Hello James, Yes, it seems to me that the fix is exactly the same, by adding the dependency to the pom.xml file of ctakes-clinical-pipeline.
Nonetheless, a more robust solution can be arranged in the future, in order to solve this problem. But as of now, with this solution, it works well. Thank you. Best regards, Manuel 2017-12-26 22:21 GMT+00:00 James Masanz <[email protected]>: > I haven't tested to verify but it looks like this would also be fixed by > adding ctakes-drug-ner to the list of dependencies in the > ctakes-clincal-pipeline pom.xml file, since this resource problem was run > into while using intellij (as opposed to downloading and running from the > convenience binary) That fix is discussed in this thread: > > https://s.apache.org/pMfO > > > On Mon, Dec 11, 2017 at 3:00 PM, Andrew Conkie <andrew.conkie@ > redstarconsulting.co.uk> wrote: > >> Hi Manuel, >> >> I've just had a similar message with another UIMA system and the issue >> was that although the path to the Type System file was correct, it didn't >> lie in the data path. If this is the same problem, it can be solved by: >> >> a) Changing the Type System import in the DrugMentionAnnotaotor file to >> use an absolute path, >> >> ie replace >> <import name="org.apache.ctakes.drugner.types.TypeSystem"/> >> >> with >> <import location="file:/C:/Users/Manel/Desktop/Tese_Mestrado_NLP/ >> cTAKES_Project_NLP_Dev/ctakes/....absolute path to the Type System file >> with .xml appended..."/> >> >> >> b) More globally - because there may be other files affected - by passing >> the file path as a startup parameter >> >> ie, setting the following as a Java env variable >> >> -Duima.datapath=C:/Users/Manel/Desktop/Tese_Mestrado_NLP/ >> cTAKES_Project_NLP_Dev/ctakes/.... the dir where all the Type System >> files are >> >> >> Interestingly, I was previously trying the Drug Annotator code myself but >> couldn't get it to work and moved onto something else. I'm planning on >> going back to it so if you had any advice that would be appreciated. >> >> Cheers >> Andrew >> >> >> >> >> On Sat, Dec 9, 2017 at 11:03 PM, Manuel Lamy <[email protected]> wrote: >> >>> Hello guys, >>> >>> I'm aiming to extend cTAKES in order to fulfill the objectives of a >>> project I'm working on. So I decided to check out the code of trunk and >>> start checking it. I followed all tthe steps of the developer's guide found >>> here: https://cwiki.apache.org/confluence/display/CTAKES/cTA >>> KES+4.0+Developer+Install+Guide >>> >>> I'm using Intellij by the way. Well, when I try to run CVD in order to >>> test some changes I made in the code, I have a problem. I want to use >>> the AggregatePlaintextFastUMLSProcessor. When I try to load it in the >>> CVD UI, I have the following error: >>> >>> ----------------- >>> >>> <exception> >>> <message>*org.apache.uima.resource.ResourceInitializationException: >>> An import could not be resolved. No file with name >>> "org/apache/ctakes/drugner/types/TypeSystem.xml" was found in the class >>> path or data path. (Descriptor: >>> file:/C:/Users/Manel/Desktop/Tese_Mestrado_NLP/cTAKES_Project_NLP_Dev/ctakes/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml)* >>> >>> *-----------------* >>> >>> The DrugMentionAnnotator.xml indeed has an import of the TypeSystem.xml >>> file. And this TypeSystem file physically exists in the path described in >>> the DrugMentionAnnotator.xml import. So, I don' really know why I have this >>> error in CVD, since the file that is originating the problem exists indeed >>> in the expectable path. >>> >>> I hope some of you guys can give me some help, because I don't know what >>> else to do in order to solve this issue. >>> >>> Thanks for your attention in advance. >>> >>> Best Regards, >>> >>> ML >>> >> >> >
