Merge branch 'release_23.2' into release_24.0

galaxyproject · Mar 13, 2024 · cbe4bc7 · cbe4bc7
2 parents c72e928 + 27feb74
commit cbe4bc7
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -4329,9 +4329,9 @@ def __init__(self, **kwd):
 
     def sniff(self, filename: str) -> bool:
         try:
-            npz = np.load(filename)
-            if isinstance(npz, np.lib.npyio.NpzFile):
-                return True
+            with np.load(filename) as npz:
+                if isinstance(npz, np.lib.npyio.NpzFile) and any(f.filename.endswith(".npy") for f in npz.zip.filelist):
+                    return True
         except Exception:
             return False
         return False

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -90,6 +90,7 @@
     visit_input_values,
 )
 from galaxy.tools.parameters.basic import (
+    ConnectedValue,
     DataCollectionToolParameter,
     DataToolParameter,
     RuntimeValue,
@@ -1520,12 +1521,12 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
                 if name:
                     input_dicts.append({"name": name, "description": annotation_str})
             for name, val in step_state.items():
-                if isinstance(val, RuntimeValue):
+                if isinstance(val, RuntimeValue) and not isinstance(val, ConnectedValue):
                     input_dicts.append({"name": name, "description": f"runtime parameter for tool {module.get_name()}"})
                 elif isinstance(val, dict):
                     # Input type is described by a dict, e.g. indexed parameters.
                     for partval in val.values():
-                        if isinstance(partval, RuntimeValue):
+                        if isinstance(partval, RuntimeValue) and not isinstance(val, ConnectedValue):
                             input_dicts.append(
                                 {"name": name, "description": f"runtime parameter for tool {module.get_name()}"}
                             )