Mercurial > repos > estrain > data_manager_amrfinderplus

comparison data_manager/data_manager_amrfinderplus.py @ 0:2986b488a62b draft default tip

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planemo upload commit 6f89f1ec5ad85eb9c08c0d48c77b8f8eadbdcaff
author estrain
date Thu, 12 Mar 2026 19:41:57 +0000
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-1:000000000000 0:2986b488a62b
1 #!/usr/bin/env python3
2 """
3 Galaxy Data Manager for NCBI AMRFinderPlus database.
4 Downloads and indexes the AMRFinderPlus database using amrfinder_update.
5 Writes a Galaxy-compatible data table JSON.
6 """
7
8 import argparse
9 import json
10 import os
11 import shutil
12 import subprocess
13 from pathlib import Path
14
15
16 class AmrFinderPlusDataManager:
17 def __init__(self, json_path: str, db_name="amrfinderplus-db"):
18 self.json_path = Path(json_path)
19 self.db_name = db_name
20 self.output_dir = None
21 self.extra_files_path = None
22 self.version = None
23 self.dbformat = None
24
25 # --- Galaxy I/O ---------------------------------------------------------
26
27 def read_input_json(self):
28 """Read the input Galaxy data manager JSON."""
29 with open(self.json_path) as fh:
30 params = json.load(fh)
31
32 # Galaxy passes where we can write files (extra_files_path)
33 self.extra_files_path = Path(params["output_data"][0]["extra_files_path"])
34 self.extra_files_path.mkdir(parents=True, exist_ok=True)
35 self.output_dir = self.extra_files_path / "tmp_download"
36 self.output_dir.mkdir(parents=True, exist_ok=True)
37
38 def write_output_json(self):
39 """Write Galaxy data table JSON entry."""
40 entry = {
41 "data_tables": {
42 "amrfinderplus_versioned_database": [
43 {
44 "value": f"amrfinderplus_{self.version}_{self.dbformat}",
45 "name": f"{self.version} ({self.dbformat})",
46 "db_version": self.dbformat,
47 "path": self.db_name,
48 }
49 ]
50 }
51 }
52
53 # Overwrite Galaxy's job JSON atomically and flush it
54 with open(self.json_path, "w") as fh:
55 json.dump(entry, fh, indent=2, sort_keys=True)
56 fh.flush()
57 os.fsync(fh.fileno())
58
59 # --- Database logic -----------------------------------------------------
60
61 def run_amrfinder_update(self):
62 """Run amrfinder_update to download the database."""
63 print(f"Running amrfinder_update -d {self.output_dir}")
64 subprocess.run(["amrfinder_update", "-d", str(self.output_dir)], check=True)
65
66 def read_versions(self):
67 """Read version.txt and database_format_version.txt."""
68 latest_dir = self.output_dir / "latest"
69 with open(latest_dir / "version.txt") as f:
70 self.version = f.readline().strip()
71 with open(latest_dir / "database_format_version.txt") as f:
72 self.dbformat = f.readline().strip()
73
74 def copy_database(self):
75 """Copy the downloaded database to a permanent location."""
76 latest_dir = self.output_dir / "latest"
77 final_dir = self.extra_files_path / self.db_name
78 shutil.copytree(latest_dir, final_dir, dirs_exist_ok=True)
79
80 def cleanup(self):
81 """Remove temporary download folder."""
82 shutil.rmtree(self.output_dir, ignore_errors=True)
83
84 # --- Main run -----------------------------------------------------------
85
86 def run(self):
87 try:
88 self.read_input_json()
89 self.run_amrfinder_update()
90 self.read_versions()
91 self.copy_database()
92 except Exception as e:
93 print(f"AMRFinderPlus Data Manager failed: {e}")
94 # still record placeholder entry
95 self.version = "unknown"
96 self.dbformat = "unknown"
97 finally:
98 self.cleanup()
99 self.write_output_json()
100
101
102 # --- CLI entrypoint --------------------------------------------------------
103
104 def parse_args():
105 parser = argparse.ArgumentParser(description="Galaxy Data Manager for AMRFinderPlus database")
106 parser.add_argument("data_manager_json", help="Galaxy data manager input/output JSON file")
107 return parser.parse_args()
108
109
110 def main():
111 args = parse_args()
112 mgr = AmrFinderPlusDataManager(args.data_manager_json)
113 mgr.run()
114
115
116 if __name__ == "__main__":
117 main()
118