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###############################################################################
# Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
###############################################################################
# Author: Martin D. Smith
"""Validate DataSet XML files"""
import os
import re
from urlparse import urlparse
import xml.etree.ElementTree as ET
import logging
XMLNS = "http://pacificbiosciences.com/PacBioDataModel.xsd"
log = logging.getLogger(__name__)
def validateResources(xmlroot, relTo='.'):
"""Validate the resources in an XML file.
Args:
xmlroot: The ET root of an xml tree
relTo: ('.') The path relative to which resources may reside. This will
work poorly if relTo is not set to the dirname of the incoming
XML file.
"""
stack = [xmlroot]
while stack:
element = stack.pop()
stack.extend(element.getchildren())
resId = element.get('ResourceId')
if resId:
parsedId = urlparse(resId)
rfn = urlparse(resId).path.strip()
if not os.path.exists(rfn):
if (not os.path.exists(os.path.join(relTo,
rfn)) and
not os.path.exists(os.path.join('.',
rfn))):
raise IOError, "{f} not found".format(f=rfn)
def validateLxml(xml_fn, xsd_fn):
try:
from lxml import etree
schema = etree.XMLSchema(etree.parse(xsd_fn))
xml_file = etree.parse(xml_fn)
if not schema.validate(xml_file):
print schema.error_log
except ImportError:
log.debug('lxml not found, validation disabled')
def validateMiniXsv(xml_fn, xsd_fn):
try:
from minixsv import pyxsval
pyxsval.parseAndValidate(xml_fn, xsd_fn)
except ImportError:
log.debug('minixsv not found, validation disabled')
def validateXml(xmlroot, skipResources=False, relTo='.'):
if not skipResources:
validateResources(xmlroot, relTo)
# Conceal the first characters of UniqueIds if they are legal numbers that
# would for some odd reason be considered invalid. Let all illegal
# characters fall through to the validator.
try:
from pbcore.io.dataset import DataSetXsd
log.debug('Validating with PyXb')
fixedString = re.sub('UniqueId="[0-9]', 'UniqueId="f',
ET.tostring(xmlroot))
fixedString = re.sub('Barcode="[0-9]', 'Barcode="f',
fixedString)
fixedString = re.sub('Pointer>[0-9]', 'Pointer>f',
fixedString)
DataSetXsd.CreateFromDocument(fixedString)
except ImportError:
log.debug('PyXb not found, validation disabled')
def validateFile(xmlfn, skipResources=False):
if ':' in xmlfn:
xmlfn = urlparse(xmlfn).path.strip()
with open(xmlfn, 'r') as xmlfile:
root = ET.parse(xmlfile).getroot()
return validateXml(root, skipResources=skipResources,
relTo=os.path.dirname(xmlfn))
def validateString(xmlString, skipResources=False, relTo='.'):
validateXml(ET.fromstring(xmlString), skipResources, relTo)
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