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From "jay vyas (JIRA)" <j...@apache.org>
Subject [jira] [Comment Edited] (CTAKES-314) BigTop/Hadoop cTAKES integration
Date Fri, 10 Oct 2014 21:14:35 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-314?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14167522#comment-14167522
] 

jay vyas edited comment on CTAKES-314 at 10/10/14 9:14 PM:
-----------------------------------------------------------

[~Pei.Chen@childrens.harvard.edu] Okay, finally got it ported into scala for the spark jobs...
Just one tiny error !   It involves a "URI is not hierarchical" exception.  any thoughts?
 This is w/ ctakes 3.2.0.

{noformat}
  def main(args: Array[String]) {
    val aed:AnalysisEngineDescription =
      org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenProcessingPipeline();
    val jcas:JCas = JCasFactory.createJCas();
    jcas.setDocumentText("My arthritis in my knee is flaring up. ");
    SimplePipeline.runPipeline(jcas, aed);

    //Print out the tokens and Parts of Speech

    val iter = {
      JCasUtil.select(jcas, classOf[BaseToken]).iterator()
    }
    while(iter.hasNext){
      val entity = iter.next();
      System.out.println("Token: " + entity.toString);
    }
  }
{noformat}

Is throwing this exception.

{noformat}

Exception in thread "main" java.lang.IllegalArgumentException: URI is not hierarchical
	at java.io.File.<init>(File.java:418)
	at org.apache.ctakes.lvg.ae.LvgAnnotator.createAnnotatorDescription(LvgAnnotator.java:565)
	at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenProcessingPipeline(ClinicalPipelineFactory.java:78)
	at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getDefaultPipeline(ClinicalPipelineFactory.java:58)
	at sparkapps.CTakesExample$.main(CTakesExample.scala:19)
	at sparkapps.CTakesExample.main(CTakesExample.scala)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)
{noformat}


was (Author: jayunit100):
[~Pei.Chen@childrens.harvard.edu] Okay, finally got it ported into scala for the spark jobs...
Just one tiny error !   It involves a "URI is not hierarchical" exception.  any thoughts?
 This is w/ ctakes 3.2.0.

{noformat}
  def main(args: Array[String]) {
    val aed:AnalysisEngineDescription =
      org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenProcessingPipeline();
    val jcas:JCas = JCasFactory.createJCas();
    jcas.setDocumentText("My arthritis in my knee is flaring up. ");
    SimplePipeline.runPipeline(jcas, aed);

    //Print out the tokens and Parts of Speech

    val iter = {
      JCasUtil.select(jcas, classOf[BaseToken]).iterator()
    }
    while(iter.hasNext){
      val entity = iter.next();
      System.out.println("Token: " + entity.toString);
    }
  }
{noformat}

{noformat}

Exception in thread "main" java.lang.IllegalArgumentException: URI is not hierarchical
	at java.io.File.<init>(File.java:418)
	at org.apache.ctakes.lvg.ae.LvgAnnotator.createAnnotatorDescription(LvgAnnotator.java:565)
	at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenProcessingPipeline(ClinicalPipelineFactory.java:78)
	at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getDefaultPipeline(ClinicalPipelineFactory.java:58)
	at sparkapps.CTakesExample$.main(CTakesExample.scala:19)
	at sparkapps.CTakesExample.main(CTakesExample.scala)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)
{noformat}

> BigTop/Hadoop cTAKES integration
> --------------------------------
>
>                 Key: CTAKES-314
>                 URL: https://issues.apache.org/jira/browse/CTAKES-314
>             Project: cTAKES
>          Issue Type: New Feature
>    Affects Versions: 3.2.0
>            Reporter: Pei Chen
>             Fix For: 3.2.3
>
>         Attachments: Napkin_cTAKES_Hadoop.JPG
>
>
> Placeholder to-
> Create a simple application that can take in different datasources (public forums, twitter,
etc.), scale up cTAKES using BigTop/Hadoop ecosystem.



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