Hi Sourabh, Does the run stop? I occasionally see that same error in another pipeline but it doesn't stop the run.
Thanks, Sean -----Original Message----- From: Sourabh Mukherjee [mailto:sourabh...@gmail.com] Sent: Friday, September 15, 2017 1:47 AM To: Apache cTAKES Dev Subject: Re: ctakes timelanes [EXTERNAL] Thanks Sean. If my understanding is correct Timelanes expect an XMI input having temoral and entity information. Hence I am using ctakes temporal package to extract the info. I tried executing EvaluationOfEventTimeRelations.java with the following parameters "--text=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/input/ --format=Anafora --xml=F:/sourabhmukherjee/thymedata-master/coloncancer/Test/ID006_clinic_016/ --xmi=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/ouput --kernelParams="c 0.001953125 t 0.03125 d 3 g 1.0 S 1 C + L 0.5 T 0.1 N 3" --patients=1-218 --useGoldAttributes" But I am getting the following error when tried to run it in eclipse Error with parameter settings: ,Kernel=tk,Cost=10.0,Gamma=1.0,secondKernel=polynomial,operator=SUM,tkWeight=0.1,lambda=0.1 org.apache.uima.resource.ResourceInitializationException: The feature org.apache.ctakes.typesystem.type.textspan.List:items is declared twice, with incompatible multipleReferencesAllowed specifications. (Descriptor: jar:file:/E:/cTakes/apache-ctakes-4.0.0/lib/ctakes-type-system-4.0.0.jar!/org/apache/ctakes/typesystem/types/TypeSystem.xml) at org.apache.uima.util.CasCreationUtils.mergeFeatures(CasCreationUtils.java:1709) at org.apache.uima.util.CasCreationUtils.addTypeToMergedTypeSystem(CasCreationUtils.java:1178) at org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1100) at org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1029) at org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription(TypeSystemDescriptionFactory.java:119) at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(AnalysisEngineFactory.java:978) at org.cleartk.util.ae.UriToDocumentTextAnnotator.getDescription(UriToDocumentTextAnnotator.java:58) at org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getXMIReadingPreprocessorAggregateBuilder(Evaluation_ImplBase.java:471) at org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getPreprocessorAggregateBuilder(Evaluation_ImplBase.java:464) at org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.train(EvaluationOfEventTimeRelations.java:303) at org.cleartk.eval.Evaluation_ImplBase.trainAndTest(Evaluation_ImplBase.java:76) at org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.main(EvaluationOfEventTimeRelations.java:211) It would be a great help if somebody helps me here since I am new to both ctakes and Java. Thanks in advance for your help. Regards, Sourabh On Wed, Sep 13, 2017 at 9:10 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Sourabh, > > The timelanes gui displays temporal information extracted by ctakes on > a timeline. That information is extracted by the ctakes-temporal module. > Without temporal information it can still display a markup of the text > and allow searching, etc. but is no more useful than many other > annotation markup tools. > > You can find the wiki page for the temporal module here: > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_ > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=CmDrS1CLFg > yz2OkgTQXYXZCzmo02rHZ7xY3OS2XLAA4&s=3peP8Yp19VD8Uxq_kihX6Rmgw90SDIRCuk > -c24oIwSY&e= > cTAKES+4.0+-+Temporal+Module > > Sean > > > -----Original Message----- > From: Sourabh Mukherjee [mailto:sourabh...@gmail.com] > Sent: Wednesday, September 13, 2017 8:21 AM > To: Apache cTAKES Dev > Subject: Re: ctakes timelanes [EXTERNAL] > > Thanks Sean. I am trying to run ctakes timelines which is present in > ctakes demo and in sandbox. > However do I need to use Temporal for this purpose ? I m unable to > find any proper document on executing temporal. > > Regards, > Sourabh > > On 08-Sep-2017 6:47 PM, "Finan, Sean" > <sean.fi...@childrens.harvard.edu> > wrote: > > > Hi Sourabh, > > Are you running the ctakes temporal module? > > Sean > > -----Original Message----- > > From: Sourabh Mukherjee [mailto:sourabh...@gmail.com] > > Sent: Friday, September 08, 2017 4:17 AM > > To: Apache cTAKES Dev > > Subject: ctakes timelanes [EXTERNAL] > > > > Hi, > > > > I followed the steps mentioned in the link " > > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da > > rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C > > F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf. > > edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx > > eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp > > T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= " > > and without any error. I am feeding the input as the xmi file ,tried > > with simple txt files too but couldn't see and timelines or any data > > at all. It is just that the UI is popping up , taking the input file > > but showing no output. Am I missing something, can somebody help me > > to understand why there is no output. Thanks in advance for the help. > > > > Regards, > > Sourabh > > >
