biodb2 down?

[jbiesinger]

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'

[Namshin Kim]

I guess the server is slow due to overload. I restarted the server but a bunch of query is being processed...

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[C. Titus Brown]

Sorry, that might be my fault -- my continuous integration setup runs a lot
of queries.

--titus

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C. Titus Brown, c...@msu.edu

[C. Titus Brown]

Hi, biodb2 still seems to be down -- is it getting overloaded due to a DoS attack, or what?

I will disable my pony-build CI builds for the moment.

thanks,
--titus

[Namshin Kim]

Hi,

 

I just restarted biodb2 server. It seems it has been down for three days. I don't think it is due to the DoS attack.

 

--

Namshin Kim