Re: [Tutor] perplexing error with shelve REVISED
It appears you have a cyclic reference in your doc object. Try adding doc.unlink() before you add it to your shelf. That fixed the problem. I did not realize that XML documents could have cyclic references. Thanks for all your help! Orest ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] perplexing error with shelve REVISED
It appears you have a cyclic reference in your doc object. Try adding doc.unlink() before you add it to your shelf. Actually, I just realized that doc.unlink() seems to delete the entire XML content, which kind of defeats the purpose of caching it. I'll check on xml-sig and the comp.lang.python group to see if there are any suggestions. Thanks again for your help! Orest ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
[Tutor] perplexing error with shelve
I have a program which queries an online database (Medline) for XML data.
It caches all data using shelve to avoid hitting the database too many
times. For some reason, I keep getting a RuntimeError: maximum recursion
depth exceeded when attempting to add a certain record. This program has
successfully handled over 40,000 records from Medline, but for whatever
reason, this particular record (PMID: 16842422) produces this error. If I
set maximum recursion depth to a larger value such as 5,000, I get a
segfault.
Below is a script that should reproduce the problem I am having. Any
guidance in solving this problem would greatly be appreciated.
Thank you,
Orest
### START SCRIPT ###
import urllib, shelve
from xml.dom import minidom
baseurl = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'
params = {
'db': 'pubmed',
'retmode': 'xml',
'rettype': 'medline'
}
badkey = '16842422'
goodkey = '16842423' #or just about any other ID
data = shelve.open('data.tmp', writeback=True)
try:
params['id'] = goodkey
url = baseurl + urllib.urlencode(params)
doc = minidom.parseString(urllib.urlopen(url).read())
print 'Successfully retrieved and parsed XML document with ID %s' %
goodkey
data[goodkey] = doc
print 'Successfully shelved XML document with ID %s' % goodkey
except RuntimeError:
print 'Should not see this error message!'
try:
params['id'] = badkey
url = baseurl + urllib.urlencode(params)
doc = minidom.parseString(urllib.urlopen(url).read())
print 'Successfully retrieved and parsed XML document with ID %s' %
badkey
data[badkey] = doc
#Should not get this message!
print 'Successfully shelved XML document with ID %s' % badkey
except RuntimeError, e:
print 'Error shelving XML document with ID %s' % badkey
print e
### END SCRIPT ###
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Re: [Tutor] perplexing error with shelve REVISED
Please post the entire traceback (omitting duplicate lines).
Sorry, I should have included the traceback. I've revised the sample script
so that it generates the traceback when run. The sample script is at the
very bottom of this email.
### SCRIPT OUTPUT ###
[kozyar]:~$ python example.py
Successfully retrieved and parsed XML document with ID 16842423
Successfully shelved XML document with ID 16842423
Successfully retrieved and parsed XML document with ID 16842422
Traceback (most recent call last):
File example.py, line 30, in module
data[badkey] = doc
File /usr/lib64/python2.5/shelve.py, line 123, in __setitem__
p.dump(value)
RuntimeError: maximum recursion depth exceeded
Exception exceptions.RuntimeError: 'maximum recursion depth exceeded' in
bound method DbfilenameShelf.__del__ of {'16842423':
xml.dom.minidom.Document instance at 0x96f290} ignored
### START SCRIPT ###
import urllib, shelve
from xml.dom import minidom
baseurl = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'
params = {
'db': 'pubmed',
'retmode': 'xml',
'rettype': 'medline'
}
badkey = '16842422'
goodkey = '16842423' #or just about any other ID
data = shelve.open('data.tmp', writeback=True)
params['id'] = goodkey
url = baseurl + urllib.urlencode(params)
doc = minidom.parseString(urllib.urlopen(url).read())
print 'Successfully retrieved and parsed XML document with ID %s' % goodkey
data[goodkey] = doc
print 'Successfully shelved XML document with ID %s' % goodkey
params['id'] = badkey
url = baseurl + urllib.urlencode(params)
doc = minidom.parseString(urllib.urlopen(url).read())
print 'Successfully retrieved and parsed XML document with ID %s' % badkey
data[badkey] = doc
#Will fail on the above line
print 'Successfully shelved XML document with ID %s' % badkey
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[Tutor] evaluating AND
Given a variable x that can either be None or a tuple of two floats [i.e. (0.32, 4.2)], which syntax is considered most appropriate under Python coding standards? if x and x[0] 0: pass =OR= if x: if x[0] 0: pass In the first, I'm obviously making the assumption that if the first condition evaluates to false, then the second condition won't be evaluated. But, is this a good/valid assumption to make? Is there a more appropriate design pattern in Python? Thanks! Orest ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Metaclass programming
This could be written
kwargs.update(zip(argnames, args))
Nice trick! Thanks for the pointer.
