First, that would be great to use the Graph instead, so I can query
it. It works the same when adding/binding attributes? I know the
difference in constructing it.
BUT I tried to add the close() and still get the same problem. So
where do I add the close call? Immediately after my for... loop, after
adding the mapping resource to the worldbase, or before/after the
worldbase.commit()? I actually am getting an EOFerror, which to me
does indicate that a buffer was not flushed to a file.
In [7]: c.events
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (454, 0))
---------------------------------------------------------------------------
KeyError Traceback (most recent call
last)
/home/kdaily/sandbox/<ipython console> in <module>()
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/
python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/
metabase.pyc in __get__(self, obj, objtype)
59 result=targetDict[obj_id] # MAP USING THE
SPECIFIED MAPPING
60 else:
---> 61 result=targetDict[obj] # NOW PERFORM MAPPING IN
THAT RESOURCE...
62 if self.targetAttr is not None:
63 result=getattr(result,self.targetAttr) # GET
ATTRIBUTE OF THE result
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/
python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/
mapping.pyc in __getitem__(self, k)
504 def __getitem__(self,k):
505 kID=getattr(k,self.IDAttr)
--> 506 return self.getTarget(self.d[kID])
507 def getTarget(self,vID):
508 if self.itemAttr is not None:
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/
python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/
mapping.pyc in __getitem__(self, k)
393 return k
394 def __getitem__(self,k):
--> 395 return self.d[self.saveKey(k)]
396 def __setitem__(self,k,v):
397 self.d[self.saveKey(k)]=v
/pkg/python/2.6.2/lib/python2.6/shelve.pyc in __getitem__(self, key)
119 value = self.cache[key]
120 except KeyError:
--> 121 f = StringIO(self.dict[key])
122 value = Unpickler(f).load()
123 if self.writeback:
/pkg/python/2.6.2/lib/python2.6/bsddb/__init__.pyc in __getitem__
(self, key)
265 def __getitem__(self, key):
266 self._checkOpen()
--> 267 return _DeadlockWrap(lambda: self.db[key]) # self.db
[key]
268
269 def __setitem__(self, key, value):
/pkg/python/2.6.2/lib/python2.6/bsddb/dbutils.pyc in DeadlockWrap
(function, *_args, **_kwargs)
66 while True:
67 try:
---> 68 return function(*_args, **_kwargs)
69 except db.DBLockDeadlockError:
70 if _deadlock_VerboseFile:
/pkg/python/2.6.2/lib/python2.6/bsddb/__init__.pyc in <lambda>()
265 def __getitem__(self, key):
266 self._checkOpen()
--> 267 return _DeadlockWrap(lambda: self.db[key]) # self.db
[key]
268
269 def __setitem__(self, key, value):
KeyError: 'int:1'
On Jun 13, 4:24 pm, Christopher Lee <l...@chem.ucla.edu> wrote:
> Hi Kenny,
> you need to close() the Mapping when you're done writing data to it.
> Its file-based storage uses Python shelve, which I believe may not
> write its data to disk until you close() it. Mapping tries to call
> close() for you automatically when garbage-collected (i.e.
> Mapping.__del__ calls self.close()), but as you have just experienced,
> that is unpredictable and unreliable (i.e. there's no sure way to know
> exactly when Python will garbage-collect your object after you drop
> all references to it).
>
> Note: I think you should Graph (one-to-many or many-to-many) instead
> of Mapping (one-to-one). See the tutorial examples or mapping module
> docs, and ask if you have questions...
>
> -- Chris
>
> On Jun 13, 2009, at 3:52 PM, Kenny Daily wrote:
>
>
>
> > So, I've gotten the mapping to work, but only sometimes?
>
> > The code is here (http://kmdaily.pastebin.com/m6d4a86c3) that I'm
> > running.
>
> > I'm checking the length of the Mapping when I'm done loading all the
> > things to map (its ~9000), adding it to worldbase, and checking the
> > length again (still 9000). Then, the code exits, and I try to load it
> > on the command line or use it again, and it has a 0 length. I look at
> > the file that its writing to, and I can see the data in it (the keys
> > and values of the objects from the AnnotationDBs that I added). The
> > object loads fine, and it accesses the database backend fine as well
> > (watching the db connections shows it connecting). Any suggestions how
> > to track the problem? Thanks!
>
> > Kenny
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