def guessXML(self, xml_content):
root = etree.fromstring(xml_content)
tag = root.tag.split("}")[1]
if isinstance(xml_content, bytes):
xml_content = str("%s" % xml_content.decode('ascii', 'ignore'))
if tag == "sbml":
sbmlReader = SBMLReader()
if sbmlReader is not None:
sbmlDoc = sbmlReader.readSBMLFromString(xml_content)
return self.SBML + ".level-%d.version-%d" % (
sbmlDoc.getLevel(), sbmlDoc.getVersion())
else:
return self.SBML
elif tag == "sedML":
sedmlDoc = readSedMLFromString(xml_content)
return self.SEDML + ".level-%d.version-%d" % (
sedmlDoc.getLevel(), sedmlDoc.getVersion())
elif tag == "numl":
numlDoc = readNUMLFromString(xml_content)
return self.NUML + ".level-%d.version-%d" % (numlDoc.getLevel(),
numlDoc.getVersion())
elif tag == "omexManifest":
return self.MANIFEST
else:
return self.XML
def tags_info(archive_path):
""" Reads the tags info from a given archive.
:param archive_path:
:return:
"""
tags_info = []
# add the file formats from omex
omex = libcombine.CombineArchive()
if omex.initializeFromArchive(archive_path) is None:
print("Invalid Combine Archive: {}", archive_path)
return None
sedml_entries = []
sbml_entries = []
for i in range(omex.getNumEntries()):
entry = omex.getEntry(i)
format = entry.getFormat()
location = entry.getLocation()
format_id = base_format(format)
if format_id in ['sbml', 'cellml', 'sed-ml', 'sedml', 'sbgn', 'sbol']:
tags_info.append({
'type': 'format',
'name': format_id,
})
if format_id == 'sbml':
sbml_entries.append(entry)
if format_id in ['sedml', 'sed-ml']:
sedml_entries.append(entry)
# add the SBML contents
# add the SED-ML contents
for entry in sedml_entries:
content = omex.extractEntryToString(entry.getLocation())
doc = libsedml.readSedMLFromString(
content) # type: libsedml.SedDocument
print(doc)
for model in doc.getListOfModels():
language = model.getLanguage()
if language:
name = language.split(':')[-1]
tags_info.append({
'type': 'sedml',
'name': 'model:{}'.format(name)
})
if len(doc.getListOfDataDescriptions()) > 0:
tags_info.append({'type': 'sedml', 'name': 'DataDescription'})
omex.cleanUp()
return tags_info
def checkKisaoAlgorithmParameter(self, exp, kisao, name, value):
""" Helper function for checking kisao parameter. """
p = exp.phrasedmlList[0]
# check that set AlgorithmParameter set correctly in SED-ML
phrasedml.clearReferencedSBML()
exp._setReferencedSBML(p)
sedml = exp._phrasedmlToSEDML(p)
doc = libsedml.readSedMLFromString(sedml)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
pdict = {
p.getKisaoID(): p
for p in algorithm.getListOfAlgorithmParameters()
}
self.assertTrue(kisao in pdict)
pkey = SEDMLCodeFactory.algorithmParameterToParameterKey(pdict[kisao])
if pkey.dtype == str:
self.assertEqual(pkey.value, value)
else:
# numerical parameter
self.assertAlmostEqual(float(pkey.value), value)
# check that integrator is set in python code
pystr = exp._toPython(p)
print(simulation.getElementName())
print(pystr)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
if pkey.dtype == str:
self.assertTrue(
".steadyStateSolver.setValue('{}', '{}')".format(
name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".steadyStateSolver.setValue('{}', {})".format(
name, value) in pystr)
else:
if pkey.dtype == str:
self.assertTrue(".integrator.setValue('{}', '{}')".format(
name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".integrator.setValue('{}', {})".format(
name, value) in pystr)
def checkKisaoIntegrator(self, exp, kisao, name):
""" Helper function for checking kisao integrator. """
p = exp.phrasedmlList[0]
# is kisao correct in SedDocument
phrasedml.clearReferencedSBML()
exp._setReferencedSBML(p)
sedml = exp._phrasedmlToSEDML(p)
doc = libsedml.readSedMLFromString(sedml)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
self.assertEqual(algorithm.getKisaoID(), kisao)
# is integrator/solver set in python code
pystr = exp._toPython(p)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
self.assertTrue(".setSteadyStateSolver('{}')".format(name) in pystr)
else:
self.assertTrue(".setIntegrator('{}')".format(name) in pystr)
def checkKisaoAlgorithmParameter(self, exp, kisao, name, value):
""" Helper function for checking kisao parameter. """
p = exp.phrasedmlList[0]
# check that set AlgorithmParameter set correctly in SED-ML
phrasedml.clearReferencedSBML()
exp._setReferencedSBML(p)
sedml = exp._phrasedmlToSEDML(p)
doc = libsedml.readSedMLFromString(sedml)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
pdict = {p.getKisaoID(): p for p in algorithm.getListOfAlgorithmParameters()}
self.assertTrue(kisao in pdict)
pkey = SEDMLCodeFactory.algorithmParameterToParameterKey(pdict[kisao])
if pkey.dtype == str:
self.assertEqual(pkey.value, value)
else:
# numerical parameter
self.assertAlmostEqual(float(pkey.value), value)
