Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems

2014-06-10 Thread John Chilton
On Tue, Jun 10, 2014 at 1:50 PM, John-Paul Robinson wrote: > Thanks for proposing a patch. > > We're looking at trying it out on our code base but are at least a few > revisions behind and may need to do a little back porting (or catching up). I think it has been a while since this stuff has been

Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems

2014-06-10 Thread John-Paul Robinson
Thanks for proposing a patch. We're looking at trying it out on our code base but are at least a few revisions behind and may need to do a little back porting (or catching up). Let me make sure I understand the intention of the patch, though. >From the code changes, I trust that the intention i

Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems

2014-06-10 Thread John Chilton
Hello All, Thanks for the well laid out e-mails and great discussion. I think John-Paul's comment about the code growing up organically is probably exactly right. (A link below has some details from Nate about this). So late last night I opened a sprawling pull request that cleaned up a lot o

Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems

2014-06-09 Thread John-Paul Robinson
We've considered the sudo solution, but it opens the window to other bugs giving galaxy the power to change ownership of other files in our shared user cluster environment. We could isolate the power to a script but then we still need to monitor this code closely. We'd prefer not to introduce tha

Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems

2014-06-09 Thread Curtis Hendrickson (Campus)
bx.psu.edu Subject: Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems Hi JPR, I had the same questions while trying to figure out a fool-proof way to allow users to import files into galaxy on our Cluster. I couldn't exactly figure out, nor did I have the

Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems

2014-06-09 Thread Kandalaft, Iyad
Hi JPR, I had the same questions while trying to figure out a fool-proof way to allow users to import files into galaxy on our Cluster. I couldn't exactly figure out, nor did I have the time to really review, why the galaxy code did these steps and why that shutil.move failed. I opted to simp