I guess the server is slow due to overload. I restarted the server but a bunch of query is being processed...
On Wed, Jun 30, 2010 at 3:47 PM, jbiesinger <jake.biesin...@gmail.com>wrote: > Is the server down or is it a metabase issue? > $ export WORLDBASEPATH=http://biodb2.bioinformatics.ucla.edu:5000 > > In [1]: from pygr import worldbase > In [2]: worldbase.Bio.Seq.Genome.MOUSE.mm9() > > WARNING: error accessing metabase > http://biodb2.bioinformatics.ucla.edu:5000. > Continuing... > Traceback (most recent call last): > File "setup/SetupMotifs_mm9.py", line 9, in <module> > genome = worldbase('Bio.Seq.Genome.MOUSE.mm9', download=True) > File "/usr/local/lib/python2.6/dist-packages/pygr/metabase.py", line > 1460, in __call__ > return self._mdb(resID, *args, **kwargs) > File "/usr/local/lib/python2.6/dist-packages/pygr/metabase.py", line > 777, in __call__ > for objdata, docstr in self.find_resource(resID, download): > File "/usr/local/lib/python2.6/dist-packages/pygr/metabase.py", line > 1047, in find_resource > % resID) > pygr.metabase.WorldbaseNotFoundError: 'unable to find > Bio.Seq.Genome.MOUSE.mm9 in WORLDBASEPATH' > > > > and another attempt resulted in: > > Traceback (most recent call last): > File "/usr/local/lib/python2.6/dist-packages/pygr/metabase.py", line > 1085, in update > self, **mdbArgs) > File "/usr/local/lib/python2.6/dist-packages/pygr/metabase.py", line > 915, in __init__ > storage = XMLRPCMetabase(dbpath, self, **kwargs) > File "/usr/local/lib/python2.6/dist-packages/pygr/metabase.py", line > 335, in __init__ > self.server = get_connection(url, 'index') > File "/usr/local/lib/python2.6/dist-packages/pygr/coordinator.py", > line 94, in __call__ > return s[name] # GET THE REQUESTED OBJECT PROXY FROM THE SERVER > File "/usr/local/lib/python2.6/dist-packages/pygr/coordinator.py", > line 75, in __getitem__ > methodDict = self.server.objectInfo(name) > File "/usr/lib/python2.6/xmlrpclib.py", line 1199, in __call__ > return self.__send(self.__name, args) > File "/usr/lib/python2.6/xmlrpclib.py", line 1489, in __request > verbose=self.__verbose > File "/usr/lib/python2.6/xmlrpclib.py", line 1237, in request > errcode, errmsg, headers = h.getreply() > File "/usr/lib/python2.6/httplib.py", line 1060, in getreply > response = self._conn.getresponse() > File "/usr/lib/python2.6/httplib.py", line 986, in getresponse > response.begin() > error: [Errno 104] Connection reset by peer > > WARNING: error accessing metabase > http://biodb2.bioinformatics.ucla.edu:5000. > Continuing... > --------------------------------------------------------------------------- > WorldbaseNotFoundError Traceback (most recent call > last) > > /home/wbiesing/projects/chipSeq/python/<ipython console> in <module>() > > /usr/local/lib/python2.6/dist-packages/pygr/metabase.pyc in > __call__(self, *args, **kwargs) > 1415 def __call__(self, *args, **kwargs): > 1416 'construct the requested resource' > -> 1417 return self._mdb(self._path, *args, **kwargs) > 1418 > 1419 def __setattr__(self, name, obj): > > /usr/local/lib/python2.6/dist-packages/pygr/metabase.pyc in > __call__(self, resID, debug, download, *args, **kwargs) > 775 try: # finally... TO RESTORE debug STATE EVEN IF > EXCEPTION OCCURS. > 776 self.update(debug=self.debug, > keepCurrentPath=True) # load if empty > --> 777 for objdata, docstr in self.find_resource(resID, > download): > 778 try: > 779 obj = self.load(resID, objdata, docstr) > > /usr/local/lib/python2.6/dist-packages/pygr/metabase.pyc in > find_resource(self, resID, download) > 1045 pass > 1046 raise WorldbaseNotFoundError('unable to find %s in > WORLDBASEPATH' > -> 1047 % resID) > 1048 > 1049 def get_worldbase_path(self): > > WorldbaseNotFoundError: 'unable to find Bio.Seq.Genome.MOUSE.mm9 in > WORLDBASEPATH' > > -- > You received this message because you are subscribed to the Google Groups > "pygr-dev" group. > To post to this group, send email to pygr-...@googlegroups.com. > To unsubscribe from this group, send email to > pygr-dev+unsubscr...@googlegroups.com<pygr-dev%2bunsubscr...@googlegroups.com> > . > For more options, visit this group at > http://groups.google.com/group/pygr-dev?hl=en. > > -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@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.
