Re: Reuse serialized XMI CAS in a dynamic application.

Tue, 16 Jun 2009 15:42:32 -0700 

I compared both type systems (the serialized type system of the CAS with the 
original type system).
It seems the problems comes from those definitions that are only present in the 
serialized one:

<typeDescription>
  <name>org.pubcurator.uima.ts.PubIdentifier[]</name>
  <description/>
  <supertypeName>uima.cas.FSArray</supertypeName>
</typeDescription>
So it seems that the TypeSystem2Xml produces an not 100% compatible type system description (at least for deserialization of a CAS). Can you think of any workarounds? Any chance to get that fixed soon? Should I create a bug report (if it is one at all)? 

Regards,
Kai



Kai Schlamp wrote:

Hi Thilo,

thanks for your help.
I tried it the way you suggested. I just tested it with one type system. And if I use my type system description directly instead of the serialized/deserialized type system it works fine. But when I use the deserialized type system (serialized by your mentioned TypeSystem2Xml) to deserialize the CAS I get a CASAdminException. Below is the Exception, the original type system description, the serialized type description via TypeSystem2Xml, and a little serialized CAS test case. 
Do you have an idea why this Exception occurs?

The Exception:
CASAdminException: Can't derive from type "uima.cas.FSArray" since it is inheritance final. at org.apache.uima.cas.impl.TypeSystemImpl.addType(TypeSystemImpl.java:581) at org.apache.uima.util.CasCreationUtils.setupTypeSystem(CasCreationUtils.java:733) at org.apache.uima.util.CasCreationUtils.doCreateCas(CasCreationUtils.java:590) at org.apache.uima.util.CasCreationUtils.createCas(CasCreationUtils.java:352) at org.apache.uima.util.CasCreationUtils.createCas(CasCreationUtils.java:304) at org.pubcurator.uima.utils.FullCasDeserializer.deserialize(FullCasDeserializer.java:56) at org.pubcurator.uima.utils.FullCasDeserializerTest.testDeserialize(FullCasDeserializerTest.java:36) 
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    at java.lang.reflect.Method.invoke(Method.java:597)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44) at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15) at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41) at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20) at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28) at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:73) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:46) 
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
    at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28) at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31) 
    at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:46) at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38) at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:467) at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:683) at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:390) at org.eclipse.pde.internal.junit.runtime.RemotePluginTestRunner.main(RemotePluginTestRunner.java:62) at org.eclipse.pde.internal.junit.runtime.CoreTestApplication.run(CoreTestApplication.java:23) 
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:574) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:368) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179) 
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:559)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:514)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1311)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1287)



Orignial Type System Description:

<?xml version="1.0" encoding="UTF-8"?>
<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier";>
  <name>PubCurator TypeSystem</name>
<description>This is the type system that PubCurator uses for data representation. All analysis engines used in PubCurator must output this type system.</description> 
  <version>1.0</version>
  <vendor>PubCurator</vendor>
  <types>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubAnnotation</name>
      <description/>
      <supertypeName>uima.tcas.Annotation</supertypeName>
      <features>
        <featureDescription>
          <name>annotator</name>
          <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotator</rangeTypeName> 
        </featureDescription>
        <featureDescription>
          <name>score</name>
          <description/>
          <rangeTypeName>uima.cas.Integer</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>identifiers</name>
          <description/>
          <rangeTypeName>uima.cas.FSArray</rangeTypeName>
          <elementType>org.pubcurator.uima.ts.PubIdentifier</elementType>
        </featureDescription>
        <featureDescription>
          <name>spans</name>
<description>One item for example can be devided in multiple spans. For example, the phrase "</description> 
          <rangeTypeName>uima.cas.FSArray</rangeTypeName>
          <elementType>org.pubcurator.uima.ts.PubSpan</elementType>
        </featureDescription>
        <featureDescription>
          <name>topic</name>
          <description/>
          <rangeTypeName>org.pubcurator.uima.ts.PubTopic</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubIdentifier</name>
      <description/>
      <supertypeName>uima.cas.TOP</supertypeName>
      <features>
        <featureDescription>
          <name>identifierType</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>identifier</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubItem</name>
      <description/>
      <supertypeName>org.pubcurator.uima.ts.PubAnnotation</supertypeName>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubItemAssociation</name>
      <description/>
      <supertypeName>org.pubcurator.uima.ts.PubAnnotation</supertypeName>
      <features>
        <featureDescription>
          <name>source</name>
          <description/>
          <rangeTypeName>org.pubcurator.uima.ts.PubItem</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>destination</name>
          <description/>
          <rangeTypeName>org.pubcurator.uima.ts.PubItem</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubAnnotator</name>
      <description/>
      <supertypeName>uima.cas.TOP</supertypeName>
      <features>
        <featureDescription>
          <name>analyzerId</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>delegateName</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>analyzerVersion</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>note</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubEntity</name>
      <description/>
      <supertypeName>uima.tcas.Annotation</supertypeName>
      <features>
        <featureDescription>
          <name>annotations</name>
          <description/>
          <rangeTypeName>uima.cas.FSArray</rangeTypeName>
          <elementType>org.pubcurator.uima.ts.PubAnnotation</elementType>
        </featureDescription>
        <featureDescription>
          <name>score</name>
          <description/>
          <rangeTypeName>uima.cas.Integer</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>annotator</name>
          <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotator</rangeTypeName> 
        </featureDescription>
        <featureDescription>
          <name>subEntities</name>
          <description/>
          <rangeTypeName>uima.cas.FSArray</rangeTypeName>
          <elementType>org.pubcurator.uima.ts.PubEntity</elementType>
        </featureDescription>
        <featureDescription>
          <name>identifiers</name>
          <description/>
          <rangeTypeName>uima.cas.FSArray</rangeTypeName>
          <elementType>org.pubcurator.uima.ts.PubIdentifier</elementType>
        </featureDescription>
        <featureDescription>
          <name>topic</name>
          <description/>
          <rangeTypeName>org.pubcurator.uima.ts.PubTopic</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubProperty</name>
      <description/>
      <supertypeName>uima.cas.TOP</supertypeName>
      <features>
        <featureDescription>
          <name>key</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>value</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubSpan</name>
      <description/>
      <supertypeName>uima.tcas.Annotation</supertypeName>
    </typeDescription>
    <typeDescription>
      <name>org.pubcurator.uima.ts.PubTopic</name>
      <description/>
      <supertypeName>uima.cas.TOP</supertypeName>
      <features>
        <featureDescription>
          <name>namespace</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>name</name>
          <description/>
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
  </types>
</typeSystemDescription>




