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Posted to user@ctakes.apache.org by Sajit Kumar <ku...@gmail.com> on 2019/04/07 15:29:02 UTC
Need help with XMI output for CPE
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
Re: Need help with XMI output for CPE
Posted by Olga Patterson <ol...@utah.edu>.
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 <ku...@gmail.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Tuesday, April 16, 2019 at 3:54 AM
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 !!!"
Re: Need help with XMI output for CPE
Posted by gandhi rajan <ga...@gmail.com>.
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 <ku...@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+
> NqkkMw42DeZA@mail.gmail.com%3E
>
> Regards,
> Sajit
>
> On Wed, Apr 17, 2019 at 10:19 AM Sajit Kumar <ku...@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, <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 <
>>>>>>>> gandhirajan.n@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 <ku...@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 !!!"
Re: Need help with XMI output for CPE
Posted by Sajit Kumar <ku...@gmail.com>.
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+NqkkMw42DeZA@mail.gmail.com%3E
Regards,
Sajit
On Wed, Apr 17, 2019 at 10:19 AM Sajit Kumar <ku...@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, <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 <
>>>>>>> gandhirajan.n@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 <ku...@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
>> !!!"
>>
>>
Re: Need help with XMI output for CPE
Posted by Sajit Kumar <ku...@gmail.com>.
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, <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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
> !!!"
>
>
Re: Need help with XMI output for CPE
Posted by gandhi rajan <ga...@gmail.com>.
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 <ku...@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.DelegatingConstructorAccessorI
> mpl.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.DelegatingConstructorAccessorI
> mpl.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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 !!!"
Re: Need help with XMI output for CPE
Posted by Sajit Kumar <ku...@gmail.com>.
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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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
> !!!"
>
>
Re: Need help with XMI output for CPE
Posted by gandhi rajan <ga...@gmail.com>.
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 <ku...@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 <ga...@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 <ku...@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 <ga...@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 <ku...@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 !!!"
Re: Need help with XMI output for CPE
Posted by Sajit Kumar <ku...@gmail.com>.
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 <ga...@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 <ku...@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 <ga...@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 <ku...@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
> !!!"
>
>
Re: Need help with XMI output for CPE
Posted by gandhi rajan <ga...@gmail.com>.
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 <ku...@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 <ga...@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 <ku...@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 !!!"
Re: Need help with XMI output for CPE
Posted by Sajit Kumar <ku...@gmail.com>.
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 <ga...@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 <ku...@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
> !!!"
>
>
Re: Need help with XMI output for CPE
Posted by gandhi rajan <ga...@gmail.com>.
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 <ku...@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 !!!"