--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_mlst.py	Thu Mar 12 20:06:31 2026 +0000
@@ -0,0 +1,152 @@
+#!/usr/bin/env python3
+"""
+Galaxy Data Manager for PubMLST.
+Downloads all PubMLST databases, creates a combined BLAST database,
+and writes a Galaxy-compatible data table JSON.
+"""
+
+import argparse
+import json
+import os
+import shutil
+import subprocess
+import sys
+import datetime
+from urllib.request import urlopen
+
+
+class MLSTDataManager:
+    def __init__(self, json_path: str):
+        self.json_path = json_path
+        self.extra_files_path = None
+        self.output_dir = None
+        self.timestamp = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
+        self.db_name = f"mlst_database_{self.timestamp}"
+
+    # ----------------------------------------------------------------------
+    # Galaxy JSON I/O
+    # ----------------------------------------------------------------------
+
+    def read_input_json(self):
+        """Read Galaxy input JSON and create the output directory."""
+        with open(self.json_path) as fh:
+            params = json.load(fh)
+        self.extra_files_path = params["output_data"][0]["extra_files_path"]
+        os.makedirs(self.extra_files_path, exist_ok=True)
+        self.output_dir = os.path.abspath(self.extra_files_path)
+
+    def write_output_json(self):
+        """Write the final Galaxy data manager JSON."""
+        entry = {
+            "data_tables": {
+                "mlst": [
+                    {
+                        "value": self.db_name,
+                        "name": self.db_name,
+                        "path": "mlst-db"
+                    }
+                ]
+            }
+        }
+
+        with open(self.json_path, "w") as fh:
+            json.dump(entry, fh, indent=2, sort_keys=True)
+            fh.flush()
+            os.fsync(fh.fileno())
+
+    # ----------------------------------------------------------------------
+    # Database steps
+    # ----------------------------------------------------------------------
+
+    def download_pubmlst_databases(self):
+        """Download all PubMLST databases."""
+        print("Downloading PubMLST databases...")
+        try:
+            subprocess.run(["mlst-download_pub_mlst", "-d", "pubmlst"], check=True)
+        except subprocess.CalledProcessError as e:
+            print(f"Error downloading databases: {e}")
+            sys.exit(1)
+
+    def make_blast_database(self):
+        """Build a BLAST database from the downloaded data."""
+        cwd = os.getcwd()
+        src_dir = os.path.join(cwd, "pubmlst")
+        dst_dir = os.path.join(self.output_dir, "pubmlst")
+
+        if os.path.exists(dst_dir):
+            shutil.rmtree(dst_dir)
+        shutil.move(src_dir, dst_dir)
+
+        blast_dir = os.path.join(self.output_dir, "blast")
+        os.makedirs(blast_dir, exist_ok=True)
+        blast_file = os.path.join(blast_dir, "mlst.fa")
+
+        print("Building combined FASTA for BLAST database...")
+        with open(blast_file, "a") as outfile:
+            for scheme in os.listdir(dst_dir):
+                scheme_path = os.path.join(dst_dir, scheme)
+                if os.path.isdir(scheme_path):
+                    for f in os.listdir(scheme_path):
+                        if f.endswith(".tfa"):
+                            with open(os.path.join(scheme_path, f)) as infile:
+                                for line in infile:
+                                    if "not a locus" not in line:
+                                        if line.startswith(">"):
+                                            outfile.write(f">{scheme}.{line[1:]}")
+                                        else:
+                                            outfile.write(line)
+
+        print("Running makeblastdb...")
+        subprocess.run([
+            "makeblastdb", "-hash_index",
+            "-in", blast_file, "-dbtype", "nucl",
+            "-title", "PubMLST", "-parse_seqids"
+        ], check=True)
+
+    def download_scheme_species_map(self):
+        """Fetch the scheme_species_map.tab file from GitHub."""
+        url = "https://raw.githubusercontent.com/tseemann/mlst/master/db/scheme_species_map.tab"
+        dst_file = os.path.join(self.output_dir, "scheme_species_map.tab")
+        print("Downloading scheme_species_map.tab...")
+        try:
+            with urlopen(url) as response, open(dst_file, "w") as out:
+                out.write(response.read().decode("utf-8"))
+            print("scheme_species_map.tab downloaded successfully")
+        except Exception as e:
+            print(f"Failed to retrieve scheme_species_map.tab: {e}")
+
+    # ----------------------------------------------------------------------
+    # Run
+    # ----------------------------------------------------------------------
+
+    def run(self):
+        try:
+            self.read_input_json()
+            self.download_pubmlst_databases()
+            self.make_blast_database()
+            self.download_scheme_species_map()
+        except Exception as e:
+            print(f"MLST Data Manager failed: {e}")
+        finally:
+            self.write_output_json()
+
+
+# ----------------------------------------------------------------------
+# CLI
+# ----------------------------------------------------------------------
+
+def parse_args():
+    parser = argparse.ArgumentParser(description="Galaxy Data Manager for PubMLST")
+    parser.add_argument("data_manager_json", help="Galaxy data manager JSON file")
+    return parser.parse_args()
+
+
+def main():
+    args = parse_args()
+    mgr = MLSTDataManager(args.data_manager_json)
+    mgr.run()
+
+
+if __name__ == "__main__":
+    main()
+