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.


> --
> Shantanu

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