Question: Fail to upload data from FTP file
0
gravatar for hzhangatus
3.5 years ago by
hzhangatus0
United States
hzhangatus0 wrote:

Dear Sir/Madam,

When I upload my fastq data about 3.5Gb by FileZilla, the status in the upload interface shows error of "Failed: Bad Request (400)".

Thanks for your help!

Looking forward to receiving your solution!

Best!

Hao

get data ftp • 1.8k views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson24k • written 3.5 years ago by hzhangatus0

That error is what you see in filezilla?  Or you see that in the Galaxy upload interface after successfully uploading the complete file via filezilla?

ADD REPLYlink written 3.5 years ago by Dannon Baker3.7k

The error occurs in the Galaxy upload interface after successfully uploading the complete file via filezilla.

ADD REPLYlink written 3.3 years ago by hzhangatus0

Does this still occur for you?  We've just recently updated this functionality.

ADD REPLYlink written 3.3 years ago by Dannon Baker3.7k

Yes, it still occur for me. Actually, I can upload data to our university's Galaxy by FileZilla, but cannot upload it to the official Galaxy, "usegalaxy.org".

ADD REPLYlink written 3.3 years ago by hzhangatus0

When I click Upload File entering to data upload interface. and click Choose FTP file, I can see the data uploaded by FileZilla. But when I choose the data and then click the start button, the error just pop up.

ADD REPLYlink written 3.3 years ago by hzhangatus0

Ok, I'll check through our logs to see if I see a failure on this side.

ADD REPLYlink written 3.3 years ago by Dannon Baker3.7k

Or I can give you my account and password to help me figure out the problem.

ADD REPLYlink written 3.3 years ago by hzhangatus0

Actually, can you open the javascript console and see if there's more of an error there when this happens for you?

ADD REPLYlink written 3.3 years ago by Dannon Baker3.7k

Thanks for you help! It's so weird that when I change a computer, then it works.

ADD REPLYlink written 3.3 years ago by hzhangatus0

Can you contact me directly with more information about which particular files you're trying to import and to what history?

I can try a few things from the admin side to help debug:  dannon.baker@gmail.com

ADD REPLYlink written 3.3 years ago by Dannon Baker3.7k

Unfortunately, the error occurs again even if I changed the computer.

The error is:

Traceback (most recent call last):
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 409, in <module>
    __main__()
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 398, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 282, in add_file
    line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
  File "/galaxy-repl/main/server/lib/galaxy/datatypes/sniff.py", line 109, in convert_newlines
    fp.write( "%s\n" % line.rstrip( "\r\n" ) )
IOError: [Errno 5] Input/output error

 

ADD REPLYlink written 3.3 years ago by hzhangatus0
0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

This appears to be an error that can be triggered when

1. the login credentials for the server are incorrect
2. the server you are attempting to FTP data to has not been set up to use FTP
3. you have FileZilla set up to use SFTP instead of FTP (FTP is the default).

How to use FTP for data upload. Note that you need to use your Galaxy registered account email address and password and if using the public Main Galaxy instance, the server URL is usegalaxy.org
http://wiki.galaxyproject.org/Support#Loading_data

If you need to set up a server to use FTP, this is explained in the admin section of our wiki. There is more to setting up a local Galaxy that has to go with it.

Please let us know if you need more help, along with more details,

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson24k
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