Fix invalid detection of hierarchical namespace stub blobs as files #4046
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Signed-off-by: Florian De Temmerman <[email protected]>
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@adamrtalbot Can you test this PR with an appropriate storage account? |
yep - I've created a storage account now. |
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Currently I'm unable to reproduce the problem at all. Given this is related to the reports in Tower, can you run a custom Nextflow version in Tower? |
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I thought the issue is with publishing directories to Gen2 Data Lake? So it should be independent of Tower. |
bentsherman
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pditommaso
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…extflow-io#4046) Signed-off-by: Florian De Temmerman <[email protected]>
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Using Azure Batch executor with storage account enabling hierarchical namespaces have problems publishing directories.
The problem is that for each directory azure will create an empty "stub blob" with a metadata field:
"hdi_isfolder": "true"Nextflow currently detects these as files and will create a download request for that stub blob using a directory path which will cause a BlobStorageException (Status code 400: InvalidInput)
This PR adds a simple to check to detect such blobs and mark those as directories.
Fixes: #4016, #2557