# check that integrator is set in python code
pystr = exp._toPython(p)
print(simulation.getElementName())
print(pystr)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
if pkey.dtype == str:
self.assertTrue(".steadyStateSolver.setValue('{}', '{}')".format(name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".steadyStateSolver.setValue('{}', {})".format(name, value) in pystr)
else:
if pkey.dtype == str:
self.assertTrue(".integrator.setValue('{}', '{}')".format(name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".integrator.setValue('{}', {})".format(name, value) in pystr)
def listDetailedContents(self):
""" List contents of the archive from the manifest.xml
:return: contentList of dictionaries with keys: filename, type
:rtype: [{}]
"""
contents = []
man = self.readManifest()
xml = et.ElementTree(et.fromstring(man))
root = xml.getroot()
for child in root:
# get content for xml element
content = None
attribute = child.attrib
formtype = attribute.get('format')
loc = attribute.get('location')
# sbml
if formtype == "http://identifiers.org/combine.specifications/sbml":
if loc.startswith('http') or loc.startswith('www'):
content = {'filename': loc, 'type': 'sbml'}
else:
content = {'filename': os.path.basename(loc), 'type': 'sbml'}
# sedml
elif formtype == "http://identifiers.org/combine.specifications/sed-ml":
zf = ZipFile(self.combinePath, 'r')
try:
sedmlRaw = zf.read(loc)
except KeyError as e:
try:
sedmlRaw = zf.read(os.path.basename(loc))
except KeyError as e:
raise e
sedmlDoc = libsedml.readSedMLFromString(sedmlRaw)
tempSedmlSource = []
for model in sedmlDoc.getListOfModels():
if os.path.splitext(os.path.basename(model.getSource()))[1] == '':
pass
else:
tempSedmlSource.append(os.path.basename(model.getSource()))
content = {'filename': os.path.basename(loc),
'type': 'sedml',
'modelsource': tempSedmlSource}
zf.close()
# manifest
elif formtype == "http://identifiers.org/combine.specifications/omex-manifest":
content = {'filename': os.path.basename(loc), 'type': 'manifest'}
# other formats
elif formtype == "image/png":
content = {'filename': os.path.basename(loc), 'type': 'png'}
elif formtype == "image/jpg" or formtype == "image/jpeg":
content = {'filename': os.path.basename(loc), 'type': 'jpg'}
elif formtype == "application/pdf":
content = {'filename': os.path.basename(loc), 'type': 'pdf'}
elif formtype == "plain/text":
content = {'filename': os.path.basename(loc), 'type': 'txt'}
elif formtype == "plain/csv":
content = {'filename': os.path.basename(loc), 'type': 'csv'}
elif formtype == "plain/dat":
content = {'filename': os.path.basename(loc), 'type': 'dat'}
contents.append(content)
return contents
def listDetailedContents(self):
""" List contents of the archive from the manifest.xml
:return: contentList of dictionaries with keys: filename, type
:rtype: [{}]
"""
contents = []
man = self.readManifest()
xml = et.ElementTree(et.fromstring(man))
root = xml.getroot()
for child in root:
# get content for xml element
content = None
attribute = child.attrib
formtype = attribute.get('format')
loc = attribute.get('location')
# sbml
if formtype == "http://identifiers.org/combine.specifications/sbml":
if loc.startswith('http') or loc.startswith('www'):
content = {'filename': loc, 'type': 'sbml'}
else:
content = {
'filename': os.path.basename(loc),
'type': 'sbml'
}
# sedml
elif formtype == "http://identifiers.org/combine.specifications/sed-ml":
zf = ZipFile(self.combinePath, 'r')
try:
sedmlRaw = zf.read(loc)
except KeyError as e:
try:
sedmlRaw = zf.read(os.path.basename(loc))
except KeyError as e:
raise e
sedmlDoc = libsedml.readSedMLFromString(sedmlRaw)
tempSedmlSource = []
for model in sedmlDoc.getListOfModels():
if os.path.splitext(os.path.basename(
model.getSource()))[1] == '':
pass
else:
tempSedmlSource.append(
os.path.basename(model.getSource()))
content = {
'filename': os.path.basename(loc),
'type': 'sedml',
'modelsource': tempSedmlSource
}
zf.close()
# manifest
elif formtype == "http://identifiers.org/combine.specifications/omex-manifest":
content = {
'filename': os.path.basename(loc),
'type': 'manifest'
}
# other formats
elif formtype == "image/png":
content = {'filename': os.path.basename(loc), 'type': 'png'}
elif formtype == "image/jpg" or formtype == "image/jpeg":
content = {'filename': os.path.basename(loc), 'type': 'jpg'}
elif formtype == "application/pdf":
content = {'filename': os.path.basename(loc), 'type': 'pdf'}
elif formtype == "plain/text":
content = {'filename': os.path.basename(loc), 'type': 'txt'}
elif formtype == "plain/csv":
content = {'filename': os.path.basename(loc), 'type': 'csv'}
elif formtype == "plain/dat":
content = {'filename': os.path.basename(loc), 'type': 'dat'}
if content != None:
contents.append(content)
return contents