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ebi-ait / hca-ebi-dev-team

Repository for hca ebi dev team agile management. See zenhub board
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[BUG] Allow any file type to be uploaded to an upload area #275

Open mshadbolt opened 4 years ago

mshadbolt commented 4 years ago

since version 0.2.11 hca-util does not allow uploading h5ad files to hca-util upload areas.

This is most likely due to the tool trying to recognise the type and rejecting uploads if it doesn't know.

Users need to be able to upload any file type they want to so there should not be this restriction on file types.

Steps to recreate:

hca-util select <any-area>
hca-util upload <a_matrix_file>.h5ad
<a_matrix_file>.h5ad  0 / 5068859764  Upload failed.
Failed upload.
lauraclarke commented 4 years ago

@rdgoite @prabh-t it would be desirable to be able to give contributors this as a route to upload matrix files which will frequently be hdf5 files in a variety of different formats. Can this bug be investigated quickly

mshadbolt commented 4 years ago

contributors could give us lots of different file types, eg .rds, .mtx, .loom so there shouldn't be any restriction on this.

prabh-t commented 4 years ago

This was due to the last update whereby "dcp-type=data" was set as the content type when the file type wasn't able to be determined. This wasn't correct as "dcp-type=data" is meant to be the parameter part (or suffix) of the type, not the actual type. We now use the generic type "application/octet-stream" when the type cannot be determined and append "; dcp-type=data" accordingly.

lauraclarke commented 4 years ago

thanks for investigating @prabh-t how long will it take to fix?

aaclan-ebi commented 4 years ago

I believe the fIx is now in latest version of hca-util v0.2.12. Moving this to Review/QA pipeline

MightyAx commented 4 years ago

I believe this ticket can be moved to Done / In Production / Closed