Closed hx-gx closed 11 years ago
Trying to run TEES 2.1.1 on Ubuntu for a hidden test set. Download the BioNLP-13' GRO task test data, which contains the .a1 and .txt files, extract to the TEES program folder, and run the following command to predict the *.a2 files.
classify.py -m GRO13 -i BioNLP-ST_2013_GRO_test-1.0-a1/ -o GRO_with_a1
However, it shows some errors and the error traceback is as follows:
Traceback (most recent call last): File "classify.py", line 190, in preprocessorParams=options.preprocessorParams, bioNLPSTParams=options.bioNLPSTParams) File "classify.py", line 78, in classify detector.classify(classifyInput, model, output, goldData=goldInput, fromStep=detectorSteps["CLASSIFY"], omitSteps=omitDetectorSteps["CLASSIFY"], workDir=workDir) File "/home/hanxu/TEES-2.1/Detectors/EventDetector.py", line 339, in classify xml = self.edgeDetector.classifyToXML(xml, self.model, None, workOutputTag, goldData=goldData, parse=self.parse) File "/home/hanxu/TEES-2.1/Detectors/SingleStageDetector.py", line 172, in classifyToXML return self.exampleWriter.write(exampleFileName, predictions, data, tag+self.tag+"pred.xml.gz", model.get(self.tag+"ids.classes"), parse, exampleStyle=exampleStyle, structureAnalyzer=self.structureAnalyzer) File "/home/hanxu/TEES-2.1/ExampleWriters/SentenceExampleWriter.py", line 30, in write return self.writeXML(examples, predictions, corpus, outputFile, classSet, parse, tokenization, goldCorpus, exampleStyle=exampleStyle, structureAnalyzer=structureAnalyzer) File "/home/hanxu/TEES-2.1/ExampleWriters/SentenceExampleWriter.py", line 94, in writeXML self.writeXMLSentence(exampleQueue, predictionsByExample, sentenceObject, classSet, classIds, goldSentence=goldSentence, exampleStyle=exampleStyle, structureAnalyzer=structureAnalyzer) # process queue File "/home/hanxu/TEES-2.1/ExampleWriters/EdgeExampleWriter.py", line 54, in writeXMLSentence entityById = self.getEntityByIdMap(sentenceElement) File "/home/hanxu/TEES-2.1/ExampleWriters/EdgeExampleWriter.py", line 34, in getEntityByIdMap assert eId not in entityById, eId AssertionError: TEES.d0.s0.e0 Counter "Write Examples" did not finish Last count: 0/43457 Last update: None
Is it because the wrong usage of TEES in the command line?
Trying to run TEES 2.1.1 on Ubuntu for a hidden test set. Download the BioNLP-13' GRO task test data, which contains the .a1 and .txt files, extract to the TEES program folder, and run the following command to predict the *.a2 files.
classify.py -m GRO13 -i BioNLP-ST_2013_GRO_test-1.0-a1/ -o GRO_with_a1
However, it shows some errors and the error traceback is as follows:
Traceback (most recent call last): File "classify.py", line 190, in
preprocessorParams=options.preprocessorParams, bioNLPSTParams=options.bioNLPSTParams)
File "classify.py", line 78, in classify
detector.classify(classifyInput, model, output, goldData=goldInput, fromStep=detectorSteps["CLASSIFY"], omitSteps=omitDetectorSteps["CLASSIFY"], workDir=workDir)
File "/home/hanxu/TEES-2.1/Detectors/EventDetector.py", line 339, in classify
xml = self.edgeDetector.classifyToXML(xml, self.model, None, workOutputTag, goldData=goldData, parse=self.parse)
File "/home/hanxu/TEES-2.1/Detectors/SingleStageDetector.py", line 172, in classifyToXML
return self.exampleWriter.write(exampleFileName, predictions, data, tag+self.tag+"pred.xml.gz", model.get(self.tag+"ids.classes"), parse, exampleStyle=exampleStyle, structureAnalyzer=self.structureAnalyzer)
File "/home/hanxu/TEES-2.1/ExampleWriters/SentenceExampleWriter.py", line 30, in write
return self.writeXML(examples, predictions, corpus, outputFile, classSet, parse, tokenization, goldCorpus, exampleStyle=exampleStyle, structureAnalyzer=structureAnalyzer)
File "/home/hanxu/TEES-2.1/ExampleWriters/SentenceExampleWriter.py", line 94, in writeXML
self.writeXMLSentence(exampleQueue, predictionsByExample, sentenceObject, classSet, classIds, goldSentence=goldSentence, exampleStyle=exampleStyle, structureAnalyzer=structureAnalyzer) # process queue
File "/home/hanxu/TEES-2.1/ExampleWriters/EdgeExampleWriter.py", line 54, in writeXMLSentence
entityById = self.getEntityByIdMap(sentenceElement)
File "/home/hanxu/TEES-2.1/ExampleWriters/EdgeExampleWriter.py", line 34, in getEntityByIdMap
assert eId not in entityById, eId
AssertionError: TEES.d0.s0.e0
Counter "Write Examples" did not finish
Last count: 0/43457
Last update: None
Is it because the wrong usage of TEES in the command line?