return type.__call__(cls, kwargs)
You are passing kwargs as a positional argument to __call__(); i.e.
passing the dict as an ordinary parameter. To use kwargs as
the keyword dict for the call, use the syntax
type.__call__(cls, **kwargs)
Great, I did not realize that ** was part of the syntax so couldn't figure
out what the issue was. It works smoothly now.
I think the problem is elsewhere in your code.
You're right. I just figured out that for some reason, when I use the
SQLAlchemy mapper() function to map my classes to the corresponding table
object, it seems to affect inspect.getargspec().
For example:
from sqlalchemy.orm import mapper
from sqlalchemy import Table, MetaData
import inspect
class Foo:
def __init__(self, x, y):
pass
print inspect.getargspec(Foo.__init__)
(['self', 'x', 'y'], None, None, None)
metadata = MetaData()
foo_table = Table('foo', metadata)
mapper(Foo, foo_table)
print inspect.getargspec(Foo.__init__)
(['instance'], 'args', 'kwargs', None)
I'm not sure why this would be the case, but is a bit frustrating since I do
need the names of the positional arguments sometimes.
Why are you doing this?
Partially as an exercise to help me better understand Python inspection as
well as metaclass programming. I also am using it in a EntitySingleton
metaclass that I adapted from the SQLAlchemy wiki
(http://www.sqlalchemy.org/trac/wiki/UsageRecipes/UniqueObject). Some of my
classes have unique constraints, and I want the metaclass to check these
unique constraints and return an object from the database if an object
meeting these constraints already exists.
For example:
class User:
__unique__ = ['firstname', 'lastname']
__metaclass__ = EntitySingleton
def __init__(self, firstname, lastname, password):
pass
The metaclass knows what the unique constraints are based on the
__unique__ list, but needs to use inspect.getargspec() to get the variable
names and match them up with the *args list that EntitySingleton.__call__
recieves. At least, that's how I'm trying to do it, but I expect this might
not be the best way to do it? Either case, when the class is mapped to a
database table, I lose all this information, so will need to figure out a
different way of approaching this.
Orest
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[Tutor] Metaclass programming
I have the following code: class meta(type): def __call__(cls, *args, **kwargs): argnames = inspect.getargspec(cls.__init__)[0] for i, value in enumerate(args): kwargs[argnames[i]] = value return type.__call__(cls, kwargs) class test(object): __metaclass__ = meta def __init__(self, x, y, **kwargs): pass However, inspect.getargspec(cls.__init__) appears to return only the arguments of the meta __init__ rather than the test __init__. Is there any way I can get access to the test __init__ function from the metaclass? Orest ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
[Tutor] Variable scope for class?
I'm trying to follow the example listed in the wiki at http://www.sqlalchemy.org/trac/wiki/UsageRecipes/UniqueObject regarding the use of a metaclass. What I don't understand is how the metaclass (EntitySingleton) has access to the variable ctx which is instantinated outside the scope of the class definition. Could anyone point me in the right direction please? Thanks, Orest ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
[Tutor] Accesing column of a 2D list
I've got a 2D list (essentially a list of lists where all sublists are of the same length). The sublists are polymorphic. One 2D list I commonly work with is: [ [datetime object, float, int, float], [datetime object, float, int, float], [datetime object, float, int, float] ] I'd like to be able to quickly accumulate the datetime column into a list. Is there a simple/straightforward syntax (such as list[:][0]) to do this, or do we need to use a for loop? I expect what I have in mind is similar to the Python array type, except it would be polymorphic. Thanks, Orest ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
