Textmarker: delete contained annotations

2013-04-30 Thread William Karl Thompson
Hi, I'm working with the cTAKES pipeline to annotate some clinical text. The cTAKES syntactic chunker generates overlapping and nested annotations with the same syntactic type. For example: [NP ascending [NP colon polyps]] What I would like to do is to use TextMarker rules to eliminate nested

Re: uimaFit way of creating an analysis description from an XML descriptor file

2013-04-30 Thread Richard Eckart de Castilho
Hi Armin, > The file is in the file system. But I don't want to create an AnalysisEngine > with AnalysisEngineFactory.createAnalysisEngineFromPath(). I'd rather like to > have an AnalysisEngineDescription. But there is not method > createAnalysisEngineDescriptionFromPath(). Right, there is non

AW: uimaFit way of creating an analysis description from an XML descriptor file

2013-04-30 Thread Armin.Wegner
Hi Richard, The file is in the file system. But I don't want to create an AnalysisEngine with AnalysisEngineFactory.createAnalysisEngineFromPath(). I'd rather like to have an AnalysisEngineDescription. But there is not method createAnalysisEngineDescriptionFromPath(). Is there an easy way to ge

Re: uimaFit way of creating an analysis description from an XML descriptor file

2013-04-30 Thread Richard Eckart de Castilho
Hi Armin, sorry I mis-read that. If the descriptor is in the classpath, try AnalysisEngineFactory.createAnalysisEngineDescription(String, Object...) The string is the "package" and the name of the descriptor without ".xml" e.g. AnalysisEngineFactory.createAnalysisEngineDescription("WhitespaceT

AW: uimaFit way of creating an analysis description from an XML descriptor file

2013-04-30 Thread Armin.Wegner
Hi Richard, I'm not talking about type system descriptors, but of analysis engine descriptors. I would like to create an AnalysisEngineDescription from an analysis engine descriptor file, e. g. like one the Textmarker Workbench created in a Textmarker Eclipse project. I'd like to add this Anal

AW: Getting the effective type system

2013-04-30 Thread Armin.Wegner
Hello Richard, using your second suggestion, I've written a very simple CAS consumer like the one in [2]. It's a one-liner and works fine: public final void process(final CAS cas) throws AnalysisEngineProcessException { try { TypeSystemUtil.typeSystem2TypeSystemDescripti