diff data_manager/omamer.py @ 0:e1502e4f8725 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/omamer.py	Wed Feb 21 19:26:53 2024 +0000
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import sys
+from pathlib import Path
+
+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": "Primates-v2.0.0.h5",
+    "Viridiplantae": "Viridiplantae-v2.0.0.h5",
+    "Metazoa": "Metazoa-v2.0.0.h5",
+    "LUCA": "LUCA-v0.2.5.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):
+    # Set output directory to default
+    output_dir = DEFAULT_OUTPUT_DIR
+
+    # Create output directory if none exists
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    # 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(output_dir, base_name)
+    download_file(url, destination_path)
+
+    data_manager_entry = {
+        "value": os.path.splitext(os.path.basename(base_name))[0],
+        "name": os.path.splitext(os.path.basename(base_name))[0],
+        "version": "2.0.2",
+        "path": str(Path(output_dir)),
+    }
+
+    # Creates a JSON dictionary representing the Data Manager configuration
+    data_manager_json = {"data_tables": {"omamer_data": [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')
+
+    args = parser.parse_args()
+
+    main(args)