def postAnalyzeFile(outputFile, bngLocation, database):
"""
Performs a postcreation file analysis based on context information
"""
#print('Transforming generated BNG file to BNG-XML representation for analysis')
consoleCommands.setBngExecutable(bngLocation)
outputDir = os.sep.join(outputFile.split(os.sep)[:-1])
if outputDir != '':
retval = os.getcwd()
os.chdir(outputDir)
consoleCommands.bngl2xml(outputFile.split(os.sep)[-1])
if outputDir != '':
os.chdir(retval)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
#print('Sending BNG-XML file to context analysis engine')
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# analysis of redundant bonds
deleteBonds = contextAnalysis.analyzeRedundantBonds(database.assumptions['redundantBonds'])
modificationFlag = True
for molecule in database.assumptions['redundantBondsMolecules']:
if molecule[0] in deleteBonds:
for bond in deleteBonds[molecule[0]]:
database.translator[molecule[1]].deleteBond(bond)
logMess('INFO:Atomization', 'Used context information to determine that the bond {0} in species {1} is not likely'.format(bond,molecule[1]))
returnArray = analyzeHelper(database.document, database.reactionDefinitions, database.useID,
outputFile, database.speciesEquivalence, database.atomize, database.translator)
with open(outputFile, 'w') as f:
f.write(returnArray.finalString)
# recompute bng-xml file
consoleCommands.bngl2xml(outputFile)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
# recompute context information
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# get those species patterns that follow uncommon motifs
motifSpecies, motifDefinitions = contextAnalysis.processContextMotifInformation(database.assumptions['lexicalVsstoch'], database)
#motifSpecies, motifDefinitions = contextAnalysis.processAllContextInformation()
if len(motifDefinitions) > 0:
logMess('WARNING:ContextAnalysis', 'Species with suspect context information were found. Information is being dumped to {0}_context.log'.format(outputFile))
with open('{0}_context.log'.format(outputFile), 'w') as f:
pprint.pprint(dict(motifSpecies), stream=f)
pprint.pprint(motifDefinitions, stream=f)
def postAnalysisHelper(outputFile, bngLocation, database):
consoleCommands.setBngExecutable(bngLocation)
outputDir = os.sep.join(outputFile.split(os.sep)[:-1])
if outputDir != '':
retval = os.getcwd()
os.chdir(outputDir)
consoleCommands.bngl2xml(outputFile.split(os.sep)[-1])
if outputDir != '':
os.chdir(retval)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
#print('Sending BNG-XML file to context analysis engine')
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# analysis of redundant bonds
deleteBonds = contextAnalysis.analyzeRedundantBonds(database.assumptions['redundantBonds'])
for molecule in database.assumptions['redundantBondsMolecules']:
if molecule[0] in deleteBonds:
for bond in deleteBonds[molecule[0]]:
database.translator[molecule[1]].deleteBond(bond)
logMess('INFO:CTX002', 'Used context information to determine that the bond {0} in species {1} is not likely'.format(bond,molecule[1]))
