def process(self,
source,
output,
parameters=None,
model=None,
sourceDataSetNames=None,
fromStep=None,
toStep=None,
omitSteps=None):
if omitSteps != None and (
(type(omitSteps) in types.StringTypes and omitSteps == "CONVERT")
or "CONVERT" in omitSteps):
raise Exception("Preprocessor step 'CONVERT' may not be omitted")
# Initialize variables and save existing default values
#self.intermediateFileTag = corpusName
#parameters = self.getParameters(parameters, model)
#parameters["CONVERT.dataSetNames"] = sourceDataSetNames
#parameters["CONVERT.corpusName"] = corpusName
#convertSetNames = self.stepArgs("CONVERT")["dataSetNames"]
#convertCorpusName = self.stepArgs("CONVERT")["corpusName"]
#self.stepArgs("CONVERT")["dataSetNames"] = sourceDataSetNames
#self.stepArgs("CONVERT")["corpusName"] = corpusName
# Run the tool chain
xml = ToolChain.process(self, source, output, parameters, model,
fromStep, toStep, omitSteps)
# Reset variables to saved default values
#self.stepArgs("CONVERT")["dataSetNames"] = convertSetNames
#self.stepArgs("CONVERT")["corpusName"] = convertCorpusName
return xml
def process(self,
source,
output,
parameters=None,
model=None,
sourceDataSetNames=None,
fromStep=None,
toStep=None,
omitSteps=None):
# Initialize variables and save existing default values
#self.intermediateFileTag = corpusName
#parameters = self.getParameters(parameters, model)
#parameters["CONVERT.dataSetNames"] = sourceDataSetNames
#parameters["CONVERT.corpusName"] = corpusName
#convertSetNames = self.stepArgs("CONVERT")["dataSetNames"]
#convertCorpusName = self.stepArgs("CONVERT")["corpusName"]
#self.stepArgs("CONVERT")["dataSetNames"] = sourceDataSetNames
#self.stepArgs("CONVERT")["corpusName"] = corpusName
# Run the tool chain
xml = ToolChain.process(self, source, output, parameters, model,
fromStep, toStep, omitSteps)
# Reset variables to saved default values
#self.stepArgs("CONVERT")["dataSetNames"] = convertSetNames
#self.stepArgs("CONVERT")["corpusName"] = convertCorpusName
return xml
def process(self,
source,
output=None,
model=None,
fromStep=None,
toStep=None,
omitSteps=None,
logPath=None):
if logPath == "AUTO":
if output != None:
logPath = output
if "*" in logPath:
logPath = logPath.split("*")[0].rstrip("-")
logPath = os.path.join(
logPath.rstrip("/").rstrip("\\") + "-log.txt")
else:
logPath = None
elif logPath == "None":
logPath = None
if logPath != None:
if not os.path.exists(os.path.dirname(logPath)):
os.makedirs(os.path.dirname(logPath))
Stream.openLog(logPath)
print >> sys.stderr, "Preprocessor steps:", [
x.name for x in self.steps
]
if len(self.steps) == 0:
raise Exception("No preprocessing steps defined")
#if omitSteps != None and((type(omitSteps) in types.StringTypes and omitSteps == "CONVERT") or "CONVERT" in omitSteps):
# raise Exception("Preprocessor step 'CONVERT' may not be omitted")
#if isinstance(source, basestring) and os.path.basename(source).isdigit(): # PMID
# print >> sys.stderr, "Preprocessing PubMed abstract", os.path.basename(source)
# source = Utils.Download.getPubMed(int(source))
# Initialize variables and save existing default values
#self.intermediateFileTag = corpusName
#parameters = self.getParameters(parameters, model)
#parameters["CONVERT.dataSetNames"] = sourceDataSetNames
#parameters["CONVERT.corpusName"] = corpusName
#convertSetNames = self.stepArgs("CONVERT")["dataSetNames"]
#convertCorpusName = self.stepArgs("CONVERT")["corpusName"]
#self.stepArgs("CONVERT")["dataSetNames"] = sourceDataSetNames
#self.stepArgs("CONVERT")["corpusName"] = corpusName
# Run the tool chain
xml = ToolChain.process(self, source, output, model, fromStep, toStep,
omitSteps)
# Reset variables to saved default values
#self.stepArgs("CONVERT")["dataSetNames"] = convertSetNames
#self.stepArgs("CONVERT")["corpusName"] = convertCorpusName
if logPath != None:
Stream.closeLog(logPath)
return xml
