def create_java_parser(jdriver=None):
try:
if jdriver:
return XMLReaderFactory.createXMLReader(jdriver)
elif jaxp:
return factory.newSAXParser().getXMLReader()
else:
return XMLReaderFactory.createXMLReader()
except ParserConfigurationException, e:
raise _exceptions.SAXReaderNotAvailable(e.getMessage())
def create_java_parser(jdriver=None):
try:
if jdriver:
return XMLReaderFactory.createXMLReader(jdriver)
elif jaxp:
return factory.newSAXParser().getXMLReader()
else:
return XMLReaderFactory.createXMLReader()
except ParserConfigurationException, e:
raise _exceptions.SAXReaderNotAvailable(e.getMessage())
def mainproc():
u'''Функция для склейки карточки с блоками правил'''
try:
rootPath = AppInfoSingleton.getAppInfo().getCurUserData().getPath(
) + '/xforms/'
except:
rootPath = 'E:/Projects/celesta/ssmmd/userscore/ssmmd/xforms/file/'
templatePath = rootPath + add #путь к карточке, в которую необходимо вставить праила
rulePath = rootPath + 'ruleTemplate.xml' #путь к блоку с правилами
bindPath = rootPath + 'bindTemplate.xml' #путь к блоку с биндами для правил
stringWriter = StringWriter()
xmlWriter = XMLOutputFactory.newInstance().createXMLStreamWriter(
stringWriter)
parser = XMLReaderFactory.createXMLReader()
handler = XformsAddRules(rulePath, bindPath, xmlWriter)
parser.setContentHandler(handler)
parser.setErrorHandler(handler)
parser.setFeature("http://xml.org/sax/features/namespace-prefixes", True)
parser.setProperty("http://xml.org/sax/properties/lexical-handler",
handler)
stream = FileInputStream(templatePath)
parser.parse(InputSource(stream))
xmlWriter.close()
stringWriter.close()
return unicode(stringWriter)
def deleteGenes(fileName, geneStarts):
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = GeneDeleter(
geneStarts, "profelis.temp.blastp.xml")
reader.parse(fileName)
os.remove(fileName)
os.rename("profelis.temp.blastp.xml", fileName)
def _createReader(self, path, value, xmlWriter):
u'''функция создания ридера для чтения файла настроек, с учетом указанного пути'''
pathList = list()
name = r"[a-zA-Z_][a-zA-Z_0-9]+"
elementPatern = regexp.compile(r"""(%s)(?:\[(?:@(%s)=(?:'([^']+)'|\"([^\"]+)\")|([0-9]+))\])?(?:/@(%s))?""" % (name, name, name), regexp.UNICODE)
lastEnd = -1
for a in elementPatern.finditer(unicode(path)):
if lastEnd + 1 != a.start(0) or (lastEnd > 0 and path[lastEnd]not in ('/', '\\')):
raise CelestaException('Bad XPath expression')
pathList.append(NodeProperties(a.groups()))
lastEnd = a.end(0)
parser = XMLReaderFactory.createXMLReader()
handler = WriteSettings(pathList, xmlWriter, value)
parser.setContentHandler(handler)
parser.setErrorHandler(handler)
parser.setFeature("http://xml.org/sax/features/namespace-prefixes", True)
parser.setProperty("http://xml.org/sax/properties/lexical-handler", handler)
stream = FileInputStream(self._getUserSettingsFilePath())
parser.parse(InputSource(stream))
stream.close()
if not handler.result:
stream = FileInputStream(self._getSettingsFilePath())
parser.parse(InputSource(stream))
stream.close()
return handler.result
def addGenes(fileName, source):
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = GeneAdder(
source, "profelis.temp.blastp.xml")
reader.parse(fileName)
os.remove(fileName)
os.rename("profelis.temp.blastp.xml", fileName)
def report(name, genes, output):
"""
name: Name of the genome.
genes: A dictionary that maps query names to Iteration objects.
output: Output file name without an extension.
