def test_XMLOutputStream_startEnd(self): oss = libsbml.ostringstream() stream = libsbml.XMLOutputStream(oss,"",False) self.assert_( stream != None ) stream.startEndElement( "id") str = oss.str() self.assert_(( "<id/>" == str )) _dummyList = [ stream ]; _dummyList[:] = []; del _dummyList pass
def test_XMLOutputStream_createStringWithProgramInfo(self): expected = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"; oss = libsbml.ostringstream() stream = libsbml.XMLOutputStream(oss,"UTF-8",True, "", "") self.assert_( stream != None ) str = oss.str() self.assert_(( expected == str )) _dummyList = [ stream ]; _dummyList[:] = []; del _dummyList pass
def test_XMLOutputStream_PredefinedEntity(self): oss = libsbml.ostringstream() stream = libsbml.XMLOutputStream(oss,"",False) stream.startElement( "testpde") stream.writeAttribute( "amp", "&" ) stream.writeAttribute( "apos", "'" ) stream.writeAttribute( "gt", ">" ) stream.writeAttribute( "lt", "<" ) stream.writeAttribute( "quot", "\"" ) stream.writeAttribute( "pdeamp", "&" ) stream.writeAttribute( "pdeapos", "'") stream.writeAttribute( "pdegt", ">" ) stream.writeAttribute( "pdelt", "<" ) stream.writeAttribute( "pdequot", """) stream.endElement( "testpde") expected = "<testpde amp=\"&\" apos=\"'\" gt=\">\" lt=\"<\" quot=\""\" pdeamp=\"&\" pdeapos=\"'\" pdegt=\">\" pdelt=\"<\" pdequot=\""\"/>"; s = oss.str() self.assert_(( expected == s )) _dummyList = [ stream ]; _dummyList[:] = []; del _dummyList pass
def test_XMLOutputStream_Elements(self): d = 2.4 l = 123456789 ui = 5 i = -3 oss = libsbml.ostringstream() stream = libsbml.XMLOutputStream(oss,"",False) stream.startElement( "fred") stream.writeAttribute( "chars", "two") stream.writeAttributeBool( "bool",True) stream.writeAttribute( "double",d) stream.writeAttribute( "long",l) stream.writeAttribute( "uint",ui) stream.writeAttribute( "int",i) stream.endElement( "fred") expected = "<fred chars=\"two\" bool=\"true\" double=\"2.4\" long=\"123456789\" uint=\"5\" int=\"-3\"/>"; s = oss.str() self.assert_(( expected == s )) _dummyList = [ stream ]; _dummyList[:] = []; del _dummyList pass
def test_XMLOutputStream_CharacterReference(self): oss = libsbml.ostringstream() stream = libsbml.XMLOutputStream(oss,"",False) stream.startElement( "testcr") stream.writeAttribute( "chars", "one" ) stream.writeAttribute( "amp", "&" ) stream.writeAttribute( "deccr", "¨" ) stream.writeAttribute( "hexcr", "¨") stream.writeAttribute( "lhexcr", "¨") stream.writeAttribute( "nodeccr1", "ژ" ) stream.writeAttribute( "nodeccr2", "&#;" ) stream.writeAttribute( "nodeccr3", "�a8;" ) stream.writeAttribute( "nodeccr4", "�A8;" ) stream.writeAttribute( "nohexcr1", "&#x;" ) stream.writeAttribute( "nohexcr2", "ꯍ" ) stream.endElement( "testcr") expected = "<testcr chars=\"one\" amp=\"&\" deccr=\"¨\" hexcr=\"¨\" lhexcr=\"¨\" nodeccr1=\"&#01688\" nodeccr2=\"&#;\" nodeccr3=\"&#00a8;\" nodeccr4=\"&#00A8;\" nohexcr1=\"&#x;\" nohexcr2=\"&#xABCD\"/>"; s = oss.str() self.assert_(( expected == s )) _dummyList = [ stream ]; _dummyList[:] = []; del _dummyList pass
def validate(self, file):
if not os.path.exists(file):
print("[Error] %s : No such file." % (infile))
self.numinvalid += 1
return
start = time.time()
sbmlDoc = libsbml.readSBML(file)
stop = time.time()
timeRead = (stop - start) * 1000
errors = sbmlDoc.getNumErrors()
seriousErrors = False
numReadErr = 0
numReadWarn = 0
errMsgRead = ""
if errors > 0:
for i in range(errors):
severity = sbmlDoc.getError(i).getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (
severity == libsbml.LIBSBML_SEV_FATAL):
seriousErrors = True
numReadErr += 1
else:
numReadWarn += 1
oss = libsbml.ostringstream()
sbmlDoc.printErrors(oss)
errMsgRead = oss.str()
# If serious errors are encountered while reading an SBML document, it
# does not make sense to go on and do full consistency checking because
# the model may be nonsense in the first place.
numCCErr = 0
numCCWarn = 0
errMsgCC = ""
skipCC = False
timeCC = 0.0
if seriousErrors:
skipCC = True
errMsgRead += "Further consistency checking and validation aborted."
