python-pbcore 1.2.11+dfsg-1 / usr / lib / python2.7 / dist-packages / pbcore / io / dataset / DataSetValidator.py

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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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