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use fsspec.download for S3 artifacts + additional logging (#2536)

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This commit is contained in:
Emanuele Bezzi
2022-07-29 11:05:36 +00:00
committed by GitHub
parent 6c86216f6b
commit d2b20129f7
2 changed files with 8 additions and 5 deletions
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server/common/utils/data_locator.py
+2 -3
View File
@@ -113,10 +113,9 @@ class DataLocator:
# do our best to create a file with the same. # do our best to create a file with the same.
ext = os.path.splitext(self.path) ext = os.path.splitext(self.path)
suffix = None if ext[1] == "" else ext[1] suffix = None if ext[1] == "" else ext[1]
with self.open() as src, tempfile.NamedTemporaryFile(prefix="cellxgene_", suffix=suffix, delete=False) as tmp: with tempfile.NamedTemporaryFile(prefix="cellxgene_", suffix=suffix, delete=False) as tmp:
tmp.write(src.read()) self.fs.download(self.uri_or_path, tmp.name)
tmp.close() tmp.close()
src.close()
tmp_path = tmp.name tmp_path = tmp.name
return LocalFilePath(tmp_path, delete=True) return LocalFilePath(tmp_path, delete=True)
server/data_anndata/anndata_adaptor.py
+6 -2
View File
@@ -174,10 +174,14 @@ class AnndataAdaptor(DataAdaptor):
except MemoryError: except MemoryError:
raise DatasetAccessError("Out of memory - file is too large for available memory.") raise DatasetAccessError("Out of memory - file is too large for available memory.")
except Exception: except Exception:
raise DatasetAccessError( import traceback
message = (
"File not found or is inaccessible. File must be an .h5ad object. " "File not found or is inaccessible. File must be an .h5ad object. "
"Please check your input and try again." "Please check your input and try again."
) )
if self.server_config.app__verbose:
message += f"\n{traceback.format_exc()}"
raise DatasetAccessError(message)
def _validate_and_initialize(self): def _validate_and_initialize(self):
if anndata_version_is_pre_070(): if anndata_version_is_pre_070():