Hello James, I just tested, it went OK. I could finally load the AggregatePlaintextFastUMLSProcessor.xml with success in CVD and run it.
I just added the dependency to the pom file as I told you. Thanks for your help. It is important to have people like your around here, with such good knowledge of the system. I'll keep updating if I have any other problem. Best regards, Manuel 2017-12-26 18:49 GMT+00:00 James Masanz <[email protected]>: > > You can try that, sure, and post back whether it works OK. I didn't want > to suggesting that until I checked if that would cause a cyclic dependency, > which I haven't checked yet. > > -- James > > On Tue, Dec 26, 2017 at 1:35 PM, Manuel Lamy <[email protected]> wrote: > >> Hello James, >> >> Thanks for your quick answer. I've been battling this problem in the last >> few days. >> >> So should I start by adding ctakes-drug-ner as a dependency of >> ctakes-clinical-pipeline module? >> >> I see where the error comes from yes. I hope to hear from you later >> concerning this problem. >> >> Thank you! >> >> Best regards, >> >> Manuel Lamy >> >> 2017-12-26 18:28 GMT+00:00 James Masanz <[email protected]>: >> >>> The runCVD profile is defined in the pom.xml file that is within >>> ctakes-clinical-pipeline, and that pom doesn't include ctakes-drug-ner in >>> its list of dependencies. I'll take a look this afternoon at a >>> recommendation. >>> >>> The AggregatePlaintextFastUMLSProcessor.xml file uses a relative path >>> when referencing DrugMentionAnnotator.xml but the class folder for >>> ctakes-drug-ner module is not in the classpath because the ctakes-drug-ner >>> is not in the list of dependencies >>> >>> >>> >>> On Fri, Dec 22, 2017 at 11:20 AM, Manuel Lamy <[email protected]> wrote: >>> >>>> Hello guys, >>>> >>>> I'm using cTAKES version 4.0.0, developer version, using Intellij. I >>>> did all the setup of the project as per the Intellij section in the >>>> *Developer >>>> Install Guide* present in the url: https://cwiki.apache.org/confl >>>> uence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide >>>> >>>> Even so, I'm unfortunately having a strange error when I try to load >>>> the *AggregatePlaintextFastUMLSProcessor.xml *in CAS Visual Debbuger >>>> (CVD module). >>>> >>>> The error is the following: >>>> >>>> >>>> [image: Imagem inline 1] >>>> I also leave the top of the stack trace from the log: >>>> >>>> *<date>2017-12-22T15:59:06</date>* >>>> * <millis>1513958346021</millis>* >>>> * <sequence>2</sequence>* >>>> * <logger>org.apache.uima</logger>* >>>> * <level>SEVERE</level>* >>>> * <class>org.apache.uima.tools.cvd.MainFrame</class>* >>>> * <method>handleException(527)</method>* >>>> * <thread>22</thread>* >>>> >>>> * <message>Annotator class "org.apache.ctakes.drugner.ae >>>> <http://org.apache.ctakes.drugner.ae>.DrugMentionAnnotator" was not found. >>>> (Descriptor: >>>> file:/C:/Users/Manel/Desktop/Tese_Mestrado_NLP/cTAKES_Dev_Tese/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml)</message>* >>>> >>>> * <exception>* >>>> * <message>org.apache.uima.resource.ResourceInitializationException: >>>> Annotator class "org.apache.ctakes.drugner.ae >>>> <http://org.apache.ctakes.drugner.ae>.DrugMentionAnnotator" was not found. >>>> (Descriptor: >>>> file:/C:/Users/Manel/Desktop/Tese_Mestrado_NLP/cTAKES_Dev_Tese/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml)</message>* >>>> * <frame>* >>>> * >>>> <class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>* >>>> * <method>initializeAnalysisComponent</method>* >>>> * <line>224</line>* >>>> * </frame>* >>>> * <frame>* >>>> * >>>> <class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>* >>>> * <method>initialize</method>* >>>> * <line>172</line>* >>>> >>>> >>>> I can't quite understand this error, since the class >>>> org.apache.ctakes.drugner.ae.DrugMentionAnnotator *physically exists *in >>>> the path referenced in the xml descriptor file. Did someone also had this >>>> problem? >>>> >>>> I'm blocked. I just can't advance in my project because all the >>>> solutions I came up with to this problem, like passing the full path, >>>> didn't work at all. >>>> >>>> I would be appreciated if someone could give me some help. Thanks in >>>> advance. >>>> >>>> Best regards, >>>> >>>> Manuel >>>> >>> >>> >> >
