Hi Peter, thanks a lot for your comments. I think it is more comfortable to be able to upload tools and xml via the webbrowser than to open a terminal and copy them, that was the idea behind my work. Especially for our institute this is very useful.
You're right about the check_argument methods. I wasn't sure to add this kind of functionality in the first place, because it can become very tricky. What I did should just be the very first step for someone who wants to continue the work (if this makes sense). That's why I added a checkbox that disable this check, so that you still can upload your tool/xml even the argument test would fail. Do you have some comments about the other parts ? Is this something you would be interested in using ? Best wishes, Bodo Vossen -----Original Message----- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Sat 5/28/2011 10:19 PM To: Vossen, Bodo Cc: firstname.lastname@example.org Subject: Re: [galaxy-dev] Implemented adding tools via admin console On Fri, May 27, 2011 at 11:21 AM, Vossen, Bodo <bodo.vos...@mpi-bn.mpg.de> wrote: > > Hi all, > > I've implemented functionality for adding tools via the admin menu. That sounds very useful in principle, although perhaps the less flexible alternative of reloading tool_conf.xml would achieve the same aim? > ... > Then it is checked if script and XML are "compatible" by > checking if they have the same number of arguments. This seems very fragile, and having looked at the code for detecting the number of arguments in a Python script it looks like it will get it wrong in many situations. Even for something quite simple like this: #sys.argv is the script file itself assert len(sys,argv)==4, "Expect 3 arguments" arg1, arg2, arg3 = sys.argv[1:] Also, what about conditional code like this? assert len(sys.argv)==4, "Expect 3 arguments" if sys.argv == "db": database = sys.argv filename = None else: database = None filename = sys.argv out_filename = sys.argv If I have read your get_parameter_number code right, it would claim there are four arguments since there are four lines of the basic form variable = sys.argv[i] Also, it cannot possibly work when there are a varying number of arguments, for example a repeat argument. If you want a test case, my Venn Diagram tool on the Tool Shed should be relevant (its a python script). > If you have any comments or question please do not > hesitate to contact me, I'm open for every kind of critics. I would remove the attempt to check the number of arguments. It is practically impossible to get this right in all cases, so I don't think it is worth doing. Having valid script/xml combinations rejected would be quite annoying. Peter
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