Problem with "upload file" tool on file uploaded through FTP server
Hi everyone, my local installation of Galaxy has an issue with using the "Upload File" tool on data that was uploaded to the ftp server. The ftp upload itself works fine: -rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa but there seems to be some issue with Galaxy moving it and I have no clue where the problem is. The final dataset /galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a file, but empty: -rw-rw-r--. 1 galaxy galaxy 0 2012-08-16 13:53 dataset_24020.dat I'm grateful for any hints. Best regards, Sarah ----- Forwarded Message ----- From: diehl@immunbio.mpg.de To: diehl@immunbio.mpg.de, diehl@immunbio.mpg.de Sent: Thursday, August 16, 2012 1:55:04 PM Subject: Galaxy tool error report from diehl@immunbio.mpg.de GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "xxx" ----------------------------------------------------------------------------- This is in reference to dataset id 24020 from history id 1393 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 115: 28S_rRNA.fa by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. xxx ----------------------------------------------------------------------------- The user 'diehl@immunbio.mpg.de' provided the following information: ----------------------------------------------------------------------------- job id: 20566 tool id: upload1 ----------------------------------------------------------------------------- job command line: python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server /galaxy/galaxy_server/database/tmp/tmpw_TcHa /galaxy/galaxy_server/database/tmp/tmpKwHCcx 24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/galaxy/galaxy_server/tools/data_source/upload.py", line 403, in <module> __main__() File "/galaxy/galaxy_server/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/galaxy/galaxy_server/tools/data_source/upload.py", line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py", line 98, in convert_newlines shutil.move( temp_name, fname ) File "/usr/local/lib/python2.7/shutil.py", line 299, in move copy2(src, real_dst) File "/usr/local/lib/python2.7/shutil.py", line 129, in copy2 copystat(src, dst) File "/usr/local/lib/python2.7/shutil.py", line 98, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/galaxy/galaxy_server/database/ftp/diehl@immunbio.mpg.de/28S_rRNA.fa' ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).
So, I fixed the problem myself ;-). For whatever reason the files need to be owned by the galaxy user. I achieved that by setting SQLDefaultUID 501 SQLDefaultGID 501 in the proftpd.conf. 501 is the UID and GID of the galaxy user and group. ----- Original Message ----- From: "Sarah Diehl" <diehl@immunbio.mpg.de> To: "galaxy-dev@lists.bx.psu.edu List" <galaxy-dev@lists.bx.psu.edu> Sent: Thursday, August 16, 2012 2:24:53 PM Subject: [galaxy-dev] Problem with "upload file" tool on file uploaded through FTP server Hi everyone, my local installation of Galaxy has an issue with using the "Upload File" tool on data that was uploaded to the ftp server. The ftp upload itself works fine: -rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa but there seems to be some issue with Galaxy moving it and I have no clue where the problem is. The final dataset /galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a file, but empty: -rw-rw-r--. 1 galaxy galaxy 0 2012-08-16 13:53 dataset_24020.dat I'm grateful for any hints. Best regards, Sarah ----- Forwarded Message ----- From: diehl@immunbio.mpg.de To: diehl@immunbio.mpg.de, diehl@immunbio.mpg.de Sent: Thursday, August 16, 2012 1:55:04 PM Subject: Galaxy tool error report from diehl@immunbio.mpg.de GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "xxx" ----------------------------------------------------------------------------- This is in reference to dataset id 24020 from history id 1393 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 115: 28S_rRNA.fa by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. xxx ----------------------------------------------------------------------------- The user 'diehl@immunbio.mpg.de' provided the following information: ----------------------------------------------------------------------------- job id: 20566 tool id: upload1 ----------------------------------------------------------------------------- job command line: python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server /galaxy/galaxy_server/database/tmp/tmpw_TcHa /galaxy/galaxy_server/database/tmp/tmpKwHCcx 24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/galaxy/galaxy_server/tools/data_source/upload.py", line 403, in <module> __main__() File "/galaxy/galaxy_server/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/galaxy/galaxy_server/tools/data_source/upload.py", line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py", line 98, in convert_newlines shutil.move( temp_name, fname ) File "/usr/local/lib/python2.7/shutil.py", line 299, in move copy2(src, real_dst) File "/usr/local/lib/python2.7/shutil.py", line 129, in copy2 copystat(src, dst) File "/usr/local/lib/python2.7/shutil.py", line 98, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/galaxy/galaxy_server/database/ftp/diehl@immunbio.mpg.de/28S_rRNA.fa' ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Sarah Diehl