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]
------------------------------------------------------------------------
---------------------------------------------------
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constituent[6]:
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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]:
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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
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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
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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
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-shared-utils-3.2.1.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/maven-slf4j-provider-3.6.0.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/org.eclipse.sisu.inject-0.3.3.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/org.eclipse.sisu.plexus-0.3.3.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-component-annotations-1.7.1.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-interpolation-1.25.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-sec-dispatcher-1.4.jar
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file:/E:/MyProjects/MAVEN_HOME/apache-maven-3.6.0/bin/../lib/plexus-utils-3.1.0.jar
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---------------------------------------------------
Exception in thread "main" java.lang.Error:
java.lang.reflect.InvocationTargetException
at com.sun.tools.xjc.reader.Ring.get(Ring.java:113)
at
com.sun.tools.xjc.reader.xmlschema.BGMBuilder.<init>(BGMBuilder.java:147)
at
com.sun.tools.xjc.reader.xmlschema.BGMBuilder.build(BGMBuilder.java:117)
at
com.sun.tools.xjc.ModelLoader.annotateXMLSchema(ModelLoader.java:425)
at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:174)
at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:119)
at com.sun.tools.xjc.Driver.run(Driver.java:333)
at
org.codehaus.mojo.jaxb2.AbstractXjcMojo.execute(AbstractXjcMojo.java:316)
at
org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:137)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:210)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:156)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:148)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
at
org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:56)
at
org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:192)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at
org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at
org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: java.lang.reflect.InvocationTargetException
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at
java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500)
at
java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:102)
... 29 more
Caused by: java.lang.Error: java.lang.reflect.InvocationTargetException
at com.sun.tools.xjc.reader.Ring.get(Ring.java:113)
at
com.sun.tools.xjc.reader.xmlschema.BindingComponent.getClassSelector(BindingComponent.java:65)
at
com.sun.tools.xjc.reader.xmlschema.ColorBinder.<init>(ColorBinder.java:62)
at
com.sun.tools.xjc.reader.xmlschema.BindGreen.<init>(BindGreen.java:63)
... 35 more
Caused by: java.lang.reflect.InvocationTargetException
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at
java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500)
at
java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:102)
... 38 more
Caused by: java.lang.NoClassDefFoundError:
javax/activation/MimeTypeParseException
at java.base/java.lang.Class.getDeclaredConstructors0(Native Method)
at
java.base/java.lang.Class.privateGetDeclaredConstructors(Class.java:3143)
at java.base/java.lang.Class.getConstructor0(Class.java:3348)
at java.base/java.lang.Class.getDeclaredConstructor(Class.java:2559)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:100)
at
com.sun.tools.xjc.reader.xmlschema.DefaultClassBinder.<init>(DefaultClassBinder.java:98)
at
com.sun.tools.xjc.reader.xmlschema.ClassSelector.<init>(ClassSelector.java:214)
... 44 more
Caused by: java.lang.ClassNotFoundException:
javax.activation.MimeTypeParseException
at
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 51 more
On Thu, Apr 11, 2019 at 9:06 AM gandhi rajan <[email protected]>
wrote:
> Hi Sajit,
>
> Could you post the error trace so that it will easy to figure out the
> problem.
>
> On Thursday, April 11, 2019, Sajit Kumar <[email protected]> wrote:
>
>> Hi Gandhi,
>>
>> I tried building ctakes on my local computer. I used the maven build
>> command to build it. The build fails for the ctakes ytex module. Any
>> suggestions to fix it. Thank you,
>>
>> Regards,
>> Sajit
>>
>> On Mon, Apr 8, 2019 at 9:24 PM gandhi rajan <[email protected]>
>> wrote:
>>
>>> Hi Sajit, I m able to find the thread safe pipeline in the latest source
>>> code in SVN under
>>>
>>> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/
>>>
>>> You can rebuild the latest code if it's not available in cTAKES 4.0
>>>
>>>
>>> Monday, April 8, 2019, Sajit Kumar <[email protected]> wrote:
>>>
>>>> Hi Gandhi,
>>>>
>>>> I did go and check Sean's mail on Thread Safe DefaultClinicialPipeline.
>>>>
>>>> https://markmail.org/message/clv3wgrztgh2swjd
>>>>
>>>> It mentions of a new ThreadSafe pipeline file suffixed with Ts. I
>>>> didn't find it the apache ctakes directory. I also tried manually including
>>>> the "threads" command in the piper file and i got a error message saying
>>>> unknown command. Can you please tell me if its available in cTakes version
>>>> 4.0 on Windows. Looking forward to hearing from you. Thanks for your help.
>>>>
>>>> Regards,
>>>> Sajit
>>>>
>>>> On Sun, Apr 7, 2019 at 10:50 PM gandhi rajan <[email protected]>
>>>> wrote:
>>>>
>>>>> Hi Sajit,
>>>>>
>>>>> As far as I know you can curtail default clinical pipeline as per your
>>>>> needs and it does support batch processing too. Please refer earlier mail
>>>>> chains from Sean regarding thread safe default clinical pipeline.
>>>>>
>>>>> On Sunday, April 7, 2019, Sajit Kumar <[email protected]>
>>>>> 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
> !!!"
>
>
