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https://github.com/chanzuckerberg/cellxgene.git
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tighten up error reporting (#1269)
* black reformat * tighten up error reporting * lint * fine tuning * additional improvements in exception handling * lint * include exception and traceback in log * fix typo
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@@ -44,9 +44,9 @@ class AnndataAdaptor(DataAdaptor):
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# try to read it. Many of these tests don't make sense for URIs (eg, extension-
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# based typing).
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if not data_locator.exists():
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raise DatasetAccessError(f"{data_locator.uri_or_path} does not exist")
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raise DatasetAccessError("does not exist")
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if not data_locator.isfile():
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raise DatasetAccessError(f"{data_locator.uri_or_path} is not a file")
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raise DatasetAccessError("is not a file")
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@staticmethod
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def file_size(data_locator):
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@@ -172,10 +172,10 @@ class AnndataAdaptor(DataAdaptor):
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)
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except MemoryError:
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raise DatasetAccessError("Out of memory - file is too large for available memory.")
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except Exception as e:
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except Exception:
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raise DatasetAccessError(
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f"{e} - file not found or is inaccessible. File must be an .h5ad object. "
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f"Please check your input and try again."
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"File not found or is inaccessible. File must be an .h5ad object. "
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"Please check your input and try again."
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)
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def _validate_and_initialize(self):
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@@ -310,9 +310,8 @@ class AnndataAdaptor(DataAdaptor):
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try:
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shape = self.get_shape()
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obs_mask = self._axis_filter_to_mask(Axis.OBS, obsFilter["obs"], shape[0])
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except (KeyError, IndexError) as e:
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raise FilterError(f"Error parsing filter: {e}") from e
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except (KeyError, IndexError):
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raise FilterError("Error parsing filter")
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with ServerTiming.time("layout.compute"):
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X_umap = scanpy_umap(self.data, obs_mask)
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normalized_layout = DataAdaptor.normalize_embedding(X_umap)
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