Serialized Type System Description:

<?xml version="1.0" encoding="UTF-8"?>
<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier";>
    <types>
        <typeDescription>
            <name>uima.tcas.Annotation</name>
            <description/>
            <supertypeName>uima.cas.AnnotationBase</supertypeName>
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>uima.tcas.DocumentAnnotation</name>
            <description/>
            <supertypeName>uima.tcas.Annotation</supertypeName>
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>language</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubAnnotation</name>
            <description/>
            <supertypeName>uima.tcas.Annotation</supertypeName>
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>annotator</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotator</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>score</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>identifiers</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubIdentifier[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>spans</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubSpan[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>topic</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubTopic</rangeTypeName> 
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubIdentifier</name>
            <description/>
            <supertypeName>uima.cas.TOP</supertypeName>
            <features>
                <featureDescription>
                    <name>identifierType</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>identifier</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubItem</name>
            <description/>
<supertypeName>org.pubcurator.uima.ts.PubAnnotation</supertypeName> 
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>annotator</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotator</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>score</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>identifiers</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubIdentifier[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>spans</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubSpan[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>topic</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubTopic</rangeTypeName> 
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubItemAssociation</name>
            <description/>
<supertypeName>org.pubcurator.uima.ts.PubAnnotation</supertypeName> 
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>annotator</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotator</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>score</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>identifiers</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubIdentifier[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>spans</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubSpan[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>topic</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubTopic</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>source</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubItem</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>destination</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubItem</rangeTypeName> 
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubAnnotator</name>
            <description/>
            <supertypeName>uima.cas.TOP</supertypeName>
            <features>
                <featureDescription>
                    <name>analyzerId</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>delegateName</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>analyzerVersion</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>note</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubEntity</name>
            <description/>
            <supertypeName>uima.tcas.Annotation</supertypeName>
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>annotations</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotation[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>score</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>annotator</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubAnnotator</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>subEntities</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubEntity[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>identifiers</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubIdentifier[]</rangeTypeName> 
                </featureDescription>
                <featureDescription>
                    <name>topic</name>
                    <description/>
<rangeTypeName>org.pubcurator.uima.ts.PubTopic</rangeTypeName> 
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubProperty</name>
            <description/>
            <supertypeName>uima.cas.TOP</supertypeName>
            <features>
                <featureDescription>
                    <name>key</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>value</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubSpan</name>
            <description/>
            <supertypeName>uima.tcas.Annotation</supertypeName>
            <features>
                <featureDescription>
                    <name>sofa</name>
                    <description/>
                    <rangeTypeName>uima.cas.Sofa</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>begin</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>end</name>
                    <description/>
                    <rangeTypeName>uima.cas.Integer</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubTopic</name>
            <description/>
            <supertypeName>uima.cas.TOP</supertypeName>
            <features>
                <featureDescription>
                    <name>namespace</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
                <featureDescription>
                    <name>name</name>
                    <description/>
                    <rangeTypeName>uima.cas.String</rangeTypeName>
                </featureDescription>
            </features>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubIdentifier[]</name>
            <description/>
            <supertypeName>uima.cas.FSArray</supertypeName>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubSpan[]</name>
            <description/>
            <supertypeName>uima.cas.FSArray</supertypeName>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubAnnotation[]</name>
            <description/>
            <supertypeName>uima.cas.FSArray</supertypeName>
        </typeDescription>
        <typeDescription>
            <name>org.pubcurator.uima.ts.PubEntity[]</name>
            <description/>
            <supertypeName>uima.cas.FSArray</supertypeName>
        </typeDescription>
    </types>
</typeSystemDescription>





Serialized CAS:
<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:cas="http:///uima/cas.ecore"; xmlns:xmi="http://www.omg.org/XMI"; xmlns:ts="http:///org/pubcurator/uima/ts.ecore"; xmlns:tcas="http:///uima/tcas.ecore"; xmi:version="2.0"><cas:NULL xmi:id="0"/><cas:Sofa xmi:id="10" sofaNum="1" sofaID="_InitialView"/><ts:PubAnnotation xmi:id="1" sofa="10" begin="10" end="20" score="1000"/><cas:View sofa="10" members="1"/></xmi:XMI>

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