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How to make a config file property unique with config parser?

How can I create a config file with unique only one unique property?
Or are there any loop for checking the config file where I find a duplicated name property value and it gives an exception?
[NAME+TIMESTAMP]
Name=UNIQUE NAME
Property=something
Property1=something1
Property2=something2
[NAME+TIMESTAMP]
Name=UNIQUE NAME
Property=something
Property1=something1
Property2=something2

Due to configParser being dict-like in most things, what we can do here is use the key of the different code-blocks to make sure that there are unique blocks.
Here is a simple test to show it in action:
import configparser
class Container:
configs=[] # keeps a list of all initialized objects.
def __init__(self, **kwargs):
for k,v in kwargs.items():
self.__setattr__(k,v) # Sets each named attribute to their given value.
Container.configs.append(self)
# Initializing some objects.
Container(
Name="Test-Object1",
Property1="Something",
Property2="Something2",
Property3="Something3",
)
Container(
Name="Test-Object2",
Property1="Something",
Property2="Something2",
Property3="Something3",
)
Container(
Name="Test-Object2",
Property1="Something Completely different",
Property2="Something Completely different2",
Property3="Something Completely different3",
)
config = configparser.ConfigParser()
for item in Container.configs: # Loops through all the created objects.
config[item.Name] = item.__dict__ # Adds all variables set on the object, using "Name" as the key.
with open("example.ini", "w") as ConfigFile:
config.write(ConfigFile)
In the above example, I create three objects that contain variables to be set by configparser. However, the third object shares the Name variable with the second Object. That means that the third one will "overwrite" the second while writing the .ini file.
example.ini:
[Test-Object1]
name = Test-Object1
property1 = Something
property2 = Something2
property3 = Something3
[Test-Object2]
name = Test-Object2
property1 = Something Completely different
property2 = Something Completely different2
property3 = Something Completely different3

JSON Serialization of Custom Objects (Encoding and Decoding)

I've been searching the internet and couldn't find a simple example to encode and decode a custom object using JSON in python.
Let's say I have the following class:
class Test:
def __init__(self, name=None, grade=None):
self.name = name
self.grade = grade
and also have a list of Test objects:
t1 = Test("course1", 80)
t2 = Test("course2", 90)
list_of_tests = [t1, t2]
How can I serialize the class Test and the object list_of_tests
using JSON? I want to be able to write it to a file and read it from a file, using python.

To be honest the easiest thing to do here is to manually create a list of dictionaries from your objects. Then you can pass that directly to the JSON functions.
data = [{'name': x.name, 'grade': x.grade} for x in list_of_tests]
with open('output.json', 'w') as out:
json.dump(data, out)
and read it back:
with open('output.json') as inp:
data = json.load(inp)
list_of_tests = [Test(x['name'], x['grade']) for x in data]

You can control how an unrecognised object is serialised by dumps(default=converter_function). For it to be valid JSON you'd have to return a plain dict with the fields you want plus some tag field identifying that it is to be treated specially by loads.
Then have another converter function to reverse the process passed to loads() as object_hook.

How can I use a dict in python to build a multi-dimension array with boto and amazon ec2?

I'm attempting to use python and boto to print a list of instances and IPs from Amazon EC2.
I'm used to PHP's nice multidimensional arrays and the similar JSON syntax but I'm having a lot of trouble in python. I tried using AutoVivification as mentioned in What's the best way to initialize a dict of dicts in Python? but am not having luck with access objects in it.
Here is my code:
import sys
import os
import boto
import string
import urllib2
from pprint import pprint
from inspect import getmembers
from datetime import datetime
class AutoVivification(dict):
"""Implementation of perl's autovivification feature."""
def __getitem__(self, item):
try:
return dict.__getitem__(self, item)
except KeyError:
value = self[item] = type(self)()
return value
conn = boto.connect_ec2_endpoint(ec2_url, AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY)
tags = conn.get_all_tags()
myInstances = AutoVivification()
for tag in tags:
if ( tag.res_type == 'instance' and tag.name == 'Name'):
if( tag.res_id ):
myInstances[tag.res_id]['myid'] = tag.res_id
myInstances[tag.res_id]['name'] = tag.value
addrs = conn.get_all_addresses()
for a in addrs:
if( a.instance_id ):
myInstances[a.instance_id]['ip'] = a.public_ip
pprint( myInstances )
for i in myInstances:
print i.name.rjust(25), i.myid
If I do pprint( myInstances ) then I am able to see the multidimensional dict that I have created, but i am not able to access the sub-arrays with i.myid - I get errors like:
AttributeError: 'unicode' object has no attribute 'myid'
AttributeError: 'unicode' object has no attribute 'name'
Doing pprint( myInstances) gives me something like:
{u'i-08148364': {'myid': u'i-18243322', 'name': u'nagios', 'ip': u'1.2.3.4'}}
so I don't understand why I can't access these items.

