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. For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en.