Hi Marco, it sounds to me like it's hanging when trying to open an XMLRPC connection to an external server. By default, if you do not set the environment variable PYGRDATAPATH, pygr.Data's search path defaults to a setting of ~,.,http://biodb2.bioinformatics.ucla.edu:5000 which translates to: your HOME directory; your current directory; and our XML-RPC server at UCLA, which serves a bunch of UCSC genome alignments and genome sequence databases (searched for any resource request in that order). In version 0.7, pygr.Data actually tries to connect to the resource databases *during* module import (i.e. when you first import pygr.Data). That would explain the hanging behavior you're seeing when you try to import pygr.Data. 0.8 eliminates that behavior; it does not connect during module import, but only when you first request some data.
Before we even look at the question of making the XMLRPC client work with your proxy setting, let's verify that you can eliminate the hanging behavior, by simply omitting the URL for the UCLA XMLRPC server from its search path. Set the environment variable PYGRDATAPATH to the following value as a test: PYGRDATAPATH=~,. Then start python and try importing pygr.Data. Let me know if that fixes the hang that you reported. Yours, Chris On Apr 28, 2009, at 7:03 AM, Giovanni Marco Dall'Olio wrote: > > Hi, > a simple question: how do I use pygr.Data on a system where I must set > an http proxy to access to Internet? > > I am using Ubuntu 8.04 with python 2.5.2 and pygr 0.7.1. > I have my $http_proxy and $HTTP_PROXY variables set correctly (other > programs work correctly). > when I do: >>>> import pygr.Data > the python prompt hangs, I don't receive any feedback on if it is > downloading something or there is any problem, and I couldn't find any > instructions in the documentation (I searched for the word 'proxy' on > your google wiki). > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