Your problem is just in how you're trying to access the items:
for i in myInstances:
# i iterates over the KEYS in myInstances
print i.name.rjust(25), i.myid
This attempts, for each key in myInstances, to print i.name.rjust(25) and so on. What you want is to access the value of the given keys (and to use the right Python syntax for accessing dictionary elements):
for i in myInstances:
# i iterates over the KEYS in myInstances
print myInstances[i]["name"].rjust(25), myInstances[i]["myid"]
Or if you don't need the keys at all, just iterate over the values in the first place:
for i in myInstances.values():
# i iterates over the VALUES in myInstances
print i["name"].rjust(25), i["myid"]
Or finally, per request, if you really want to iterate over keys and values at once:
for k, v in myInstances.iteritems():
print k, v["name"].rjust(25), v["myid"]

Plone: Change default schemata of a content type

I am using the Products.FacultyStaffDirectory product to manage contacts in my website.
One of the content types, i.e. FacultyStaffDirectory, has the description field in the 'categorization' tab when you are in edit mode. Now I need to remove the description field and put it in the default tab.
To do this, I'm using archetypes.schemaextender product to edit the field. In particular, I am using ISchemaModifier.
I have implemented the code but the field is still being shown in the categorization tab. May be something I missed. Below is the code:
This is the class that contains the description field that I want to modify:
# -*- coding: utf-8 -*-
__author__ = """WebLion <support#weblion.psu.edu>"""
__docformat__ = 'plaintext'
from AccessControl import ClassSecurityInfo
from Products.Archetypes.atapi import *
from zope.interface import implements
from Products.FacultyStaffDirectory.interfaces.facultystaffdirectory import IFacultyStaffDirectory
from Products.FacultyStaffDirectory.config import *
from Products.CMFCore.permissions import View, ManageUsers
from Products.CMFCore.utils import getToolByName
from Products.ATContentTypes.content.base import ATCTContent
from Products.ATContentTypes.content.schemata import ATContentTypeSchema, finalizeATCTSchema
from Products.membrane.at.interfaces import IPropertiesProvider
from Products.membrane.utils import getFilteredValidRolesForPortal
from Acquisition import aq_inner, aq_parent
from Products.FacultyStaffDirectory import FSDMessageFactory as _
schema = ATContentTypeSchema.copy() + Schema((
LinesField('roles_',
accessor='getRoles',
mutator='setRoles',
edit_accessor='getRawRoles',
vocabulary='getRoleSet',
default = ['Member'],
multiValued=1,
write_permission=ManageUsers,
widget=MultiSelectionWidget(
label=_(u"FacultyStaffDirectory_label_FacultyStaffDirectoryRoles", default=u"Roles"),
description=_(u"FacultyStaffDirectory_description_FacultyStaffDirectoryRoles", default=u"The roles all people in this directory will be granted site-wide"),
i18n_domain="FacultyStaffDirectory",
),
),
IntegerField('personClassificationViewThumbnailWidth',
accessor='getClassificationViewThumbnailWidth',
mutator='setClassificationViewThumbnailWidth',
schemata='Display',
default=100,
write_permission=ManageUsers,
widget=IntegerWidget(
label=_(u"FacultyStaffDirectory_label_personClassificationViewThumbnailWidth", default=u"Width for thumbnails in classification view"),
description=_(u"FacultyStaffDirectory_description_personClassificationViewThumbnailWidth", default=u"Show all person thumbnails with a fixed width (in pixels) within the classification view"),
i18n_domain="FacultyStaffDirectory",
),
),
))
FacultyStaffDirectory_schema = OrderedBaseFolderSchema.copy() + schema.copy() # + on Schemas does only a shallow copy
finalizeATCTSchema(FacultyStaffDirectory_schema, folderish=True)
class FacultyStaffDirectory(OrderedBaseFolder, ATCTContent):
"""
"""
security = ClassSecurityInfo()
implements(IFacultyStaffDirectory, IPropertiesProvider)
meta_type = portal_type = 'FSDFacultyStaffDirectory'
# Make this permission show up on every containery object in the Zope instance. This is a Good Thing, because it easy to factor up permissions. The Zope Developer's Guide says to put this here, not in the install procedure (http://www.zope.org/Documentation/Books/ZDG/current/Security.stx). This is because it isn't "sticky", in the sense of being persisted through the ZODB. Thus, it has to run every time Zope starts up. Thus, when you uninstall the product, the permission doesn't stop showing up, but when you actually remove it from the Products folder, it does.
security.setPermissionDefault('FacultyStaffDirectory: Add or Remove People', ['Manager', 'Owner'])
# moved schema setting after finalizeATCTSchema, so the order of the fieldsets
# is preserved. Also after updateActions is called since it seems to overwrite the schema changes.
# Move the description field, but not in Plone 2.5 since it's already in the metadata tab. Although,
# decription and relateditems are occasionally showing up in the "default" schemata. Move them
# to "metadata" just to be safe.
if 'categorization' in FacultyStaffDirectory_schema.getSchemataNames():
FacultyStaffDirectory_schema.changeSchemataForField('description', 'categorization')
else:
FacultyStaffDirectory_schema.changeSchemataForField('description', 'metadata')