def process(self, source, output, parameters=None, model=None, sourceDataSetNames=None, fromStep=None, toStep=None, omitSteps=None):
# Initialize variables and save existing default values
#self.intermediateFileTag = corpusName
#parameters = self.getParameters(parameters, model)
#parameters["CONVERT.dataSetNames"] = sourceDataSetNames
#parameters["CONVERT.corpusName"] = corpusName
#convertSetNames = self.stepArgs("CONVERT")["dataSetNames"]
#convertCorpusName = self.stepArgs("CONVERT")["corpusName"]
#self.stepArgs("CONVERT")["dataSetNames"] = sourceDataSetNames
#self.stepArgs("CONVERT")["corpusName"] = corpusName
# Run the tool chain
xml = ToolChain.process(self, source, output, parameters, model, fromStep, toStep, omitSteps)
# Reset variables to saved default values
#self.stepArgs("CONVERT")["dataSetNames"] = convertSetNames
#self.stepArgs("CONVERT")["corpusName"] = convertCorpusName
return xml
def process(self, source, output, parameters=None, model=None, sourceDataSetNames=None, fromStep=None, toStep=None, omitSteps=None):
if omitSteps != None and((type(omitSteps) in types.StringTypes and omitSteps == "CONVERT") or "CONVERT" in omitSteps):
raise Exception("Preprocessor step 'CONVERT' may not be omitted")
# Initialize variables and save existing default values
#self.intermediateFileTag = corpusName
#parameters = self.getParameters(parameters, model)
#parameters["CONVERT.dataSetNames"] = sourceDataSetNames
#parameters["CONVERT.corpusName"] = corpusName
#convertSetNames = self.stepArgs("CONVERT")["dataSetNames"]
#convertCorpusName = self.stepArgs("CONVERT")["corpusName"]
#self.stepArgs("CONVERT")["dataSetNames"] = sourceDataSetNames
#self.stepArgs("CONVERT")["corpusName"] = corpusName
# Run the tool chain
xml = ToolChain.process(self, source, output, parameters, model, fromStep, toStep, omitSteps)
# Reset variables to saved default values
#self.stepArgs("CONVERT")["dataSetNames"] = convertSetNames
#self.stepArgs("CONVERT")["corpusName"] = convertCorpusName
return xml
def process(self, source, output=None, model=None, fromStep=None, toStep=None, omitSteps=None, logPath=None):
if logPath == "AUTO":
if output != None:
logPath = output
if "*" in logPath:
logPath = logPath.split("*")[0].rstrip("-")
logPath = os.path.join(logPath.rstrip("/").rstrip("\\") + "-log.txt")
else:
logPath = None
elif logPath == "None":
logPath = None
if logPath != None:
if not os.path.exists(os.path.dirname(logPath)):
os.makedirs(os.path.dirname(logPath))
Stream.openLog(logPath)
print >> sys.stderr, "Preprocessor steps:", [x.name for x in self.steps]
if len(self.steps) == 0:
raise Exception("No preprocessing steps defined")
#if omitSteps != None and((type(omitSteps) in types.StringTypes and omitSteps == "CONVERT") or "CONVERT" in omitSteps):
# raise Exception("Preprocessor step 'CONVERT' may not be omitted")
#if isinstance(source, basestring) and os.path.basename(source).isdigit(): # PMID
# print >> sys.stderr, "Preprocessing PubMed abstract", os.path.basename(source)
# source = Utils.Download.getPubMed(int(source))
# Initialize variables and save existing default values
#self.intermediateFileTag = corpusName
#parameters = self.getParameters(parameters, model)
#parameters["CONVERT.dataSetNames"] = sourceDataSetNames
#parameters["CONVERT.corpusName"] = corpusName
#convertSetNames = self.stepArgs("CONVERT")["dataSetNames"]
#convertCorpusName = self.stepArgs("CONVERT")["corpusName"]
#self.stepArgs("CONVERT")["dataSetNames"] = sourceDataSetNames
#self.stepArgs("CONVERT")["corpusName"] = corpusName
# Run the tool chain
xml = ToolChain.process(self, source, output, model, fromStep, toStep, omitSteps)
# Reset variables to saved default values
#self.stepArgs("CONVERT")["dataSetNames"] = convertSetNames
#self.stepArgs("CONVERT")["corpusName"] = convertCorpusName
if logPath != None:
Stream.closeLog(logPath)
return xml
