Hi Sajit, It was a flaky test case that was passing on and off. You can ignore that test case and proceed with your build as there is not enough for ytex from the developers.
On Friday, April 19, 2019, Sajit Kumar <kumar.sajit...@gmail.com> wrote: > 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 >>> !!!" >>> >>> -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
