Error getting display data for dataset

[innovate-invent]

Galaxy 20.09. I encountered this exception while trying to download a dataset.

galaxy.webapps.galaxy.api.datasets ERROR 2021-02-04 21:56:10,169 [p:33,w:1,m:0] [uWSGIWorker1Core2] Error getting display data for dataset (645e48ac270ad0b4) from history (9b56708fd00f54a7)
Traceback (most recent call last):
  File "/srv/galaxy/lib/galaxy/webapps/galaxy/api/datasets.py", line 422, in display
    rval = hda.datatype.display_data(trans, hda, preview, filename, to_ext, **display_kwd)
  File "/srv/galaxy/lib/galaxy/datatypes/tabular.py", line 89, in display_data
    return self._serve_raw(trans, dataset, to_ext, **kwd)
  File "/srv/galaxy/lib/galaxy/datatypes/data.py", line 347, in _serve_raw
    trans.response.headers['Content-Length'] = int(os.stat(dataset.file_name).st_size)
FileNotFoundError: [Errno 2] No such file or directory: ''
10.0.1.237 - - [04/Feb/2021:21:56:10 +0000] "GET /api/histories/9b56708fd00f54a7/contents/645e48ac270ad0b4/display?to_ext=gff3&key=8bf3d2af3355a63e96b9865779342a95 HTTP/1.1" 500 - "-" "python-requests/2.25.1"

[mvdbeek]

Is that a new or purged dataset ?

[innovate-invent]

This is a dataset freshly generated by a workflow

[innovate-invent]

I don't know if this is related but I encountered this issue while uploading via nginx upload module:

Traceback (most recent call last):
  File "/srv/galaxy/tools/data_source/upload.py", line 342, in <module>
    __main__()
  File "/srv/galaxy/tools/data_source/upload.py", line 335, in __main__
    metadata.append(add_file(dataset, registry, output_path))
  File "/srv/galaxy/tools/data_source/upload.py", line 134, in add_file
    stdout, ext, datatype, is_binary, converted_path = handle_upload(
  File "/srv/galaxy/lib/galaxy/datatypes/upload_util.py", line 42, in handle_upload
    ext, converted_path, compression_type = sniff.handle_uploaded_dataset_file_internal(
  File "/srv/galaxy/lib/galaxy/datatypes/sniff.py", line 739, in handle_uploaded_dataset_file_internal
    is_binary = check_binary(converted_path)
  File "/srv/galaxy/lib/galaxy/util/checkers.py", line 54, in check_binary
    temp = open(name, "rb")
FileNotFoundError: [Errno 2] No such file or directory: '/data/database/tmp/upload_file_data_tqu3di8x'

I checked and the file was not actually there. I am not sure why it wouldn't be unless there was a race between two replicates trying to serve the same request or something.

[maikenp]

We see the same problem on our galaxy server, did you get it solved?

get -i 89

in the terminal in an interactive tool. Gives the same error as you showed in the Feb 4 post.

Edit: I realized that it does not work with collections, if I unhide the history, and use the ids of each file, it works. So my problem was just using the wrong id.

[innovate-invent]

This is very likely due to #11335

[mvdbeek]

I guess that should then also be fixed with #12763