Below is my piper file and the sample text I am using is ctakes-smoking-status/data/test/doc2_07543210_sample_current.txt: load FullTokenizerPipeline
// Add non-core annotators add ContextDependentTokenizerAnnotator addDescription POSTagger // Add Chunkers load ChunkerSubPipe // Default fast dictionary lookup load DictionarySubPipe // Add Cleartk Entity Attribute annotators load AttributeCleartkSubPipe // ClassifiableEntries - errors out at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:134) set SectionsToIgnore=20109,20138 set AllowedClassifications=SMOKER,CURRENT_SMOKER,NON_SMOKER,PAST_SMOKER,UNKNOWN set UimaDescriptorStep1=file: org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml set UimaDescriptorStep2=file: org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml add ClassifiableEntries UimaDescriptorStep1Key=UimaDescriptorStep1 UimaDescriptorStep2Key=UimaDescriptorStep2 // KuRuleBasedClassifierAnnotator- works but commented out for now //add KuRuleBasedClassifierAnnotator SmokingWordsFile=/org/apache/ctakes/smokingstatus/data/KU/keywords.txt UnknownWordsFile=/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt // PcsClassifierAnnotator_libsvm - errors out at libsvm.svm.svm_predict(svm.java:2343) set StopWordsFileRes=file: org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt set PathOfModelRes=file: org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model set PCSKeyWordFileResc=file: org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt //add PcsClassifierAnnotator_libsvm PathOfModel=PathOfModelResc StopWordsFile=StopWordsFileRes PCSKeyWordFile=PCSKeyWordFileResc // SideEffectAnnotator - errors out set sideEffectDic=file: org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt //add SideEffectAnnotator sideEffectTable=sideEffectDic addLast util.log.FinishedLogger On Thu, Jun 2, 2022 at 2:39 PM Finan, Sean <sean.fi...@childrens.harvard.edu.invalid> wrote: > Hi Muhammad, > > Can you please copy & paste the contents of your piper file? > > Thanks, > Sean > ________________________________________ > From: Muhammad Ali Syed <ms...@ncsu.edu.INVALID> > Sent: Thursday, June 2, 2022 2:30 PM > To: dev@ctakes.apache.org > Subject: SmokingStatus & Side effects - piper file [EXTERNAL] > > * External Email - Caution * > > > Hi there, > > I am exploring cTakes Smoking Status & Side Effects components and have not > come across any piper file version of their implementation. When trying to > incrementally add AEs to FullTokenizerPipeline.piper from these 2 > components I am running into issues such as: > - getting ResourceInitializationExceptions - when adding > ClassifiableEntries (did set UimaDescriptorStep1Key > and UimaDescriptorStep2Key) I tried add individual AEs from step1 and step2 > and ran into other issues > - exceptions such as in PcsClassifierAnnotator_libsvm (added to pipeline > after adding > KuRuleBasedClassifierAnnotator): java.lang.NullPointerException at > libsvm.svm.svm_predict(svm.java:2343) > > My question is: can these 2 components (containing multiple AEs) be > implemented by piper files as of now? In other words, can any pipeline, > that can be created using XML descriptor files, be also created by piper > files? > > Is there any sample piper code for pipelines that include either of these > components? > > Regards, >
