit e8c8f102cab10531ed588be4ecb8a0d01e797f09
author tduigou
date Tue, 06 Jan 2026 11:38:30 +0000
parents f80ed73f9f9a
children
line wrap: on
line diff
--- a/maystro.py	Wed Jul 23 09:40:00 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-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()