Thanks for letting me and everyone else know that the workaround is working. I think we'll have to consider a better home (different pom file) for those profiles so they work with all modules/components. But I'm glad we have a workaround for now.
-- James On Tue, Dec 26, 2017 at 1:55 PM, Manuel Lamy <[email protected]> wrote: > 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 >>>>> >>>> >>>> >>> >> >
