--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_amrfinderplus.py	Thu Mar 12 19:41:57 2026 +0000
@@ -0,0 +1,118 @@
+#!/usr/bin/env python3
+"""
+Galaxy Data Manager for NCBI AMRFinderPlus database.
+Downloads and indexes the AMRFinderPlus database using amrfinder_update.
+Writes a Galaxy-compatible data table JSON.
+"""
+
+import argparse
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+
+class AmrFinderPlusDataManager:
+    def __init__(self, json_path: str, db_name="amrfinderplus-db"):
+        self.json_path = Path(json_path)
+        self.db_name = db_name
+        self.output_dir = None
+        self.extra_files_path = None
+        self.version = None
+        self.dbformat = None
+
+    # --- Galaxy I/O ---------------------------------------------------------
+
+    def read_input_json(self):
+        """Read the input Galaxy data manager JSON."""
+        with open(self.json_path) as fh:
+            params = json.load(fh)
+
+        # Galaxy passes where we can write files (extra_files_path)
+        self.extra_files_path = Path(params["output_data"][0]["extra_files_path"])
+        self.extra_files_path.mkdir(parents=True, exist_ok=True)
+        self.output_dir = self.extra_files_path / "tmp_download"
+        self.output_dir.mkdir(parents=True, exist_ok=True)
+
+    def write_output_json(self):
+        """Write Galaxy data table JSON entry."""
+        entry = {
+            "data_tables": {
+                "amrfinderplus_versioned_database": [
+                    {
+                        "value": f"amrfinderplus_{self.version}_{self.dbformat}",
+                        "name": f"{self.version} ({self.dbformat})",
+                        "db_version": self.dbformat,
+                        "path": self.db_name,
+                    }
+                ]
+            }
+        }
+
+        # Overwrite Galaxy's job JSON atomically and flush it
+        with open(self.json_path, "w") as fh:
+            json.dump(entry, fh, indent=2, sort_keys=True)
+            fh.flush()
+            os.fsync(fh.fileno())
+
+    # --- Database logic -----------------------------------------------------
+
+    def run_amrfinder_update(self):
+        """Run amrfinder_update to download the database."""
+        print(f"Running amrfinder_update -d {self.output_dir}")
+        subprocess.run(["amrfinder_update", "-d", str(self.output_dir)], check=True)
+
+    def read_versions(self):
+        """Read version.txt and database_format_version.txt."""
+        latest_dir = self.output_dir / "latest"
+        with open(latest_dir / "version.txt") as f:
+            self.version = f.readline().strip()
+        with open(latest_dir / "database_format_version.txt") as f:
+            self.dbformat = f.readline().strip()
+
+    def copy_database(self):
+        """Copy the downloaded database to a permanent location."""
+        latest_dir = self.output_dir / "latest"
+        final_dir = self.extra_files_path / self.db_name
+        shutil.copytree(latest_dir, final_dir, dirs_exist_ok=True)
+
+    def cleanup(self):
+        """Remove temporary download folder."""
+        shutil.rmtree(self.output_dir, ignore_errors=True)
+
+    # --- Main run -----------------------------------------------------------
+
+    def run(self):
+        try:
+            self.read_input_json()
+            self.run_amrfinder_update()
+            self.read_versions()
+            self.copy_database()
+        except Exception as e:
+            print(f"AMRFinderPlus Data Manager failed: {e}")
+            # still record placeholder entry
+            self.version = "unknown"
+            self.dbformat = "unknown"
+        finally:
+            self.cleanup()
+            self.write_output_json()
+
+
+# --- CLI entrypoint --------------------------------------------------------
+
+def parse_args():
+    parser = argparse.ArgumentParser(description="Galaxy Data Manager for AMRFinderPlus database")
+    parser.add_argument("data_manager_json", help="Galaxy data manager input/output JSON file")
+    return parser.parse_args()
+
+
+def main():
+    args = parse_args()
+    mgr = AmrFinderPlusDataManager(args.data_manager_json)
+    mgr.run()
+
+
+if __name__ == "__main__":
+    main()
+