FacultyStaffDirectory_schema.changeSchemataForField('relatedItems', 'metadata')
_at_rename_after_creation = True
schema = FacultyStaffDirectory_schema
# Methods
security.declarePrivate('at_post_create_script')
def at_post_create_script(self):
"""Actions to perform after a FacultyStaffDirectory is added to a Plone site"""
# Create some default contents
# Create some base classifications
self.invokeFactory('FSDClassification', id='faculty', title='Faculty')
self.invokeFactory('FSDClassification', id='staff', title='Staff')
self.invokeFactory('FSDClassification', id='grad-students', title='Graduate Students')
# Create a committees folder
self.invokeFactory('FSDCommitteesFolder', id='committees', title='Committees')
# Create a specialties folder
self.invokeFactory('FSDSpecialtiesFolder', id='specialties', title='Specialties')
security.declareProtected(View, 'getDirectoryRoot')
def getDirectoryRoot(self):
"""Return the current FSD object through acquisition."""
return self
security.declareProtected(View, 'getClassifications')
def getClassifications(self):
"""Return the classifications (in brains form) within this FacultyStaffDirectory."""
portal_catalog = getToolByName(self, 'portal_catalog')
return portal_catalog(path='/'.join(self.getPhysicalPath()), portal_type='FSDClassification', depth=1, sort_on='getObjPositionInParent')
security.declareProtected(View, 'getSpecialtiesFolder')
def getSpecialtiesFolder(self):
"""Return a random SpecialtiesFolder contained in this FacultyStaffDirectory.
If none exists, return None."""
specialtiesFolders = self.getFolderContents({'portal_type': 'FSDSpecialtiesFolder'})
if specialtiesFolders:
return specialtiesFolders[0].getObject()
else:
return None
security.declareProtected(View, 'getPeople')
def getPeople(self):
"""Return a list of people contained within this FacultyStaffDirectory."""
portal_catalog = getToolByName(self, 'portal_catalog')
results = portal_catalog(path='/'.join(self.getPhysicalPath()), portal_type='FSDPerson', depth=1)
return [brain.getObject() for brain in results]
security.declareProtected(View, 'getSortedPeople')
def getSortedPeople(self):
""" Return a list of people, sorted by SortableName
"""
people = self.getPeople()
return sorted(people, cmp=lambda x,y: cmp(x.getSortableName(), y.getSortableName()))
security.declareProtected(View, 'getDepartments')
def getDepartments(self):
"""Return a list of FSDDepartments contained within this site."""
portal_catalog = getToolByName(self, 'portal_catalog')
results = portal_catalog(portal_type='FSDDepartment')
return [brain.getObject() for brain in results]
security.declareProtected(View, 'getAddableInterfaceSubscribers')
def getAddableInterfaceSubscribers():
"""Return a list of (names of) content types marked as addable using the
IFacultyStaffDirectoryAddable interface."""
return [type['name'] for type in listTypes() if IFacultyStaffDirectoryAddable.implementedBy(type['klass'])]
security.declarePrivate('getRoleSet')
def getRoleSet(self):
"""Get the roles vocabulary to use."""
portal_roles = getFilteredValidRolesForPortal(self)
allowed_roles = [r for r in portal_roles if r not in INVALID_ROLES]
return allowed_roles
#
# Validators
#
security.declarePrivate('validate_id')
def validate_id(self, value):
"""Ensure the id is unique, also among groups globally."""
if value != self.getId():
parent = aq_parent(aq_inner(self))
if value in parent.objectIds():
return _(u"An object with id '%s' already exists in this folder") % value
groups = getToolByName(self, 'portal_groups')
if groups.getGroupById(value) is not None:
return _(u"A group with id '%s' already exists in the portal") % value
registerType(FacultyStaffDirectory, PROJECTNAME)
Below is the portion of code from the class that I have implemented to change the description field's schemata:
from Products.Archetypes.public import ImageField, ImageWidget, StringField, StringWidget, SelectionWidget, TextField, RichWidget
from Products.FacultyStaffDirectory.interfaces.facultystaffdirectory import IFacultyStaffDirectory
from archetypes.schemaextender.field import ExtensionField
from archetypes.schemaextender.interfaces import ISchemaModifier, ISchemaExtender, IBrowserLayerAwareExtender
from apkn.templates.interfaces import ITemplatesLayer
from zope.component import adapts
from zope.interface import implements
class _ExtensionImageField(ExtensionField, ImageField): pass
class _ExtensionStringField(ExtensionField, StringField): pass
class _ExtensionTextField(ExtensionField, TextField): pass
class FacultyStaffDirectoryExtender(object):
"""
Adapter to add description field to a FacultyStaffDirectory.
"""
adapts(IFacultyStaffDirectory)
implements(ISchemaModifier, IBrowserLayerAwareExtender)
layer = ITemplatesLayer
fields = [
]
def __init__(self, context):
self.context = context
def getFields(self):
return self.fields
def fiddle(self, schema):
desc_field = schema['description'].copy()
desc_field.schemata = "default"
schema['description'] = desc_field
And here is the code from my configure.zcml:
<adapter
name="apkn-FacultyStaffDirectoryExtender"
factory="apkn.templates.extender.FacultyStaffDirectoryExtender"
provides="archetypes.schemaextender.interfaces.ISchemaModifier"
/>
Is there something that I'm missing in this?

