[jira] [Comment Edited] (UIMA-5586) uv3: DocumentAnnotation subclasses not handled as in UIMAv2 during deserialization

["Richard Eckart de Castilho (JIRA)" <de...@uima.apache.org>]

    [ https://issues.apache.org/jira/browse/UIMA-5586?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16176191#comment-16176191 ] 

Richard Eckart de Castilho edited comment on UIMA-5586 at 9/22/17 9:42 AM:
---------------------------------------------------------------------------

Possibly related to this issue is another observation. When deserializing some binary CAS formats, there is a NPE in certain cases. Here is an example that might serve for reproduction:

{noformat}
    @Test
    public void test6LenientPlainUima() throws Exception
    {
        CAS source = JCasFactory.createJCas().getCas();
        CAS target = JCasFactory.createJCas().getCas();

        new DocumentMetaData(source.getJCas(), 0, 0).addToIndexes();

        @SuppressWarnings("resource")
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        CasIOUtils.save(source, bos, COMPRESSED_FILTERED);
        bos.close();
        
        CasIOUtils.load(new ByteArrayInputStream(bos.toByteArray()), target);
    }
{noformat}

The NPE only seems to be thrown when the `DocumentMetaData` is added via JCas:

{noformat}
java.lang.NullPointerException
	at org.apache.uima.cas.impl.CASImpl.getView(CASImpl.java:2224)
	at org.apache.uima.cas.impl.BinaryCasSerDes6.deserializeAfterVersion(BinaryCasSerDes6.java:1892)
	at org.apache.uima.cas.impl.BinaryCasSerDes.reinit(BinaryCasSerDes.java:595)
	at org.apache.uima.util.CasIOUtils.load(CasIOUtils.java:382)
	at org.apache.uima.util.CasIOUtils.load(CasIOUtils.java:313)
	at org.apache.uima.util.CasIOUtils.load(CasIOUtils.java:237)
        ...
{noformat}

I have set up a similar test using only the plain CAS API which seems to work fine:

{noformat}
    @Test
    public void test6LenientPlainUima2() throws Exception
    {
        TypeSystemDescription tsd = new TypeSystemDescription_impl();
        TypeDescription td = tsd.addType("DocumentMetaData", "", CAS.TYPE_NAME_DOCUMENT_ANNOTATION);
        td.addFeature("feat", "", CAS.TYPE_NAME_STRING);
        
        CAS source = CasCreationUtils.createCas(tsd, null, null, null);
        CAS target = CasCreationUtils.createCas(tsd, null, null, null);

        AnnotationFS dmd = source
                .createAnnotation(source.getTypeSystem().getType("DocumentMetaData"), 0, 0);
        source.addFsToIndexes(dmd);
        assertEquals("DocumentMetaData", source.getDocumentAnnotation().getType().getName());

        @SuppressWarnings("resource")
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        CasIOUtils.save(source, bos, COMPRESSED_FILTERED);
        bos.close();
        
        CasIOUtils.load(new ByteArrayInputStream(bos.toByteArray()), target);
    }
{noformat}


was (Author: rec):
Possibly related to this issue is another observation. When deserializing some binary CAS formats, there is a NPE in certain cases. Here is an example that might serve for reproduction:

{noformat}
    @Test
    public void test6LenientPlainUima() throws Exception
    {
        CAS source = JCasFactory.createJCas().getCas();
        CAS target = JCasFactory.createJCas().getCas();

        new DocumentMetaData(source.getJCas(), 0, 0).addToIndexes();

        @SuppressWarnings("resource")
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        CasIOUtils.save(source, bos, COMPRESSED_FILTERED);
        bos.close();
        
        CasIOUtils.load(new ByteArrayInputStream(bos.toByteArray()), target);
    }
{noformat}

The NPE only seems to be thrown when the `DocumentMetaData` is added via JCas.

I have set up a similar test using only the plain CAS API which seems to work fine:

{noformat}
    @Test
    public void test6LenientPlainUima2() throws Exception
    {
        TypeSystemDescription tsd = new TypeSystemDescription_impl();
        TypeDescription td = tsd.addType("DocumentMetaData", "", CAS.TYPE_NAME_DOCUMENT_ANNOTATION);
        td.addFeature("feat", "", CAS.TYPE_NAME_STRING);
        
        CAS source = CasCreationUtils.createCas(tsd, null, null, null);
        CAS target = CasCreationUtils.createCas(tsd, null, null, null);

        AnnotationFS dmd = source
                .createAnnotation(source.getTypeSystem().getType("DocumentMetaData"), 0, 0);
        source.addFsToIndexes(dmd);
        assertEquals("DocumentMetaData", source.getDocumentAnnotation().getType().getName());

        @SuppressWarnings("resource")
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        CasIOUtils.save(source, bos, COMPRESSED_FILTERED);
        bos.close();
        
        CasIOUtils.load(new ByteArrayInputStream(bos.toByteArray()), target);
    }
{noformat}

> uv3: DocumentAnnotation subclasses not handled as in UIMAv2 during deserialization
> ----------------------------------------------------------------------------------
>
>                 Key: UIMA-5586
>                 URL: https://issues.apache.org/jira/browse/UIMA-5586
>             Project: UIMA
>          Issue Type: Bug
>          Components: Core Java Framework
>    Affects Versions: 3.0.0SDK-beta
>            Reporter: Richard Eckart de Castilho
>
> Consider the case that you have custom subclass of the uima `DocumentAnnotation`, let's call it `DocumentMetaData`. Next, we have an XMI file which contains an annotation of the `DocumentMetaData` type.
> When loading such an XMI file in UIMAv2, the CAS ends up with a single `DocumentMetaData` annotation which is accessible via `cas.getDocumentAnnotation()`.
> When loading the same file with UIMAv3, the CAS ends up with both, a `DocumentAnnotation` and a `DocumentMetaData` annotation and `cas.getDocumentAnnotation()` returns the former.
> The same appears to happen when deserializing a CAS from various binary formats.



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