update script

galaxyproject · Jun 5, 2024 · 31c3fdf · 31c3fdf
1 parent 1200b86
commit 31c3fdf
Showing 1 changed file with 12 additions and 5 deletions.
diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
@@ -28,16 +28,16 @@
 # BIOTOOLS_API_URL = "https://130.226.25.21"
 
 USEGALAXY_STAR_SERVER_URLS = {
-    "UseGalaxy.org": "https://usegalaxy.org",
+    "UseGalaxy.org (Main)": "https://usegalaxy.org",
     "UseGalaxy.org.au": "https://usegalaxy.org.au",
     "UseGalaxy.eu": "https://usegalaxy.eu",
-    "UseGalaxy.org.fr": "https://usegalaxy.fr",
+    "UseGalaxy.fr": "https://usegalaxy.fr",
 }
 
 project_path = Path(__file__).resolve().parent.parent  # galaxy_tool_extractor folder
 usage_stats_path = project_path.joinpath("data", "usage_stats")
 conf_path = project_path.joinpath("data", "conf.yml")
-public_servers = project_path.joinpath("data","available_public_servers.csv")
+public_servers = project_path.joinpath("data", "available_public_servers.csv")
 
 GALAXY_TOOL_STATS = {
     "No. of tool users (2022-2023) (usegalaxy.eu)": usage_stats_path.joinpath("tool_usage_per_user_2022_23_EU.csv"),
@@ -721,7 +721,10 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
                     file=sys.stderr,
                 )
 
+        #######################################################
         # add additional information to the List[Dict] object
+        #######################################################
+
         edam_ontology = get_ontology("https://edamontology.org/EDAM_1.25.owl").load()
 
         for tool in tools:
@@ -740,9 +743,13 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
             public_servers_df = pd.read_csv(public_servers)
             for index, row in public_servers_df.iterrows():
                 name = row["name"]
-                url = row["url"]
-                tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
 
+                if not name.lower() in [
+                    n.lower() for n in USEGALAXY_STAR_SERVER_URLS.keys()
+                ]:  # do not query UseGalaxy servers again
+
+                    url = row["url"]
+                    tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
 
         export_tools_to_json(tools, args.all_tools_json)
         export_tools_to_tsv(tools, args.all_tools, format_list_col=True, add_usage_stats=True)