I've used the demos as a resource for building web applications with Ctakes and would suggest taking a look at http://healthnlp.github.io/examples/
-----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, May 16, 2016 3:00 PM To: dev@ctakes.apache.org Subject: RE: ctakes 3.2.2 AggregatePlaintextFastUMLSProcessor webproject integration Hi Jan, It looks like ou are basically trying to run the equivalent of: ctakes-clinical-pipeline/desc/../analysis_engine/CuisOnlyPlaintextUMLSProcessor.xml You could try swapping out the Aggregate... for that one and see what happens. Sean -----Original Message----- From: Jan Zieher [mailto:jzie...@gmx.de] Sent: Monday, May 16, 2016 2:08 PM To: dev@ctakes.apache.org Subject: ctakes 3.2.2 AggregatePlaintextFastUMLSProcessor webproject integration Hey, I created a java webproject in netbeans 8.1 and integrated ctakes with the libs of the 3.2.2 binaries download, its desc and resource folder into the WEB-INF folder. I would like to run the AggregatePlaintextFastUMLSProcessor AE. Through debugging the code below worked, if I comment the following engines in the AE descriptor. <node>HistoryCleartkAnalysisEngine</node> <node>PolarityCleartkAnalysisEngine</node> <node>SubjectCleartkAnalysisEngine</node> <node>UncertaintyCleartkAnalysisEngine</node> String s = this.getServletContext().getRealPath("/WEB-INF/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml"); File aed = new File(s); JCas jcas; try { pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createEngineDescriptionFromPath(s); AnalysisEngine ae = AnalysisEngineFactory.createEngine(pipelineIncludingUmlsDictionaries); jcas = JCasFactory.createJCas(); jcas.setDocumentText("Fx of obesity but no fx of coronary artery diseases"); SimplePipeline.runPipeline(jcas, ae); // Print out the IdentifiedAnnotation objects for (IdentifiedAnnotation entity : JCasUtil.select(jcas, IdentifiedAnnotation.class)) { System.out.println("Entity: " + entity.getCoveredText() + " === Polarity: " + entity.getPolarity()+ "Class:"+ entity.getClass()); } } catch (UIMAException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } If I uncomment the cleartk engines I get this class not found error, although the class exists in the ctakes-assertion-3.2.2.jar. org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed. (Descriptor: file:/C:/Users/..../Documents/NetBeansProjects/mta.parser/target/mta.parser-1.0-SNAPSHOT/WEB-INF/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml) My first question is are these engines very necessary for the nlp results ? Could this class not found error also belong to path problems caused by the webcontent location ? Has anyone a project or description how to set up such a webproject ? I would be very happy if someone could help me. Best regards, Jan IMPORTANT WARNING: The information in this message (and the documents attached to it, if any) is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken, or omitted to be taken, in reliance on it is prohibited and may be unlawful. If you have received this message in error, please delete all electronic copies of this message (and the documents attached to it, if any), destroy any hard copies you may have created and notify me immediately by replying to this email. Thank you. Geisinger Health System utilizes an encryption process to safeguard Protected Health Information and other confidential data contained in external e-mail messages. If email is encrypted, the recipient will receive an e-mail instructing them to sign on to the Geisinger Health System Secure E-mail Message Center to retrieve the encrypted e-mail.
