diff --git a/data_managers/data_manager_omamer/data_manager/macros.xml b/data_managers/data_manager_omamer/data_manager/macros.xml
deleted file mode 100644
index 0ae6f5e06cf..00000000000
--- a/data_managers/data_manager_omamer/data_manager/macros.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-
- 2.0.2
- 2
-
-
-
- python
- requests
-
-
-
diff --git a/data_managers/data_manager_omamer/data_manager/omamer.py b/data_managers/data_manager_omamer/data_manager/omamer.py
deleted file mode 100644
index c819f0077e1..00000000000
--- a/data_managers/data_manager_omamer/data_manager/omamer.py
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/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)
diff --git a/data_managers/data_manager_omamer/data_manager/omamer.xml b/data_managers/data_manager_omamer/data_manager/omamer.xml
index 1359137beaf..dace8599178 100644
--- a/data_managers/data_manager_omamer/data_manager/omamer.xml
+++ b/data_managers/data_manager_omamer/data_manager/omamer.xml
@@ -1,24 +1,48 @@
-
-
- macros.xml
-
+
+
+ wget
+
+
+
+
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-
-
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@@ -28,10 +52,13 @@
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