def fiddle(self, schema):
schema['description'].schemata = 'default'
should be sufficient. The copy() operation does not make any sense here.
In order to check if the fiddle() method is actually used: use pdb or add debug print statements.

It turns out that there was nothing wrong with the code.
I got it to work by doing the following:
Restarted the plone website
Re-installed the product
Clear and rebuilt my catalog
This got it working somehow.

Parsing a file with multiple xmls in it

Is there a way to parse a file which contains multiple xmls in it?
eg., if I have a file called stocks.xml and within the stocks.xml i have more than one xml content, is there any way to parse this xml file ?.
-- stocks.xml
<?xml version="1.0" encoding="ASCII"?><PRODUCT><ID>A001</ID>..</PRODUCT><SHOP-1><QUANTITY>nn</QUANITY><SHOP-1><QUANTITY>nn</QUANITY>
<?xml version="1.0" encoding="ASCII"?><PRODUCT><ID>A002</ID>..</PRODUCT><SHOP-1><QUANTITY>nn</QUANITY><SHOP-1><QUANTITY>nn</QUANITY>

If you can assume that each xml document begins with <?xml version="1.0" ..., simply read the file line-by-line looking for a lines that match that pattern (or, read all the data and then do a search through the data).
Once you find a line, keep it, and append subsequent lines until the next xml document is found or you hit EOF. lather, rinse, repeat.
You now have one xml document in a string. You can then parse the string using the normal XML parsing tools, or you write it to a file.
This will work fine in most cases, but of course it could fall down if one of your embedded xml documents contains data that exactly matches the same pattern as the beginning of a document. Most likely you don't have to worry about that, and if you do there are ways to avoid that with a little more cleverness.
The right solution really depends on your needs. If you're creating a general purpose must-work-at-all-times solution this might not be right for you. For real world, special purpose problems it's probably more than Good Enough, and often Good Enough is indeed Good Enough.

