emr-vis-nlp
commented
9 years ago It may not be parenthesis specifically as ""("CLIA") as" indicates any-adenoma to be false." worked just fine...
On Wed, Jul 22, 2015 at 6:40 PM, Gaurav Trivedi notifications@github.com wrote:
Both wordtree and highlight span feedback fail if the span includes a parenthesis. For example
Insitu Hybridization Assays (ISH & FISH)
Error trace:
22-Jul-2015 18:36:12.279 SEVERE [http-nio-8080-exec-17] com.sun.jersey.spi.container.ContainerResponse.mapMappableContainerException The RuntimeException could not be mapped to a response, re-throwing to the HTTP container java.lang.ArrayIndexOutOfBoundsException: 89 at edu.pitt.cs.nih.backend.featureVector.Preprocess.separatePathologyHeaderFooter(Preprocess.java:302) at edu.pitt.cs.nih.backend.featureVector.ColonoscopyDS_SVMLightFormat.getFullDSFeatureVector(ColonoscopyDS_SVMLightFormat.java:308) at edu.pitt.cs.nih.backend.featureVector.ColonoscopyDS_SVMLightFormat.createFullDS(ColonoscopyDS_SVMLightFormat.java:96) at edu.pitt.cs.nih.backend.featureVector.ColonoscopyDS_SVMLightFormat.createLearningFileSet(ColonoscopyDS_SVMLightFormat.java:850) at edu.pitt.cs.nih.backend.feedback.TextFileFeedbackManagerLibSVM.createLearningFiles(TextFileFeedbackManagerLibSVM.java:339) at edu.pitt.cs.nih.backend.feedback.TextFileFeedbackManager_LibSVM_WordTree.processFeedback(TextFileFeedbackManager_LibSVM_WordTree.java:78) at frontEnd.serverSide.controller.Feedback_Controller.processFeedback(Feedback_Controller.java:194) at frontEnd.serverSide.controller.Feedback_Controller.getFeedback(Feedback_Controller.java:42) at frontEnd.serverSide.WSInterface.getFeedback(WSInterface.java:185) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:540) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:715) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:503) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:136) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:526) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:655) at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1566) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1523) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:744)
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trivedigaurav
Both wordtree and highlight span feedback fail if the span includes a parenthesis. For example
Error trace: