Need help with "Upload File" tool

Question: Need help with "Upload File" tool

4.0 years ago by

devi.jaganathan • 0

United States

devi.jaganathan • 0 wrote:

I am unable to upload file size of 10.7 and 10.2 GB. It ended up in error thrice. I used filezilla ( FTP) to upload

could someone help me with this error

Thanks,

Devi

Tool name: Upload File
Tool version: 1.1.4
Tool ID: upload1

upload-file • 1.3k views

ADD COMMENT • link •

modified 4.0 years ago by Martin Čech ♦♦ 4.9k • written 4.0 years ago by devi.jaganathan • 0

Could you let us know what exactly the error stated?

ADD REPLY • link written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k

Hi Daniel,

this was the error generated:

Traceback (most recent call last):
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 407, in <module>
    __main__()
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 396, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 134, in add_file
    chunk = gzipped_file.read( CHUNK_SIZE )
  File "/galaxy/main/python/lib/python2.7/gzip.py", line 261, in read
    self._read(readsize)
  File "/galaxy/main/python/lib/python2.7/gzip.py", line 312, in _read
    uncompress = self.decompress.decompress(buf)
zlib.error: Error -3 while decompressing: invalid literal/length code

Thanks,

Devi

ADD REPLY • link written 4.0 years ago by devi.jaganathan • 0

Is this hapenning to both files or only to one? Your archive might be corrupted. I would try unzipping it locally and if it works uploading it to the FTP folder again.

ADD REPLY • link modified 4.0 years ago • written 4.0 years ago by Martin Čech ♦♦ 4.9k

Hi i actually had four files, two got uploaded (file size 5.4 and 5.2), the file size with 10.2 and 10.7 both dint get uploaded. However i can see the files when i login but not able to import to history.

I tried uploading it thrice but dint seem to work.

And also i was wondering what do you mean by archive corrupted (how can i correct it)

Thanks,

Devi

ADD REPLY • link modified 4.0 years ago • written 4.0 years ago by devi.jaganathan • 0

The error message states that there was a problem decompressing. I assume that you are trying to import a compressed file (an archive) from your FTP folder and Galaxy is failing to decompress it. This would be most probably caused by the archive itself because Galaxy uses standard implementation of decompressing.

If you have the file locally please try to decompress it on your machine to see whether it is possible to decompress it at all.

ADD REPLY • link written 4.0 years ago by Martin Čech ♦♦ 4.9k

Hi sorry i am not able to decompress it on my machine (i have the data in hard drive). The file type is "IZArc GZ Archive (.gz)"

could you please tell me how to decompress this type of files

ADD REPLY • link written 4.0 years ago by devi.jaganathan • 0

What OS are you using? Is the data publicly available?

ADD REPLY • link written 4.0 years ago by Martin Čech ♦♦ 4.9k

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