You should see this python program by Michiel de Hoon
And if you want to parse multiple files, then a rule to detect that we are in other xml must be developed, for example,at first you read <stocks> .... and at the end you must reead </stocks> when you find that then if there is something else,well, continue reading and do the same parser until reach eof.
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parser for XML results returned by NCBI's Entrez Utilities. This
parser is used by the read() function in Bio.Entrez, and is not intended
be used directly.
"""
# The question is how to represent an XML file as Python objects. Some
# XML files returned by NCBI look like lists, others look like dictionaries,
# and others look like a mix of lists and dictionaries.
#
# My approach is to classify each possible element in the XML as a plain
# string, an integer, a list, a dictionary, or a structure. The latter is a
# dictionary where the same key can occur multiple times; in Python, it is
# represented as a dictionary where that key occurs once, pointing to a list
# of values found in the XML file.
#
# The parser then goes through the XML and creates the appropriate Python
# object for each element. The different levels encountered in the XML are
# preserved on the Python side. So a subelement of a subelement of an element
# is a value in a dictionary that is stored in a list which is a value in
# some other dictionary (or a value in a list which itself belongs to a list
# which is a value in a dictionary, and so on). Attributes encountered in
# the XML are stored as a dictionary in a member .attributes of each element,
# and the tag name is saved in a member .tag.
#
# To decide which kind of Python object corresponds to each element in the
# XML, the parser analyzes the DTD referred at the top of (almost) every
# XML file returned by the Entrez Utilities. This is preferred over a hand-
# written solution, since the number of DTDs is rather large and their
# contents may change over time. About half the code in this parser deals
# wih parsing the DTD, and the other half with the XML itself.
import os.path
import urlparse
import urllib
import warnings
from xml.parsers import expat
# The following four classes are used to add a member .attributes to integers,
# strings, lists, and dictionaries, respectively.
class IntegerElement(int):
def __repr__(self):
text = int.__repr__(self)
try:
attributes = self.attributes
except AttributeError:
return text
return "IntegerElement(%s, attributes=%s)" % (text, repr(attributes))
class StringElement(str):
def __repr__(self):
text = str.__repr__(self)
try:
attributes = self.attributes
except AttributeError:
return text
return "StringElement(%s, attributes=%s)" % (text, repr(attributes))
class UnicodeElement(unicode):
def __repr__(self):
text = unicode.__repr__(self)
try:
attributes = self.attributes
except AttributeError:
return text
return "UnicodeElement(%s, attributes=%s)" % (text, repr(attributes))
class ListElement(list):
def __repr__(self):
text = list.__repr__(self)
try:
attributes = self.attributes
except AttributeError:
return text
return "ListElement(%s, attributes=%s)" % (text, repr(attributes))
class DictionaryElement(dict):
def __repr__(self):
text = dict.__repr__(self)
try:
attributes = self.attributes
except AttributeError:
return text
return "DictElement(%s, attributes=%s)" % (text, repr(attributes))
# A StructureElement is like a dictionary, but some of its keys can have
# multiple values associated with it. These values are stored in a list
# under each key.
class StructureElement(dict):
def __init__(self, keys):
dict.__init__(self)
for key in keys:
dict.__setitem__(self, key, [])
self.listkeys = keys
def __setitem__(self, key, value):
if key in self.listkeys:
self[key].append(value)
else:
dict.__setitem__(self, key, value)
def __repr__(self):
text = dict.__repr__(self)
try:
attributes = self.attributes
except AttributeError:
return text
return "DictElement(%s, attributes=%s)" % (text, repr(attributes))
class NotXMLError(ValueError):
def __init__(self, message):
self.msg = message
def __str__(self):
return "Failed to parse the XML data (%s). Please make sure that the input data are in XML format." % self.msg
