I am trying to understand how FTP and data library upload options are working in Galaxy. When a non-binary file is uploaded through FTP option, it goes through three move operations: 
 1. First it is copied to a temporary namespace line-by-line converting newlines
 2. Then the temporary file is moved back to the FTP directory with the same name [1]
 3. Later the newline sanitized FTP file is moved to datasets directory

These move operations in Python are carried as copy and delete tasks. I don't see the same approach being taken with data libraries or other file-system import/upload options. I looked at library_common code, but I couldn't follow it [2]. I was wondering if someone could help in understanding how file upload is implemented for different upload mechanisms and datatypes.

Also, can FTP upload option reduce the number of move operations? For example, can the original FTP file or temporary file copied/moved directly to the datasets directory? This will be helpful in supporting FTP-type upload where 'galaxy' user isn't the primary owner of user's files (move operations perform chmod  and it requires primary ownership).

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Thanks,
Shantanu

1. https://bitbucket.org/galaxy/galaxy-central/src/530fb4f8204f2106e11f419c381fd53d2319ce24/lib/galaxy/datatypes/sniff.py?at=default#cl-83
2. https://bitbucket.org/galaxy/galaxy-central/src/530fb4f8204f/lib/galaxy/webapps/galaxy/controllers/library_common.py?at=default