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https://github.com/galaxyproject/galaxy.git
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Merge branch 'release_24.0' into dev
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@@ -250,10 +250,11 @@ function onDisplay() {
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// but we're using a __vkey__ bit as a workaround
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// Only conditionally force to keep urls clean most of the time.
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if (route.path === itemUrls.value.display) {
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// @ts-ignore
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// @ts-ignore - monkeypatched router, drop with migration.
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router.push(itemUrls.value.display, { title: props.name, force: true });
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} else if (itemUrls.value.display) {
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router.push({ path: itemUrls.value.display, params: { title: props.name } });
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// @ts-ignore - monkeypatched router, drop with migration.
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router.push(itemUrls.value.display, { title: props.name });
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}
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}
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}
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@@ -4329,9 +4329,9 @@ class Npz(CompressedArchive):
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def sniff(self, filename: str) -> bool:
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try:
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npz = np.load(filename)
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if isinstance(npz, np.lib.npyio.NpzFile):
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return True
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with np.load(filename) as npz:
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if isinstance(npz, np.lib.npyio.NpzFile) and any(f.filename.endswith(".npy") for f in npz.zip.filelist):
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return True
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except Exception:
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return False
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return False
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@@ -90,6 +90,7 @@ from galaxy.tools.parameters import (
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visit_input_values,
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)
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from galaxy.tools.parameters.basic import (
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ConnectedValue,
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DataCollectionToolParameter,
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DataToolParameter,
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RuntimeValue,
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@@ -1520,12 +1521,12 @@ class WorkflowContentsManager(UsesAnnotations):
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if name:
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input_dicts.append({"name": name, "description": annotation_str})
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for name, val in step_state.items():
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if isinstance(val, RuntimeValue):
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if isinstance(val, RuntimeValue) and not isinstance(val, ConnectedValue):
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input_dicts.append({"name": name, "description": f"runtime parameter for tool {module.get_name()}"})
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elif isinstance(val, dict):
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# Input type is described by a dict, e.g. indexed parameters.
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for partval in val.values():
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if isinstance(partval, RuntimeValue):
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if isinstance(partval, RuntimeValue) and not isinstance(val, ConnectedValue):
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input_dicts.append(
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{"name": name, "description": f"runtime parameter for tool {module.get_name()}"}
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)
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