class CorruptedXMLError(ValueError):
def __init__(self, message):
self.msg = message
def __str__(self):
return "Failed to parse the XML data (%s). Please make sure that the input data are not corrupted." % self.msg
class ValidationError(ValueError):
"""Validating parsers raise this error if the parser finds a tag in the XML that is not defined in the DTD. Non-validating parsers do not raise this error. The Bio.Entrez.read and Bio.Entrez.parse functions use validating parsers by default (see those functions for more information)"""
def __init__(self, name):
self.name = name
def __str__(self):
return "Failed to find tag '%s' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False." % self.name
class DataHandler:
home = os.path.expanduser('~')
local_dtd_dir = os.path.join(home, '.biopython', 'Bio', 'Entrez', 'DTDs')
del home
from Bio import Entrez
global_dtd_dir = os.path.join(str(Entrez.__path__[0]), "DTDs")
del Entrez
def __init__(self, validate):
self.stack = []
self.errors = []
self.integers = []
self.strings = []
self.lists = []
self.dictionaries = []
self.structures = {}
self.items = []
self.dtd_urls = []
self.validating = validate
self.parser = expat.ParserCreate(namespace_separator=" ")
self.parser.SetParamEntityParsing(expat.XML_PARAM_ENTITY_PARSING_ALWAYS)
self.parser.XmlDeclHandler = self.xmlDeclHandler
def read(self, handle):
"""Set up the parser and let it parse the XML results"""
try:
self.parser.ParseFile(handle)
except expat.ExpatError, e:
if self.parser.StartElementHandler:
# We saw the initial <!xml declaration, so we can be sure that
# we are parsing XML data. Most likely, the XML file is
# corrupted.
raise CorruptedXMLError(e)
else:
# We have not seen the initial <!xml declaration, so probably
# the input data is not in XML format.
raise NotXMLError(e)
try:
return self.object
except AttributeError:
if self.parser.StartElementHandler:
# We saw the initial <!xml declaration, and expat didn't notice
# any errors, so self.object should be defined. If not, this is
# a bug.
raise RuntimeError("Failed to parse the XML file correctly, possibly due to a bug in Bio.Entrez. Please contact the Biopython developers at biopython-dev#biopython.org for assistance.")
else:
# We did not see the initial <!xml declaration, so probably
# the input data is not in XML format.
raise NotXMLError("XML declaration not found")
def parse(self, handle):
BLOCK = 1024
while True:
#Read in another block of the file...
text = handle.read(BLOCK)
if not text:
# We have reached the end of the XML file
if self.stack:
# No more XML data, but there is still some unfinished
# business
raise CorruptedXMLError
try:
for record in self.object:
yield record
except AttributeError:
if self.parser.StartElementHandler:
# We saw the initial <!xml declaration, and expat
# didn't notice any errors, so self.object should be
# defined. If not, this is a bug.
raise RuntimeError("Failed to parse the XML file correctly, possibly due to a bug in Bio.Entrez. Please contact the Biopython developers at biopython-dev#biopython.org for assistance.")
else:
# We did not see the initial <!xml declaration, so
# probably the input data is not in XML format.
raise NotXMLError("XML declaration not found")
self.parser.Parse("", True)
self.parser = None
return
try:
self.parser.Parse(text, False)
except expat.ExpatError, e:
if self.parser.StartElementHandler:
# We saw the initial <!xml declaration, so we can be sure
# that we are parsing XML data. Most likely, the XML file
# is corrupted.
raise CorruptedXMLError(e)
else:
# We have not seen the initial <!xml declaration, so
# probably the input data is not in XML format.
raise NotXMLError(e)
if not self.stack:
# Haven't read enough from the XML file yet
continue
records = self.stack[0]
if not isinstance(records, list):
raise ValueError("The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse")
while len(records) > 1: # Then the top record is finished
record = records.pop(0)
yield record
def xmlDeclHandler(self, version, encoding, standalone):
# XML declaration found; set the handlers
self.parser.StartElementHandler = self.startElementHandler
self.parser.EndElementHandler = self.endElementHandler
