--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/omamer.py	Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import sys
+
+import requests
+
+# URL for downloading OMAmer datasets
+OMAMER_DATASETS_URL = "https://omabrowser.org/All/{dataset}"
+
+# List of OMAmer data sets with versions
+OMAMER_DATASETS = {
+    "Primates_v2.0.0": "Primates-v2.0.0.h5",
+    "Viridiplantae_v2.0.0": "Viridiplantae-v2.0.0.h5",
+    "Metazoa_v2.0.0": "Metazoa-v2.0.0.h5",
+    "LUCA_v0.2.5": "LUCA-v0.2.5.h5",
+    "LUCA_v2.0.0": "LUCA-v2.0.0.h5",
+    "Saccharomyceta": "Saccharomyceta.h5",
+    "Homininae": "Homininae.h5",
+}
+
+DEFAULT_OUTPUT_DIR = "database_omamer"
+
+
+def download_file(url, dest):
+    try:
+        with requests.get(url, stream=True) as r:
+            r.raise_for_status()
+            with open(dest, 'wb') as f:
+                for chunk in r.iter_content(chunk_size=8192):
+                    f.write(chunk)
+        print(f"Downloaded: {url} to {dest}")
+    except requests.exceptions.RequestException as e:
+        print(f"Error downloading {url}: {e}")
+        sys.exit(1)
+
+
+def main(args):
+
+    with open(args.json) as fh:
+        params = json.load(fh)
+    target_directory = params["output_data"][0]["extra_files_path"]
+
+    # Create output directory if none exists
+    if not os.path.exists(target_directory):
+        os.makedirs(target_directory)
+
+    # Check if the selected dataset exists
+    if args.name not in OMAMER_DATASETS:
+        print(f"Error: Selected dataset '{args.name}' not found.")
+        sys.exit(1)
+
+    # Download the selected OMAmer dataset
+    dataset = OMAMER_DATASETS[args.name]
+    url = OMAMER_DATASETS_URL.format(dataset=dataset)
+    base_name = os.path.splitext(dataset)[0]
+    destination_path = os.path.join(target_directory, dataset)
+    download_file(url, destination_path)
+
+    data_manager_entry = {
+        "value": dataset,
+        "name": base_name,
+        "version": args.version,
+        "path": dataset,
+    }
+
+    # Creates a JSON dictionary representing the Data Manager configuration
+    data_manager_json = {"data_tables": {"omamer": [data_manager_entry]}}
+
+    # Writes this JSON dictionary to the specified output file
+    with open(args.json, "w") as fh:
+        json.dump(data_manager_json, fh, indent=2, sort_keys=True)
+
+
+if __name__ == "__main__":
+    # Set up argparse to specify expected command line arguments
+    parser = argparse.ArgumentParser(description='Download data for OMAmer')
+    parser.add_argument('--name', default='Primates', choices=OMAMER_DATASETS.keys(), help='Select dataset to download')
+    parser.add_argument('--json', help='Path to JSON file')
+    parser.add_argument("--version", help="Omamer version")
+
+    args = parser.parse_args()
+
+    main(args)