Hi Gandhi, I was able to fix most of the issues. However, now i have the DateAnnotatorTest failing for ctakes-ytex.uima. I see that you also faced this issue. I tried deleting the tmp/ctakes-* and then rebuilding but didnt help. Do you have a solution or suggestion? Please find below the link for the mail chain on this issue. Looking forward to hearing from you. Thanks.
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201711.mbox/%3CCAGycqjz0E8_=zxsv1-owgsnppmvg6jcgwwys1+nqkkmw42d...@mail.gmail.com%3E Regards, Sajit On Wed, Apr 17, 2019 at 10:19 AM Sajit Kumar <kumar.sajit...@gmail.com> wrote: > Hi Gandhi, > > I have all the code checked out and I am following the instructions given > in developer install guide. I don't see anything missing. Can you please > help. I am not sure why the threadsafe files are not part of the standard > windows distributable. I just need to be able to run the thread safe > clinical pipeline. I am trying all this to just get that. Hope you can > help. Thanks. > > Regards, > Sajit > > On Wed, 17 Apr, 2019, 08:59 gandhi rajan, <gandhiraja...@gmail.com> wrote: > >> I m able to see some class not found exception which means some >> dependency is missing. Ytex compilation dint had any issue when I last >> compiled cTAKES. Ensure you have the code checked out from latest trunk and >> all dependencies are in place. >> >> On Tuesday, April 16, 2019, Sajit Kumar <kumar.sajit...@gmail.com> wrote: >> >>> Hi Gandhi, >>> >>> Sorry for the delay in my response. I was facing other issues with >>> cTakes that i needed to look at. Please find below the snapshot of the >>> build error. Please let me know how to resolve this/ >>> >>> [INFO] >>> [INFO] -------------------< org.apache.ctakes:ctakes-ytex >>> >-------------------- >>> [INFO] Building Apache cTAKES YTEX 4.0.1-SNAPSHOT >>> [48/53] >>> [INFO] --------------------------------[ jar >>> ]--------------------------------- >>> [INFO] >>> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-ytex >>> --- >>> [INFO] >>> [INFO] --- jaxb2-maven-plugin:1.6:xjc (default) @ ctakes-ytex --- >>> [INFO] Generating source... >>> [INFO] parsing a schema... >>> [INFO] >>> ------------------------------------------------------------------------ >>> [INFO] Reactor Summary for Apache cTAKES 4.0.1-SNAPSHOT: >>> [INFO] >>> [INFO] Apache cTAKES ...................................... SUCCESS [ >>> 22.575 s] >>> [INFO] ctakes-gui-res ..................................... SUCCESS [ >>> 7.031 s] >>> [INFO] Apache cTAKES Resources coreference ................ SUCCESS [ >>> 9.224 s] >>> [INFO] Apache cTAKES Resources temporal ................... SUCCESS [ >>> 1.894 s] >>> [INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [ >>> 1.301 s] >>> [INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [ >>> 9.357 s] >>> [INFO] Apache cTAKES Resources core ....................... SUCCESS [ >>> 1.481 s] >>> [INFO] Apache cTAKES common type system ................... SUCCESS [ >>> 21.150 s] >>> [INFO] Apache cTAKES utils ................................ SUCCESS [ >>> 6.307 s] >>> [INFO] Apache cTAKES core ................................. SUCCESS [ >>> 31.469 s] >>> [INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [ >>> 6.291 s] >>> [INFO] Apache cTAKES document preprocessor ................ SUCCESS [ >>> 2.744 s] >>> [INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ >>> 22.646 s] >>> [INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [ >>> 2.410 s] >>> [INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [ >>> 0.653 s] >>> [INFO] Apache cTAKES named entity contexts ................ SUCCESS [ >>> 4.114 s] >>> [INFO] Apache cTAKES Resources assertion .................. SUCCESS [ >>> 2.419 s] >>> [INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [ >>> 2.386 s] >>> [INFO] Apache cTAKES Constituency Parser .................. SUCCESS [ >>> 3.270 s] >>> [INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ >>> 40.950 s] >>> [INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [ >>> 2.449 s] >>> [INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [ >>> 10.470 s] >>> [INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ >>> 48.173 s] >>> [INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [ >>> 6.177 s] >>> [INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [ >>> 2.369 s] >>> [INFO] Apache cTAKES chunker .............................. SUCCESS [ >>> 3.725 s] >>> [INFO] Apache cTAKES Assertion ............................ SUCCESS [ >>> 14.576 s] >>> [INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [ >>> 1.173 s] >>> [INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [ >>> 4.467 s] >>> [INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ >>> 13.851 s] >>> [INFO] Apache cTAKES Temporal Information Extraction ...... SUCCESS >>> [02:54 min] >>> [INFO] Apache cTAKES CoReference Resolver ................. SUCCESS [ >>> 16.710 s] >>> [INFO] ctakes-gui ......................................... SUCCESS [ >>> 11.218 s] >>> [INFO] Apache cTAKES fhir support ......................... SUCCESS [ >>> 6.980 s] >>> [INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ >>> 22.809 s] >>> [INFO] Apache cTAKES dictionary lookup .................... SUCCESS [ >>> 4.770 s] >>> [INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [ >>> 1.422 s] >>> [INFO] Apache cTAKES Drug NER ............................. SUCCESS [ >>> 8.732 s] >>> [INFO] Apache cTAKES Resources side-effect ................ SUCCESS [ >>> 1.497 s] >>> [INFO] Apache cTAKES Side Effects ......................... SUCCESS [ >>> 4.015 s] >>> [INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [ >>> 1.446 s] >>> [INFO] Apache cTAKES Smoking Status ....................... SUCCESS [ >>> 4.992 s] >>> [INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [ >>> 1.386 s] >>> [INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [ >>> 3.186 s] >>> [INFO] ctakes-examples-res ................................ SUCCESS [ >>> 2.084 s] >>> [INFO] ctakes-examples .................................... SUCCESS [ >>> 5.038 s] >>> [INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [ >>> 1.863 s] >>> [INFO] Apache cTAKES YTEX ................................. FAILURE [ >>> 11.041 s] >>> [INFO] Apache cTAKES YTEX UIMA ............................ SKIPPED >>> [INFO] Apache cTAKES YTEX Web ............................. SKIPPED >>> [INFO] Apache cTAKES Distribution ......................... SKIPPED >>> [INFO] Apache cTAKES Regression-test ...................... SKIPPED >>> [INFO] Apache cTAKES template filler ...................... SKIPPED >>> [INFO] >>> ------------------------------------------------------------------------ >>> [INFO] BUILD FAILURE >>> [INFO] >>> ------------------------------------------------------------------------ >>> [INFO] Total time: 11:07 min >>> [INFO] Finished at: 2019-04-16T15:15:55+05:30 >>> [INFO] >>> ------------------------------------------------------------------------ >>> --------------------------------------------------- >>> constituent[0]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../conf/logging/ >>> constituent[1]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/animal-sniffer-annotations-1.14.jar >>> constituent[2]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/aopalliance-1.0.jar >>> constituent[3]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/cdi-api-1.0.jar >>> constituent[4]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/checker-compat-qual-2.0.0.jar >>> constituent[5]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/commons-cli-1.4.jar >>> constituent[6]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/commons-io-2.5.jar >>> constituent[7]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/commons-lang3-3.8.1.jar >>> constituent[8]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/error_prone_annotations-2.1.3.jar >>> constituent[9]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/guava-25.1-android.jar >>> constituent[10]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/guice-4.2.1-no_aop.jar >>> constituent[11]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/j2objc-annotations-1.1.jar >>> constituent[12]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/jansi-1.17.1.jar >>> constituent[13]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/javax.inject-1.jar >>> constituent[14]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/jcl-over-slf4j-1.7.25.jar >>> constituent[15]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/jsr250-api-1.0.jar >>> constituent[16]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/jsr305-3.0.2.jar >>> constituent[17]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-artifact-3.6.0.jar >>> constituent[18]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-builder-support-3.6.0.jar >>> constituent[19]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-compat-3.6.0.jar >>> constituent[20]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-core-3.6.0.jar >>> constituent[21]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-embedder-3.6.0.jar >>> constituent[22]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-model-3.6.0.jar >>> constituent[23]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-model-builder-3.6.0.jar >>> constituent[24]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-plugin-api-3.6.0.jar >>> constituent[25]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-repository-metadata-3.6.0.jar >>> constituent[26]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-api-1.3.1.jar >>> constituent[27]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-connector-basic-1.3.1.jar >>> constituent[28]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-impl-1.3.1.jar >>> constituent[29]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-provider-3.6.0.jar >>> constituent[30]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-spi-1.3.1.jar >>> constituent[31]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-transport-wagon-1.3.1.jar >>> constituent[32]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-resolver-util-1.3.1.jar >>> constituent[33]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-settings-3.6.0.jar >>> constituent[34]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-settings-builder-3.6.0.jar >>> constituent[35]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-shared-utils-3.2.1.jar >>> constituent[36]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-slf4j-provider-3.6.0.jar >>> constituent[37]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/org.eclipse.sisu.inject-0.3.3.jar >>> constituent[38]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/org.eclipse.sisu.plexus-0.3.3.jar >>> constituent[39]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-cipher-1.7.jar >>> constituent[40]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-component-annotations-1.7.1.jar >>> constituent[41]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-interpolation-1.25.jar >>> constituent[42]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-sec-dispatcher-1.4.jar >>> constituent[43]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-utils-3.1.0.jar >>> constituent[44]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/slf4j-api-1.7.25.jar >>> constituent[45]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/wagon-file-3.2.0.jar >>> constituent[46]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/wagon-http-3.2.0-shaded.jar >>> constituent[47]: >>> file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/wagon-provider-api-3.2.0.jar >>> --------------------------------------------------- >>> Exception in thread "main" java.lang.Error: >>> java.lang.reflect.InvocationTargetException >>> at com.sun.tools.xjc.reader.Ring.get(Ring.java:113) >>> at >>> com.sun.tools.xjc.reader.xmlschema.BGMBuilder.<init>(BGMBuilder.java:147) >>> at >>> com.sun.tools.xjc.reader.xmlschema.BGMBuilder.build(BGMBuilder.java:117) >>> at >>> com.sun.tools.xjc.ModelLoader.annotateXMLSchema(ModelLoader.java:425) >>> at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:174) >>> at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:119) >>> at com.sun.tools.xjc.Driver.run(Driver.java:333) >>> at >>> org.codehaus.mojo.jaxb2.AbstractXjcMojo.execute(AbstractXjcMojo.java:316) >>> at >>> org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:137) >>> at >>> org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:210) >>> at >>> org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:156) >>> at >>> org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:148) >>> at >>> org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117) >>> at >>> org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81) >>> at >>> org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:56) >>> at >>> org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128) >>> at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:305) >>> at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192) >>> at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105) >>> at org.apache.maven.cli.MavenCli.execute(MavenCli.java:956) >>> at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288) >>> at org.apache.maven.cli.MavenCli.main(MavenCli.java:192) >>> at >>> java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native >>> Method) >>> at >>> java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) >>> at >>> java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >>> at java.base/java.lang.reflect.Method.invoke(Method.java:567) >>> at >>> org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289) >>> at >>> org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229) >>> at >>> org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415) >>> at >>> org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356) >>> Caused by: java.lang.reflect.InvocationTargetException >>> at >>> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>> Method) >>> at >>> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) >>> at >>> java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) >>> at >>> java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500) >>> at >>> java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481) >>> at com.sun.tools.xjc.reader.Ring.get(Ring.java:102) >>> ... 29 more >>> Caused by: java.lang.Error: java.lang.reflect.InvocationTargetException >>> at com.sun.tools.xjc.reader.Ring.get(Ring.java:113) >>> at >>> com.sun.tools.xjc.reader.xmlschema.BindingComponent.getClassSelector(BindingComponent.java:65) >>> at >>> com.sun.tools.xjc.reader.xmlschema.ColorBinder.<init>(ColorBinder.java:62) >>> at >>> com.sun.tools.xjc.reader.xmlschema.BindGreen.<init>(BindGreen.java:63) >>> ... 35 more >>> Caused by: java.lang.reflect.InvocationTargetException >>> at >>> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>> Method) >>> at >>> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) >>> at >>> java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) >>> at >>> java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500) >>> at >>> java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481) >>> at com.sun.tools.xjc.reader.Ring.get(Ring.java:102) >>> ... 