Writes a report of the contents of the blast searchs for the queries in
genes into "name.html", "name.blastp.xml", and "name.xls".
"""
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = BlastMerger(["extendedBlasts/" + name + ".blastp.xml", "intergenicBlasts/" + name + ".blastp.xml"], genes.keys(), output + ".blastp.xml", True)
reader.parse("initialBlasts/" + name + ".blastp.xml")
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = HTMLWriter(output + ".blastp.html")
reader.parse(output + ".blastp.xml")
writeSpreadsheet(genes.values(), output)
def parseBlast(fileName): """ A function for parsing XML blast output. """ reader = XMLReaderFactory.createXMLReader() reader.entityResolver = reader.contentHandler = BlastHandler() reader.parse(fileName) return dict(map(lambda iteration: (iteration.query, iteration), reader.getContentHandler().iterations))
def startElement(self, uri, tag, name, attributes):
if tag == "Iteration" and not self.added:
self.added = True
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = GeneWriter(self.output)
try:
reader.parse(self.source)
except BreakParsingException:
print "Hello"
self.output.write("<" + tag + ">")
def startElement(self, uri, tag, name, attributes):
if tag == "Iteration" and not self.added:
self.added = True
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = GeneWriter(
self.output)
try:
reader.parse(self.source)
except BreakParsingException:
print "Hello"
self.output.write("<" + tag + ">")
def parseBlast(fileName):
"""
A function for parsing XML blast output.
"""
reader = XMLReaderFactory.createXMLReader()
reader.contentHandler = BlastHandler()
reader.entityResolver = BlastHandler()
reader.parse(fileName)
for iteration in reader.contentHandler.iterations:
iteration.xmlFile = fileName
return reader.contentHandler.database, reader.contentHandler.evalue, reader.contentHandler.iterations
def parseBlast(fileName):
"""
A function for parsing XML blast output.
"""
reader = XMLReaderFactory.createXMLReader()
reader.contentHandler = BlastHandler()
reader.entityResolver = BlastHandler()
reader.parse(fileName)
for iteration in reader.contentHandler.iterations:
iteration.xmlFile = fileName
return reader.contentHandler.database, reader.contentHandler.evalue, reader.contentHandler.iterations
def load(self, filename, language):
parser = XMLReaderFactory.createXMLReader()
#if (filename.endsWith(".gz")):
#input_src = InputSource(GZipInputStream(FileInputStream(filename)))
#else:
input_src = InputSource(filename)
parser.contentHandler = ParseHandler(language)
parser.parse(input_src)
HibernateUtil.commitTransaction()
HibernateUtil.closeSession()
def uploadXML(self, action="ui"):
'''
функция реализует загрузку данных из xml в базу данных
'''
parser = XMLReaderFactory.createXMLReader()
handler = UploadXMLHandler(self.tableInstance, action)
parser.setContentHandler(handler)
parser.setErrorHandler(handler)
parser.setFeature("http://xml.org/sax/features/namespace-prefixes",
True)
parser.setProperty("http://xml.org/sax/properties/lexical-handler",
handler)
parser.parse(InputSource(self.dataStream))
def __init__(self, rulePath, bindPath, xmlWriter):
self.rulePath = rulePath
self.bindPath = bindPath
self.xmlWriter = xmlWriter
self.parser = XMLReaderFactory.createXMLReader()
handler = RulesWriter(self.xmlWriter)
self.parser.setContentHandler(handler)
self.parser.setErrorHandler(handler)
self.parser.setFeature(
"http://xml.org/sax/features/namespace-prefixes", True)
self.parser.setProperty(
"http://xml.org/sax/properties/lexical-handler", handler)
self.state = 0
def endElement(self, uri, tag, name):
if tag == "BlastOutput_iterations":
if self.sources:
self.output.write(" ")
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = BlastMerger(self.sources[1:], self.genes, self.output, False, self, self.iteration)
try:
reader.parse(self.sources[0])
except BreakParsingException:
if self.parent:
raise BreakParsingException()
else:
pass
else:
raise BreakParsingException()
if self.iterationQueryDef:
self.iterationQueryDef = False
if self.iterationQueryDefString[:self.iterationQueryDefString.rfind(":")] in self.genes:
self.printing = True
self.holding = False
self.output.write("".join(self.text))
self.text = []
else:
self.printing = False
self.holding = False
self.text = []
if self.printing:
if self.holding:
self.text += re.sub("\n\s*\n", "\n", "".join(self.whitespace)) + "</" + tag + ">"
else:
self.output.write(re.sub("\n\s*\n", "\n", "".join(self.whitespace)) + "</" + tag + ">")
self.whitespace = []
if tag == "Iteration":
self.holding = False
self.printing = True
def report(name, genes, output):
"""
name: Name of the genome.
