On Jan 14, 2013, at 11:45 PM, Shantanu Pavgi (Campus) wrote: > > On Jan 9, 2013, at 12:41 PM, Nate Coraor wrote: > >> Hi Shantanu, >> >> The code in question is actually in the upload tool, >> tools/data_source/upload.py. In general, you should be able to minimize the >> number of copy and delete steps if you put new_file_path, file_path, and >> ftp_upload_dir in the same filesystem. >> >> --nate >> > > Thanks for the reply Nate. I understand that both data libraries and FTP > upload methods call upload tool, but I am not following how it is being > called by them. For example, FTP upload seems to be doing newline conversion > as mentioned earlier, whereas, data library seems to be skipping it (or doing > it in a different manner, i.e., not in-place??). Which files should I be > looking at to follow FTP and data library upload calls to understand such > differences?
Data library uploads, if instructed not to copy data in to Galaxy, will not modify the file on disk. The code from the library side begins at lib/galaxy/webapps/galaxy/controllers/library_common.py, and then moves through lib/galaxy/tools/actions/upload_common.py, where the library upload becomes a job. From there it goes to the job running system, where tools/data_source/upload.py is executed. --nate > > -- > Shantanu ___________________________________________________________ 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/
