YTEX is not supported. So to make cTAKES compile, I changed all poms that reference YTEX so that all YTEX related packages are skipped for compiling.
From: Sajit Kumar <[email protected]> Reply-To: "[email protected]" <[email protected]> Date: Tuesday, April 16, 2019 at 3:54 AM To: "[email protected]" <[email protected]> Subject: Re: Need help with XMI output for CPE 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 !!!"