38 more >>> Caused by: java.lang.NoClassDefFoundError: >>> javax/activation/MimeTypeParseException >>> at java.base/java.lang.Class.getDeclaredConstructors0(Native >>> Method) >>> at >>> java.base/java.lang.Class.privateGetDeclaredConstructors(Class.java:3143) >>> at java.base/java.lang.Class.getConstructor0(Class.java:3348) >>> at >>> java.base/java.lang.Class.getDeclaredConstructor(Class.java:2559) >>> at com.sun.tools.xjc.reader.Ring.get(Ring.java:100) >>> at >>> com.sun.tools.xjc.reader.xmlschema.DefaultClassBinder.<init>(DefaultClassBinder.java:98) >>> at >>> com.sun.tools.xjc.reader.xmlschema.ClassSelector.<init>(ClassSelector.java:214) >>> ... 44 more >>> Caused by: java.lang.ClassNotFoundException: >>> javax.activation.MimeTypeParseException >>> at >>> org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50) >>> at >>> org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271) >>> at >>> org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247) >>> at >>> org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239) >>> ... 51 more >>> >>> On Thu, Apr 11, 2019 at 9:06 AM gandhi rajan <gandhiraja...@gmail.com> >>> wrote: >>> >>>> Hi Sajit, >>>> >>>> Could you post the error trace so that it will easy to figure out the >>>> problem. >>>> >>>> On Thursday, April 11, 2019, Sajit Kumar <kumar.sajit...@gmail.com> >>>> wrote: >>>> >>>>> Hi Gandhi, >>>>> >>>>> I tried building ctakes on my local computer. I used the maven build >>>>> command to build it. The build fails for the ctakes ytex module. Any >>>>> suggestions to fix it. Thank you, >>>>> >>>>> Regards, >>>>> Sajit >>>>> >>>>> On Mon, Apr 8, 2019 at 9:24 PM gandhi rajan <gandhiraja...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi Sajit, I m able to find the thread safe pipeline in the latest >>>>>> source code in SVN under >>>>>> >>>>>> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/ >>>>>> >>>>>> You can rebuild the latest code if it's not available in cTAKES 4.0 >>>>>> >>>>>> >>>>>> Monday, April 8, 2019, Sajit Kumar <kumar.sajit...@gmail.com> wrote: >>>>>> >>>>>>> Hi Gandhi, >>>>>>> >>>>>>> I did go and check Sean's mail on Thread Safe >>>>>>> DefaultClinicialPipeline. >>>>>>> >>>>>>> https://markmail.org/message/clv3wgrztgh2swjd >>>>>>> >>>>>>> It mentions of a new ThreadSafe pipeline file suffixed with Ts. I >>>>>>> didn't find it the apache ctakes directory. I also tried manually >>>>>>> including >>>>>>> the "threads" command in the piper file and i got a error message saying >>>>>>> unknown command. Can you please tell me if its available in cTakes >>>>>>> version >>>>>>> 4.0 on Windows. Looking forward to hearing from you. Thanks for your >>>>>>> help. >>>>>>> >>>>>>> Regards, >>>>>>> Sajit >>>>>>> >>>>>>> On Sun, Apr 7, 2019 at 10:50 PM gandhi rajan < >>>>>>> gandhiraja...@gmail.com> wrote: >>>>>>> >>>>>>>> Hi Sajit, >>>>>>>> >>>>>>>> As far as I know you can curtail default clinical pipeline as per >>>>>>>> your needs and it does support batch processing too. Please refer >>>>>>>> earlier >>>>>>>> mail chains from Sean regarding thread safe default clinical pipeline. >>>>>>>> >>>>>>>> On Sunday, April 7, 2019, Sajit Kumar <kumar.sajit...@gmail.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I am trying to batch process the clinical notes from MIMIC >>>>>>>>> database. I tried using the CPE tool provided with cTakes for this.I >>>>>>>>> am >>>>>>>>> only interested in extracting the CUIs from the notes. So i created a >>>>>>>>> CPE >>>>>>>>> file using CuisOnlyUMLSProcessor as the CAS Consumer. The XML >>>>>>>>> output using FileWriterCasConsumer works without a problem. >>>>>>>>> >>>>>>>>> However, I wanted the output as XMI instead of the XML as provided >>>>>>>>> by the standard templates. For this i tried using the writer xml's >>>>>>>>> provided >>>>>>>>> in \desc\ctakes-core\desc\cas_consumer directory. I also tried >>>>>>>>> changing the >>>>>>>>> implementation name in these files to >>>>>>>>> org.apache.uima.tools.components.XmiWriterCasConsumer. >>>>>>>>> I get exceptions and am not able to generate a XMI output. >>>>>>>>> >>>>>>>>> I have seen people suggesting to use the Default Clinical pipeline >>>>>>>>> to do a batch processing. However, this has 2 drawbacks. I am stuck >>>>>>>>> using >>>>>>>>> the standard processors and end up with lot of details that i dont >>>>>>>>> need. >>>>>>>>> Also the CPE configuration file provides a multi-threading option >>>>>>>>> thereby >>>>>>>>> help speed up the process. I have close to 200K files to process. >>>>>>>>> >>>>>>>>> Please help to resolve this issue. Thank you. >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Sajit >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Regards, >>>>>>>> Gandhi >>>>>>>> >>>>>>>> "The best way to find urself is to lose urself in the service of >>>>>>>> others !!!" >>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Regards, >>>>>> Gandhi >>>>>> >>>>>> "The best way to find urself is to lose urself in the service of >>>>>> others !!!" >>>>>> >>>>>> >>>> >>>> -- >>>> Regards, >>>> Gandhi >>>> >>>> "The best way to find urself is to lose urself in the service of others >>>> !!!" >>>> >>>> >> >> -- >> Regards, >> Gandhi >> >> "The best way to find urself is to lose urself in the service of others >> !!!" >> >>
