def __init__(self, rawTextFileName, intermediateXMLFileName):
preprocessor = Preprocessor(rawTextFileName, intermediateXMLFileName)
preprocessor.posTaggedText()
preprocessor.getParseTree()
preprocessor.getMetaMapConcepts()
self.intermediate = intermediateXMLFileName
self.vectors = []
def main(aRawTextFileName=None,
aIntermediateXMLFileName=None,
aConfigFile=None):
assemblerList = []
if aRawTextFileName is None and aIntermediateXMLFileName is None:
sysArgs = sys.argv[1:]
if len(sysArgs) >= 3:
"""when calling ProjectAeris, it should be done with a raw text file and an output xml file location as the first and second arguments respectively"""
rawTextFileName = sysArgs[0]
intermediateXMLFileName = sysArgs[1]
configFileName = sysArgs[2]
else:
print "Missing some command-line arguments"
return
else:
rawTextFileName = aRawTextFileName
intermediateXMLFileName = aIntermediateXMLFileName
configFileName = aConfigFile
print 'initial preprocess done!'
preprocessOne = Preprocessor(
rawTextFileName=rawTextFileName,
intermediateXMLFileName=intermediateXMLFileName)
configFile = configFileName
allAssemblerDict = {
'Event Date': EventDateAssembler(rawTextFileName,
intermediateXMLFileName),
'Age': AgeAssembler(rawTextFileName, intermediateXMLFileName),
'Dosage': DosageAssembler(rawTextFileName, intermediateXMLFileName),
'Drugname': DrugnameAssembler(rawTextFileName,
intermediateXMLFileName),
'Weight': WeightAssembler(rawTextFileName, intermediateXMLFileName),
'Gender': GenderAssembler(rawTextFileName, intermediateXMLFileName),
'Reaction': ReactionAssembler(rawTextFileName, intermediateXMLFileName)
}
#Place to test new preprocess methods
preprocessOne.getMetaMapConcepts()
# preprocessOne.posTaggedText()
# preprocessOne.getParseTree()
# print preprocessOne.rawText()
#Place to test new preprocess methods
#The following is to actually run the extractors
config = json.load(open(configFile))
entities = config.keys()
for entity in entities:
if entity not in allAssemblerDict:
raise KeyError("An entity you entered doesn't exist")
else:
assemblerList.append((entity, allAssemblerDict[entity]))
for name, assembler in assemblerList:
if config[name]:
assembler.setExtractorList(config[name])
assembler.runExtractors()
assembler.writeToSemiFinalXML()
assembler.launchTestSuite()