genes: A dictionary that maps query names to Iteration objects.
output: Output file name without an extension.
Writes a report of the contents of the blast searchs for the queries in
genes into "<name>.dat" and "<name>.xls".
"""
dataOutput = open(output + ".dat", "w")
spreadsheetOutput = open(output + ".xls", "w")
reader = XMLReaderFactory.createXMLReader()
reader.setContentHandler(Collector(genes.keys(), dataOutput))
reader.setEntityResolver(reader.getContentHandler())
reader.parse("initialBlasts/" + name + ".blastp.xml")
reader.parse("extendedBlasts/" + name + ".blastp.xml")
reader.parse("intergenicBlasts/" + name + ".blastp.xml")
writeSpreadsheet(genes.values(), spreadsheetOutput)
dataOutput.close()
spreadsheetOutput.close()
def writeHTML(fileName):
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = HTMLWriter(fileName[:-4] + ".html" if fileName[-4:] == ".xml" else fileName + ".html")
reader.parse(fileName)
def addGenes(fileName, source):
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = GeneAdder(source, "profelis.temp.blastp.xml")
reader.parse(fileName)
os.remove(fileName)
os.rename("profelis.temp.blastp.xml", fileName)
def deleteGenes(fileName, geneStarts):
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = GeneDeleter(geneStarts, "profelis.temp.blastp.xml")
reader.parse(fileName)
os.remove(fileName)
os.rename("profelis.temp.blastp.xml", fileName)
def __init__(self, encoding, namespace_separator):
self.encoding = encoding
self.CurrentLineNumber = 1
self.CurrentColumnNumber = 0
self._NextLineNumber = 1
self._NextColumnNumber = 0
self.ErrorLineNumber = -1
self.ErrorColumnNumber = -1
self.ErrorCode = None
if namespace_separator is None:
self.namespace_separator = namespace_separator
elif isinstance(namespace_separator, basestring):
self.namespace_separator = str(namespace_separator)
if len(self.namespace_separator) > 1:
error = ("namespace_separator must be at most one character, "
"omitted, or None")
raise ValueError(error)
else:
error = ("ParserCreate() argument 2 must be string or None, "
"not %s" % type(namespace_separator).__name__)
raise TypeError(error)
# See http://bugs.jython.org/issue1537
try:
self._reader = XMLReaderFactory.createXMLReader(
_mangled_xerces_parser_name)
except:
self._reader = XMLReaderFactory.createXMLReader(
_xerces_parser_name)
if self.namespace_separator is None:
try:
feature = "http://xml.org/sax/features/namespaces"
self._reader.setFeature(feature, False)
except SAXNotRecognizedException:
error = ("namespace support cannot be disabled; "
"set namespace_separator to a string of length 1.")
