Hello,
I would like to report on a Galaxy issue and the my proposed solution for it,
hopefully it will be helpful to other Galaxy users that encounter [are
encountering] the same problem.
I tried to upload to my local Galaxy a file that I has been transferred by a
FTP client.
Then, when Galaxy tried to "pull out" this file from the FTP server, the
operation failed with this traceback:
File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 403, in
<module>
__main__()
File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 392, in
__main__
add_file( dataset, registry, json_file, output_path )
File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 289, in
add_file
line_count, converted_path = sniff.convert_newlines( dataset.path,
in_place=in_place )
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 98, in
convert_newlines
shutil.move( temp_name, fname )
File "/usr/lib64/python2.6/shutil.py", line 260, in move
copy2(src, real_dst)
File "/usr/lib64/python2.6/shutil.py", line 96, in copy2
copystat(src, dst)
File "/usr/lib64/python2.6/shutil.py", line 66, in copystat
os.utime(dst, (st.st_atime, st.st_mtime))
OSError: [Errno 1] Operation not permitted:
'/home/galaxy_upload/data_upload/...'
The source file that I tried to copy had read/write permissions for all,
therefore, logically, this operation should not have failed...
I read a bit about this issue and I found out that python command shutil.move
might raise an OSError when it tries to move a file to a partition where the
user (galaxy in this case) has write permission but he is not the owner.
More specifically, the exception fails to modify the copystat data.
I have found a post suggesting to simply IGNORE this OSError that was raised
from copystat...
Therefore, I added the following "try" statement to
"galaxy-dist/lib/galaxy/datatypes/sniff.py on line 98:
try:
shutil.move( temp_name, fname )
# Return number of lines in file.
except OSError:
pass
return ( i + 1, None )
and it solved the problem completely!
This is the link to the post that I took the solution from:
http://bugs.python.org/issue1438480
I'm also attaching a modified "sniff.py".
Hopefully, this will be helpful to other galaxy developers,
Best,
Liram
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