Mercurial > repos > estrain > data_manager_amrfinderplus

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