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jbjorne / TEES

Turku Event Extraction System
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Running issue #7

Closed chengkun-wu closed 10 years ago

chengkun-wu commented 11 years ago

Trying to run TEES2.1 on Mac OS Mountain Lion.

Then TEES finished the preprocessing steps but met some errors afterwards.

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 "/Users/dtcuser/Dropbox/PhD/Year 2/codes/biocontext-1.0/TEES-master/Detectors/EventDetector.py", line 336, in classify xml = self.triggerDetector.classifyToXML(self.classifyData, self.model, None, workOutputTag, goldData=goldData, parse=self.parse, recallAdjust=float(self.getStr("recallAdjustParameter", self.model))) File "/Users/dtcuser/Dropbox/PhD/Year 2/codes/biocontext-1.0/TEES-master/Detectors/SingleStageDetector.py", line 163, in classifyToXML classifier.classify(exampleFileName, tag+self.tag+"classifications", classifierModel, finishBeforeReturn=True) File "/Users/dtcuser/Dropbox/PhD/Year 2/codes/biocontext-1.0/TEES-master/Classifiers/ExternalClassifier.py", line 171, in classify classifyCommand = os.path.join(classifyDir, self.classifyCommand).replace("%e", examples).replace("%m", model).replace("%c", predictionsPath).strip() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/posixpath.py", line 67, in join elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith'

I first suspected that it might be the python version I’m using, so I also tried python 2.7, but I got the same error message.

jbjorne commented 11 years ago

That looks like the issue might be with the SVM-classifier not being installed correctly. Please try to reinstall (by running configure.py) the classifier, and select the option to compile from source (the binary is only compatible with linux). Keep an eye for any error messages when installing the classifier.

chengkun-wu commented 10 years ago

Thanks for the reply. I have managed to get it right. Indeed, the SVM-classifier was not installed probably.