self.parser.CharacterDataHandler = self.characterDataHandler
self.parser.ExternalEntityRefHandler = self.externalEntityRefHandler
self.parser.StartNamespaceDeclHandler = self.startNamespaceDeclHandler
def startNamespaceDeclHandler(self, prefix, un):
raise NotImplementedError("The Bio.Entrez parser cannot handle XML data that make use of XML namespaces")
def startElementHandler(self, name, attrs):
self.content = ""
if name in self.lists:
object = ListElement()
elif name in self.dictionaries:
object = DictionaryElement()
elif name in self.structures:
object = StructureElement(self.structures[name])
elif name in self.items: # Only appears in ESummary
name = str(attrs["Name"]) # convert from Unicode
del attrs["Name"]
itemtype = str(attrs["Type"]) # convert from Unicode
del attrs["Type"]
if itemtype=="Structure":
object = DictionaryElement()
elif name in ("ArticleIds", "History"):
object = StructureElement(["pubmed", "medline"])
elif itemtype=="List":
object = ListElement()
else:
object = StringElement()
object.itemname = name
object.itemtype = itemtype
elif name in self.strings + self.errors + self.integers:
self.attributes = attrs
return
else:
# Element not found in DTD
if self.validating:
raise ValidationError(name)
else:
# this will not be stored in the record
object = ""
if object!="":
object.tag = name
if attrs:
object.attributes = dict(attrs)
if len(self.stack)!=0:
current = self.stack[-1]
try:
current.append(object)
except AttributeError:
current[name] = object
self.stack.append(object)
def endElementHandler(self, name):
value = self.content
if name in self.errors:
if value=="":
return
else:
raise RuntimeError(value)
elif name in self.integers:
value = IntegerElement(value)
elif name in self.strings:
# Convert Unicode strings to plain strings if possible
try:
value = StringElement(value)
except UnicodeEncodeError:
value = UnicodeElement(value)
elif name in self.items:
self.object = self.stack.pop()
if self.object.itemtype in ("List", "Structure"):
return
elif self.object.itemtype=="Integer" and value:
value = IntegerElement(value)
else:
# Convert Unicode strings to plain strings if possible
try:
value = StringElement(value)
except UnicodeEncodeError:
value = UnicodeElement(value)
name = self.object.itemname
else:
self.object = self.stack.pop()
return
value.tag = name
if self.attributes:
value.attributes = dict(self.attributes)
del self.attributes
current = self.stack[-1]
if current!="":
try:
current.append(value)
except AttributeError:
current[name] = value
def characterDataHandler(self, content):
self.content += content
def elementDecl(self, name, model):
"""This callback function is called for each element declaration:
<!ELEMENT name (...)>
encountered in a DTD. The purpose of this function is to determine
whether this element should be regarded as a string, integer, list
dictionary, structure, or error."""
if name.upper()=="ERROR":
self.errors.append(name)
return
if name=='Item' and model==(expat.model.XML_CTYPE_MIXED,
expat.model.XML_CQUANT_REP,
None, ((expat.model.XML_CTYPE_NAME,
expat.model.XML_CQUANT_NONE,
'Item',
()
),
)
):
# Special case. As far as I can tell, this only occurs in the
# eSummary DTD.
self.items.append(name)
return
# First, remove ignorable parentheses around declarations
while (model[0] in (expat.model.XML_CTYPE_SEQ,
expat.model.XML_CTYPE_CHOICE)
and model[1] in (expat.model.XML_CQUANT_NONE,
expat.model.XML_CQUANT_OPT)
and len(model[3])==1):
model = model[3][0]
# PCDATA declarations correspond to strings
if model[0] in (expat.model.XML_CTYPE_MIXED,
expat.model.XML_CTYPE_EMPTY):
self.strings.append(name)
return
# List-type elements
if (model[0] in (expat.model.XML_CTYPE_CHOICE,
expat.model.XML_CTYPE_SEQ) and
model[1] in (expat.model.XML_CQUANT_PLUS,
expat.model.XML_CQUANT_REP)):
self.lists.append(name)
return
# This is the tricky case. Check which keys can occur multiple
# times. If only one key is possible, and it can occur multiple
# times, then this is a list. If more than one key is possible,
# but none of them can occur multiple times, then this is a
# dictionary. Otherwise, this is a structure.
# In 'single' and 'multiple', we keep track which keys can occur
# only once, and which can occur multiple times.
single = []
