Re: [galaxy-dev] So I think I fixed a bug.
Hi All my bad, Error in email. the fix was else: sniff.convert_newlines( dp ) shutil.move( dp, os.path.join( files_path, name ) ) +# My fix jboocock # +os.chmod(files_path +"/" + name, 0644) tab was off Cheers James. On 8/24/2012 1:28 AM, James wrote: Hi All, diff -r ba56d4746f7a tools/data_source/upload.py --- a/tools/data_source/upload.pyFri Aug 03 13:31:48 2012 -0400 +++ b/tools/data_source/upload.pyFri Aug 24 01:26:36 2012 +1200 @@ -357,6 +357,7 @@ else: sniff.convert_newlines( dp ) shutil.move( dp, os.path.join( files_path, name ) ) +os.chmod(files_path +"/"+name, "0644") # Move the dataset to its "real" path shutil.move( dataset.primary_file, output_path ) # Write the job info Fixes permissions not been created for filenames correctly so an apache instance can access the extra files. Cheers James. Research Assistant Biochemistry Department University of Otago New Zealand ___ 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/
Re: [galaxy-dev] So I think I fixed a bug.
Hi All, diff -r ba56d4746f7a tools/data_source/upload.py --- a/tools/data_source/upload.pyFri Aug 03 13:31:48 2012 -0400 +++ b/tools/data_source/upload.pyFri Aug 24 01:26:36 2012 +1200 @@ -357,6 +357,7 @@ else: sniff.convert_newlines( dp ) shutil.move( dp, os.path.join( files_path, name ) ) +os.chmod(files_path +"/"+name, "0644") # Move the dataset to its "real" path shutil.move( dataset.primary_file, output_path ) # Write the job info Fixes permissions not been created for filenames correctly so an apache instance can access the extra files. Cheers James. Research Assistant Biochemistry Department University of Otago New Zealand ___ 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/
Re: [galaxy-dev] So I think I fixed a bug.
For a simple patch like yours, just pasting and sending your diff to the list works well: %hg diff ... For bigger patches/enhancements, a bitbucket fork + pull request is highly encouraged. Best, J. On Aug 23, 2012, at 4:47 AM, James wrote: > Hi All, > > Today I found a bug relating to the file permissions in composite datatypes. > When > the extrafiles directory was created and the server was running through > apache, the permission did not > allow a galaxy user to download by following the HTML link. Found it was > related to meta data files > not using the os.chmod function to set the permissions of the user data in > upload.py. Added that > line of code and it works and the file permissions match that of other files > in the database. > > Somehelp with submitting a patch would be welcome ( although one line patch > it would be helpful to me.) > > Cheers > James Boocock > ___ > 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/ ___ 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/
