From e2ffaf014cad6eb0a86db29b3145aa69bb5b9318 Mon Sep 17 00:00:00 2001
From: paulzierep <paul.zierep@googlemail.com>
Date: Thu, 13 Jun 2024 09:22:08 +0200
Subject: [PATCH] fix and test for fix (#115)

* fix and test for fix

* check cached server

* lint -improved exception
---
 bin/extract_galaxy_tools.py         | 15 +++++++++----
 bin/tests/test_get_public_server.py | 35 +++++++++++++++++++++++++++++
 2 files changed, 46 insertions(+), 4 deletions(-)
 create mode 100644 bin/tests/test_get_public_server.py

diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
index b0e42de0..aa71d70a 100644
--- a/bin/extract_galaxy_tools.py
+++ b/bin/extract_galaxy_tools.py
@@ -484,10 +484,17 @@ def get_all_installed_tool_ids_on_server(galaxy_url: str) -> List[str]:
     """
     galaxy_url = galaxy_url.rstrip("/")
     base_url = f"{galaxy_url}/api"
-    r = requests.get(f"{base_url}/tools", params={"in_panel": False})
-    r.raise_for_status()
-    tool_dict_list = r.json()
-    return [tool_dict["id"] for tool_dict in tool_dict_list]
+
+    try:
+        r = requests.get(f"{base_url}/tools", params={"in_panel": False})
+        r.raise_for_status()
+        tool_dict_list = r.json()
+        tools = [tool_dict["id"] for tool_dict in tool_dict_list]
+        return tools
+    except Exception as ex:
+        print(f"Server query failed with: \n {ex}")
+        print(f"Could not query tools on server {galaxy_url}, all tools from this server will be set to 0!")
+        return []
 
 
 def check_tools_on_servers(tool_ids: List[str], galaxy_server_url: str) -> int:
diff --git a/bin/tests/test_get_public_server.py b/bin/tests/test_get_public_server.py
new file mode 100644
index 00000000..a78f3225
--- /dev/null
+++ b/bin/tests/test_get_public_server.py
@@ -0,0 +1,35 @@
+######################################
+# Initial start for function based unit tests
+# need to set this up using a proper testing framework
+######################################
+
+import os
+import sys
+
+sys.path.append(os.path.dirname(os.path.dirname(os.path.realpath(__file__))))
+
+from extract_galaxy_tools import (
+    check_tools_on_servers,
+    USEGALAXY_SERVER_URLS,
+)
+
+server_url = USEGALAXY_SERVER_URLS["UseGalaxy.eu"]
+tool_ids = ["abricate"]
+
+count = check_tools_on_servers(tool_ids, server_url)
+print(count)
+
+tool_ids = ["bla"]
+count = check_tools_on_servers(tool_ids, server_url)
+print(count)
+
+server_url = "https://jolo.eu"
+tool_ids = ["bla"]
+count = check_tools_on_servers(tool_ids, server_url)
+print(count)
+
+# test the cache !
+server_url = "https://jolo.eu"
+tool_ids = ["bla", "blub"]
+count = check_tools_on_servers(tool_ids, server_url)
+print(count)