self.numinvalid += 1
else:
sbmlDoc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY,
self.ucheck)
start = time.time()
failures = sbmlDoc.checkConsistency()
stop = time.time()
timeCC = (stop - start) * 1000
if failures > 0:
isinvalid = False
for i in range(failures):
severity = sbmlDoc.getError(i).getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (
severity == libsbml.LIBSBML_SEV_FATAL):
numCCErr += 1
isinvalid = True
else:
numCCWarn += 1
if isinvalid:
self.numinvalid += 1
oss = libsbml.ostringstream()
sbmlDoc.printErrors(oss)
errMsgCC = oss.str()
#
# print results
#
print(" filename : %s" % (file))
print(" file size (byte) : %d" % (os.path.getsize(file)))
print(" read time (ms) : %f" % (timeRead))
if not skipCC:
print(" c-check time (ms) : %f" % (timeCC))
else:
print(" c-check time (ms) : skipped")
print(" validation error(s) : %d" % (numReadErr + numCCErr))
if not skipCC:
print(" (consistency error(s)): %d" % (numCCErr))
else:
print(" (consistency error(s)): skipped")
print(" validation warning(s) : %d" % (numReadWarn + numCCWarn))
if not skipCC:
print(" (consistency warning(s)): %d" % (numCCWarn))
else:
print(" (consistency warning(s)): skipped")
if errMsgRead or errMsgCC:
print()
print("===== validation error/warning messages =====\n")
if errMsgRead:
print(errMsgRead)
if errMsgCC:
print("*** consistency check ***\n")
print(errMsgCC)
def validate(self, file):
if not os.path.exists(file):
print "[Error] %s : No such file." % (infile)
self.numinvalid += 1
return
start = time.time()
sbmlDoc = libsbml.readSBML(file)
stop = time.time()
timeRead = (stop - start)*1000
errors = sbmlDoc.getNumErrors()
seriousErrors = False
numReadErr = 0
numReadWarn = 0
errMsgRead = ""
if errors > 0:
for i in range(errors):
severity = sbmlDoc.getError(i).getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (severity == libsbml.LIBSBML_SEV_FATAL):
seriousErrors = True
numReadErr += 1
else:
numReadWarn += 1
oss = libsbml.ostringstream()
sbmlDoc.printErrors(oss)
errMsgRead = oss.str()
# If serious errors are encountered while reading an SBML document, it
# does not make sense to go on and do full consistency checking because
# the model may be nonsense in the first place.
numCCErr = 0
numCCWarn = 0
errMsgCC = ""
skipCC = False;
timeCC = 0.0
if seriousErrors:
skipCC = True;
errMsgRead += "Further consistency checking and validation aborted."
self.numinvalid += 1;
else:
sbmlDoc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, self.ucheck)
start = time.time()
failures = sbmlDoc.checkConsistency()
stop = time.time()
timeCC = (stop - start)*1000
if failures > 0:
isinvalid = False;
for i in range(failures):
severity = sbmlDoc.getError(i).getSeverity()
if (severity == libsbml.LIBSBML_SEV_ERROR) or (severity == libsbml.LIBSBML_SEV_FATAL):
numCCErr += 1
isinvalid = True;
else:
numCCWarn += 1
if isinvalid:
self.numinvalid += 1;
oss = libsbml.ostringstream()
sbmlDoc.printErrors(oss)
errMsgCC = oss.str()
#
# print results
#
print " filename : %s" % (file)
print " file size (byte) : %d" % (os.path.getsize(file))
print " read time (ms) : %f" % (timeRead)
if not skipCC :
print " c-check time (ms) : %f" % (timeCC)
else:
print " c-check time (ms) : skipped"
print " validation error(s) : %d" % (numReadErr + numCCErr)
if not skipCC :
print " (consistency error(s)): %d" % (numCCErr)
else:
print " (consistency error(s)): skipped"
print " validation warning(s) : %d" % (numReadWarn + numCCWarn)
if not skipCC :
print " (consistency warning(s)): %d" % (numCCWarn)
else:
print " (consistency warning(s)): skipped"
