From 19bfc0e77ca193e81bf375baccd68a143882b02f Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 24 Mar 2026 18:27:35 +0100
Subject: [PATCH 1/2] fix and update the omamer DM

fixes https://github.com/galaxyproject/tools-iuc/issues/6585

the new links match sha256 of the current data available at eu
the `value` for the datasets All.Jul2023 is unchanges, only name (now date
+ name) and version (now the date contained in the link) differs.
---
 .../data_manager/macros.xml                   | 12 ---
 .../data_manager/omamer.py                    | 86 -------------------
 .../data_manager/omamer.xml                   | 64 ++++++++++----
 .../data_manager_omamer/test-data/2024.json   | 12 +++
 .../data_manager_omamer/test-data/out.json    |  6 +-
 5 files changed, 61 insertions(+), 119 deletions(-)
 delete mode 100644 data_managers/data_manager_omamer/data_manager/macros.xml
 delete mode 100644 data_managers/data_manager_omamer/data_manager/omamer.py
 create mode 100644 data_managers/data_manager_omamer/test-data/2024.json

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 @@
-
-<macros>
-    <token name="@TOOL_VERSION@">2.0.2</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="3.11">python</requirement>
-            <requirement type="package" version="2.27.1">requests</requirement>
-        </requirements>
-    </xml>
-</macros>
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..862a339ee10 100644
--- a/data_managers/data_manager_omamer/data_manager/omamer.xml
+++ b/data_managers/data_manager_omamer/data_manager/omamer.xml
@@ -1,24 +1,49 @@
-<tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
-    <macros>
-        <import>macros.xml</import>
-    </macros>
+<tool id="data_manager_omamer" name="OMAmer data manager" version="2.0.3+galaxy0" tool_type="manage_data" profile="24.2">
+    <requirements>
+        <requirement type="package" version="1.25.0">wget</requirement>
+    </requirements>
     <version_command></version_command>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/omamer.py'
-        --name '$name'
-        --json '$output_file'
-        --version '@TOOL_VERSION@'
+        mkdir '$output_file.extra_files_path'/ &&
+        cd '$output_file.extra_files_path' &&
+        wget https://omabrowser.org/${name}.h5 &&
+        cp '$dmjson' '$output_file'
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#set $version, $basename = str($name).split("/")
+## handling of 'legacy' data (2.0.2 of the DM used different values which we keep here)
+#if $version == "All.Jul2023"
+    #set $value = $basename + ".h5"
+#else
+    #set $value = $basename.replace("/", '-')
+#end if
+{
+  "data_tables": {
+    "omamer": [
+      {
+        "name": "$version $basename",
+        "path": "${basename}.h5",
+        "value": "$value",
+        "version": "$version"
+      }
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="output_dir" type="text" label="Output Directory" value=""/>
         <param name="name" type="select" label="Database">
-            <option value="Primates_v2.0.0">Primates_v2.0.0</option>
-            <option value="Viridiplantae_v2.0.0">Viridiplantae_v2.0.0</option>
-            <option value="Metazoa_v2.0.0">Metazoa_v2.0.0</option>
-            <option value="LUCA_v0.2.5">LUCA_v0.2.5</option>
-            <option value="LUCA_v2.0.0">LUCA_v2.0.0</option>
-            <option value="Saccharomyceta">Saccharomyceta</option>
-            <option value="Homininae">Homininae</option>
+            <option value="All.Jul2024/LUCA">All.Jul2024 LUCA</option>
+            <option value="All.Jul2024/Primates">All.Jul2024 Primates (only for testing the DM???)</option>
+
+            <option value="All.Jul2023/Primates-v2.0.0">All.Jul2023 Primates_v2.0.0</option>
+            <option value="All.Jul2023/Viridiplantae-v2.0.0">All.Jul2023 Viridiplantae_v2.0.0</option>
+            <option value="All.Jul2023/Metazoa-v2.0.0">All.Jul2023 Metazoa_v2.0.0</option>
+            <option value="All.Jul2023/LUCA-v0.2.5">All.Jul2023 LUCA_v0.2.5</option>
+            <option value="All.Jul2023/LUCA-v2.0.0">All.Jul2023 LUCA_v2.0.0</option>
+            <option value="All.Jul2023/Saccharomyceta">All.Jul2023 Saccharomyceta</option>
+            <option value="All.Jul2023/Homininae">All.Jul2023 Homininae</option>
         </param>
     </inputs>
 
@@ -28,10 +53,13 @@
 
     <tests>
         <test>
-            <param name="output_dir" value="test_galaxy"/>
-            <param name="name" value="Primates_v2.0.0"/>
+            <param name="name" value="All.Jul2023/Primates-v2.0.0"/>
             <output name="output_file" file="out.json"/>
         </test>
+        <test>
+            <param name="name" value="All.Jul2024/Primates"/>
+            <output name="output_file" file="2024.json"/>
+        </test>
     </tests>
 
     <help><![CDATA[
diff --git a/data_managers/data_manager_omamer/test-data/2024.json b/data_managers/data_manager_omamer/test-data/2024.json
new file mode 100644
index 00000000000..aeed3e01136
--- /dev/null
+++ b/data_managers/data_manager_omamer/test-data/2024.json
@@ -0,0 +1,12 @@
+{
+  "data_tables": {
+    "omamer": [
+      {
+        "name": "All.Jul2024 Primates",
+        "path": "Primates.h5",
+        "value": "Primates",
+        "version": "All.Jul2024"
+      }
+    ]
+  }
+}
diff --git a/data_managers/data_manager_omamer/test-data/out.json b/data_managers/data_manager_omamer/test-data/out.json
index 8498ef61f79..761ab8e94c9 100644
--- a/data_managers/data_manager_omamer/test-data/out.json
+++ b/data_managers/data_manager_omamer/test-data/out.json
@@ -2,11 +2,11 @@
   "data_tables": {
     "omamer": [
       {
-        "name": "Primates-v2.0.0",
+        "name": "All.Jul2023 Primates-v2.0.0",
         "path": "Primates-v2.0.0.h5",
         "value": "Primates-v2.0.0.h5",
-        "version": "2.0.2"
+        "version": "All.Jul2023"
       }
     ]
   }
-}
\ No newline at end of file
+}

From b6c9fce190fad611e03f55eb0b3585fd4d1b3a98 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 26 Mar 2026 17:32:55 +0100
Subject: [PATCH 2/2] try curl

---
 data_managers/data_manager_omamer/data_manager/omamer.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/data_managers/data_manager_omamer/data_manager/omamer.xml b/data_managers/data_manager_omamer/data_manager/omamer.xml
index 862a339ee10..dace8599178 100644
--- a/data_managers/data_manager_omamer/data_manager/omamer.xml
+++ b/data_managers/data_manager_omamer/data_manager/omamer.xml
@@ -5,8 +5,7 @@
     <version_command></version_command>
     <command detect_errors="exit_code"><![CDATA[
         mkdir '$output_file.extra_files_path'/ &&
-        cd '$output_file.extra_files_path' &&
-        wget https://omabrowser.org/${name}.h5 &&
+        curl https://omabrowser.org/${name}.h5 -o '$output_file.extra_files_path/${name}.h5' &&
         cp '$dmjson' '$output_file'
     ]]></command>
     <configfiles>