def testGetXMLString(self):
def test(xml):
reader = tesbml.SBMLReader()
document = reader.readSBMLFromString(xml)
util.checkSBMLDocument(document)
model = document.getModel()
self.assertTrue('Reaction' in str(type(model.getReaction(0))))
def getString(path):
with open(path, 'r') as fd:
lines = '\n'.join(fd.readlines())
return lines
#
for path in [cn.TEST_FILE2, cn.TEST_FILE3]:
test(util.getXML(path))
test(util.getXML(getString(path)))
def testIsSBMLModel(self):
return
self.assertFalse(util.isSBMLModel("dummy"))
xml = util.getXML(cn.TEST_FILE2)
reader = tesbml.SBMLReader()
document = reader.readSBMLFromString(xml)
util.checkSBMLDocument(document)
model = document.getModel()
self.assertTrue(util.isSBMLModel(model))
def initialize(self, model_reference):
"""
Initializes the instance variables in the model.
:param str or libsbml.model: for str may be path or model string
and file/str may be xml or antimony.
"""
if util.isSBMLModel(model_reference):
model = model_reference
else:
xml = util.getXML(model_reference)
reader = libsbml.SBMLReader()
document = reader.readSBMLFromString(xml)
util.checkSBMLDocument(document, model_reference=model_reference)
model = document.getModel()
# Do the initializations
self.reactions = self._getReactions(model)
self.molecules = self._getMolecules()
self.moietys = self._getMoietys()
def prettyPrint(model_reference, file_out=sys.stdout, **kwargs):
"""
Prints the reactions in a model.
:param str model_reference: file, xml string, antimony string
:param dict kwargs: arguments to Reaction.getId
"""
xml = util.getXML(model_reference)
reader = libsbml.SBMLReader()
document = reader.readSBMLFromString(xml)
util.checkSBMLDocument(document)
model = document.getModel()
simple = SimpleSBML()
simple.initialize(model)
stgs = []
for reaction in simple.reactions:
stg = reaction.getId(**kwargs)
stgs.append(stg)
file_out.write("%s\n" % stg)
return stgs
def lint(model_reference=None,
file_out=sys.stdout,
mass_balance_check=GAMES,
config_fid=None,
is_report=True,
implicit_games=False):
"""
Reports on errors found in a model
:param str model_reference:
libsbml_model file in
file, antimony string, xml string
:param TextIOWrapper model_fid: fid for an XML file
:param TextIOWrapper file_out:
:param str mass_balance_check: how check for mass balance
:param TextIOWrapper config_fid: readable stream
:param bool is_report: print result
:return MoietyComparatorResult/null/None:
"""
config.setConfiguration(fid=config_fid)
config_dct = config.getConfiguration()
if util.isSBMLModel(model_reference):
model = model_reference
else:
xml = util.getXML(model_reference)
reader = libsbml.SBMLReader()
document = reader.readSBMLFromString(xml)
util.checkSBMLDocument(document)
model = document.getModel()
#
simple = SimpleSBML()
simple.initialize(model)
if mass_balance_check == cn.MOIETY_ANALYSIS:
result = MoietyComparator.analyzeReactions(simple)
if is_report:
for line in result.report.split('\n'):
file_out.write("%s\n" % line)
return result
elif mass_balance_check == GAMES:
if implicit_games:
for ignored in config_dct[cn.CFG_IGNORED_MOLECULES]:
simple = removeIgnored(simple, ignored)
m = GAMES_PP(simple)
games_result = m.analyze(simple.reactions)
if games_result and is_report:
gr = GAMESReport(
m, explain_threshold=config_dct[cn.CFG_GAMES_THRESHOLD])
errortype_dic = {
TYPE_I: gr.reportTypeOneError,
TYPE_II: gr.reportTypeTwoError,
TYPE_III: gr.reportTypeThreeError,
CANCELING: gr.reportCancelingError,
ECHELON: gr.reportEchelonError
}
for errors in m.error_summary:
for category in errortype_dic.keys():
if errors.type == category:
func = errortype_dic[category]
report, _ = func(errors.errors, explain_details=True)
print(report)
return games_result
else:
print("Specified method doesn't exist")
return None