Fix wf and tutorial extraction

galaxyproject · Nov 7, 2024 · ae45d26 · ae45d26
1 parent 5d196c9
commit ae45d26
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/sources/bin/extract_all_tutorials.sh b/sources/bin/extract_all_tutorials.sh
@@ -5,7 +5,7 @@ then
         python sources/bin/extract_gtn_tutorials.py \
                 extract \
                 --all "communities/all/resources/test_tutorials.json" \
-                --tools "communities/all/resources/tools.json" \
+                --tools "communities/all/resources/test_tools.json" \
                 --api $PLAUSIBLE_API_KEY \
                 --test
 else

diff --git a/sources/bin/extract_all_workflows.sh b/sources/bin/extract_all_workflows.sh
@@ -4,7 +4,7 @@ if [ ! -z $1 ]
 then
         python sources/bin/extract_galaxy_workflows.py extract \
                 --all communities/all/resources/test_workflows.json \
-                --tools communities/all/resources/tools.json \
+                --tools communities/all/resources/test_tools.json \
                 --test
 else
         python sources/bin/extract_galaxy_workflows.py extract \

diff --git a/sources/bin/shared.py b/sources/bin/shared.py
@@ -83,11 +83,11 @@ def read_suite_per_tool_id(tool_fp: str) -> Dict:
     tool_suites = load_json(tool_fp)
     tools = {}
     for suite in tool_suites:
-        for tool in suite["Galaxy tool ids"]:
+        for tool in suite["Suite ID"]:
             tools[tool] = {
-                "Galaxy wrapper id": suite["Galaxy wrapper id"],
-                "Galaxy wrapper owner": suite["Galaxy wrapper id"],
-                "EDAM operation": suite["EDAM operation"],
+                "Suite ID": suite["Suite ID"],
+                "Suite owner": suite["Suite owner"],
+                "EDAM operations": suite["EDAM operations"],
             }
     return tools
 
@@ -154,7 +154,7 @@ def get_edam_operation_from_tools(selected_tools: list, all_tools: dict) -> List
     edam_operation = set()
     for t in selected_tools:
         if t in all_tools:
-            edam_operation.update(set(all_tools[t]["EDAM operation"]))
+            edam_operation.update(set(all_tools[t]["EDAM operations"]))
         else:
             print(f"{t} not found in all tools")
     return list(edam_operation)