raise ValueError(error)
self._base = None
self._buffer_text = True
self._returns_unicode = True
self._data = StringBuilder()
self._handler = XMLEventHandler(self)
self._reader.setContentHandler(self._handler)
self._reader.setErrorHandler(self._handler)
self._reader.setDTDHandler(self._handler)
self._reader.setEntityResolver(self._handler)
sax_properties = ("lexical-handler", "declaration-handler")
for name in sax_properties:
try:
name = "http://xml.org/sax/properties/" + name
self._reader.setProperty(name, self._handler)
except SAXNotRecognizedException:
error = "can't set property %r" % name
raise NotImplementedError(error)
apache_features = (("nonvalidating/load-external-dtd", False), )
for name, value in apache_features:
try:
name = "http://apache.org/xml/features/" + name
self._reader.setFeature(name, value)
except SAXNotRecognizedException:
error = "can't set feature %r" % name
raise NotImplementedError(error)
# experimental
#f = "http://xml.org/sax/features/external-general-entities"
f = "http://xml.org/sax/features/external-parameter-entities"
#self._reader.setFeature(f, False)
# check
f = "http://xml.org/sax/features/use-entity-resolver2"
assert self._reader.getFeature(f)
def xmlToText(input, output): reader = XMLReaderFactory.createXMLReader() translater = BlastTranslater(output) reader.setContentHandler(translater) reader.setEntityResolver(translater) reader.parse(input)
def __init__(self, encoding, namespace_separator):
self.encoding = encoding
self.CurrentLineNumber = 1
self.CurrentColumnNumber = 0
self._NextLineNumber = 1
self._NextColumnNumber = 0
self.ErrorLineNumber = -1
self.ErrorColumnNumber = -1
self.ErrorCode = None
if namespace_separator is None:
self.namespace_separator = namespace_separator
elif isinstance(namespace_separator, basestring):
self.namespace_separator = str(namespace_separator)
if len(self.namespace_separator) > 1:
error = ("namespace_separator must be at most one character, "
"omitted, or None")
raise ValueError(error)
else:
error = ("ParserCreate() argument 2 must be string or None, "
"not %s" % type(namespace_separator).__name__)
raise TypeError(error)
self._reader = XMLReaderFactory.createXMLReader(_xerces_parser)
if self.namespace_separator is None:
try:
feature = "http://xml.org/sax/features/namespaces"
self._reader.setFeature(feature, False)
except SAXNotRecognizedException:
error = ("namespace support cannot be disabled; "
"set namespace_separator to a string of length 1.")
raise ValueError(error)
self._base = None
self._buffer_text = True
self._returns_unicode = True
self._data = StringBuilder()
self._handler = XMLEventHandler(self)
self._reader.setContentHandler(self._handler)
self._reader.setErrorHandler(self._handler)
self._reader.setDTDHandler(self._handler)
self._reader.setEntityResolver(self._handler)
sax_properties = ("lexical-handler", "declaration-handler")
for name in sax_properties:
try:
name = "http://xml.org/sax/properties/" + name
self._reader.setProperty(name, self._handler)
except SAXNotRecognizedException:
error = "can't set property %r" % name
raise NotImplementedError(error)
apache_features = (("nonvalidating/load-external-dtd", False),)
for name, value in apache_features:
try:
name = "http://apache.org/xml/features/" + name
self._reader.setFeature(name, value)
except SAXNotRecognizedException:
error = "can't set feature %r" % name
raise NotImplementedError(error)
# experimental
#f = "http://xml.org/sax/features/external-general-entities"
f = "http://xml.org/sax/features/external-parameter-entities"
#self._reader.setFeature(f, False)
# check
f = "http://xml.org/sax/features/use-entity-resolver2"
assert self._reader.getFeature(f)
def xmlToText(input, output):
reader = XMLReaderFactory.createXMLReader()
translater = BlastTranslater(output)
reader.setContentHandler(translater)
reader.setEntityResolver(translater)
reader.parse(input)
def writeHTML(fileName):
reader = XMLReaderFactory.createXMLReader()
reader.entityResolver = reader.contentHandler = HTMLWriter(
fileName[:-4] + ".html" if fileName[-4:] == ".xml" else fileName +
".html")
reader.parse(fileName)