multiple = []
# The 'count' function is called recursively to make sure all the
# children in this model are counted. Error keys are ignored;
# they raise an exception in Python.
def count(model):
quantifier, name, children = model[1:]
if name==None:
if quantifier in (expat.model.XML_CQUANT_PLUS,
expat.model.XML_CQUANT_REP):
for child in children:
multiple.append(child[2])
else:
for child in children:
count(child)
elif name.upper()!="ERROR":
if quantifier in (expat.model.XML_CQUANT_NONE,
expat.model.XML_CQUANT_OPT):
single.append(name)
elif quantifier in (expat.model.XML_CQUANT_PLUS,
expat.model.XML_CQUANT_REP):
multiple.append(name)
count(model)
if len(single)==0 and len(multiple)==1:
self.lists.append(name)
elif len(multiple)==0:
self.dictionaries.append(name)
else:
self.structures.update({name: multiple})
def open_dtd_file(self, filename):
path = os.path.join(DataHandler.local_dtd_dir, filename)
try:
handle = open(path, "rb")
except IOError:
pass
else:
return handle
path = os.path.join(DataHandler.global_dtd_dir, filename)
try:
handle = open(path, "rb")
except IOError:
pass
else:
return handle
return None
def externalEntityRefHandler(self, context, base, systemId, publicId):
"""The purpose of this function is to load the DTD locally, instead
of downloading it from the URL specified in the XML. Using the local
DTD results in much faster parsing. If the DTD is not found locally,
we try to download it. If new DTDs become available from NCBI,
putting them in Bio/Entrez/DTDs will allow the parser to see them."""
urlinfo = urlparse.urlparse(systemId)
#Following attribute requires Python 2.5+
#if urlinfo.scheme=='http':
if urlinfo[0]=='http':
# Then this is an absolute path to the DTD.
url = systemId
elif urlinfo[0]=='':
# Then this is a relative path to the DTD.
# Look at the parent URL to find the full path.
url = self.dtd_urls[-1]
source = os.path.dirname(url)
url = os.path.join(source, systemId)
self.dtd_urls.append(url)
# First, try to load the local version of the DTD file
location, filename = os.path.split(systemId)
handle = self.open_dtd_file(filename)
if not handle:
# DTD is not available as a local file. Try accessing it through
# the internet instead.
message = """\
Unable to load DTD file %s.
Bio.Entrez uses NCBI's DTD files to parse XML files returned by NCBI Entrez.
Though most of NCBI's DTD files are included in the Biopython distribution,
sometimes you may find that a particular DTD file is missing. While we can
access the DTD file through the internet, the parser is much faster if the
required DTD files are available locally.
For this purpose, please download %s from
%s
and save it either in directory
%s
or in directory
%s
in order for Bio.Entrez to find it.
Alternatively, you can save %s in the directory
Bio/Entrez/DTDs in the Biopython distribution, and reinstall Biopython.
Please also inform the Biopython developers about this missing DTD, by
reporting a bug on http://bugzilla.open-bio.org/ or sign up to our mailing
list and emailing us, so that we can include it with the next release of
Biopython.
Proceeding to access the DTD file through the internet...
""" % (filename, filename, url, self.global_dtd_dir, self.local_dtd_dir, filename)
warnings.warn(message)
try:
handle = urllib.urlopen(url)
except IOError:
raise RuntimeException("Failed to access %s at %s" % (filename, url))
parser = self.parser.ExternalEntityParserCreate(context)
parser.ElementDeclHandler = self.elementDecl
parser.ParseFile(handle)
handle.close()
self.dtd_urls.pop()
return 1

So you have a file containing multiple XML documents one after the other? Here is an example which strips out the <?xml ?> PIs and wraps the data in a root tag to parse the whole thing as a single XML document:
import re
import lxml.etree
re_strip_pi = re.compile('<\?xml [^?>]+\?>', re.M)
data = '<root>' + open('stocks.xml', 'rb').read() + '</root>'
match = re_strip_pi.search(data)
data = re_strip_pi.sub('', data)
tree = lxml.etree.fromstring(match.group() + data)
for prod in tree.xpath('//PRODUCT'):
print prod

You can't have multiple XML documents in one XML file. Split the documents - composed in whatever way - into single XML files and parse them one-by-one.