[jira] [Created] (UIMA-5590) Eclipse debug logical view for CAS indexes misleading/missing

[Marshall Schor (JIRA)]

Marshall Schor created UIMA-5590:


 Summary: Eclipse debug logical view for CAS indexes 
misleading/missing
 Key: UIMA-5590
 URL: https://issues.apache.org/jira/browse/UIMA-5590
 Project: UIMA
  Issue Type: Improvement
  Components: Core Java Framework, Eclipse plugins
Reporter: Marshall Schor
Priority: Minor


The uimaj-ep-debug plugin adds logical view support for UIMA things in Eclipse 
debug expression window.

For a CAS (really, a particular CAS view), it shows the indexes, but it 
includes the "sofa index" which is always empty for all views (except for the 
base view).  If you forget this, you might find this misleading.

If you use the logical view on the base cas, the indexes are blank.



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Re: testing uv3 with dk-pro?

[Marshall Schor]

ok, taking a look.

-Marshall


On 9/26/2017 6:33 AM, Richard Eckart de Castilho wrote:
> The fix in UIMA-5586 resolves various unit test failures in DKPro Core
> when building against UIMAv3.
>
> However, I still get the an NPE during deserialization in some cases when JCas
> is used and when a custom document annotation class is used. I
> have moved this to a separate issue:
>
> https://issues.apache.org/jira/browse/UIMA-5588
>
> Best,
>
> -- Richard
>
>> On 25.09.2017, at 19:18, Marshall Schor  wrote:
>>
>> this is now fixed; additional testing much appreciated!  -Marshall
>

[jira] [Created] (UIMA-5589) DUCC may preempt too many shares in some cases

[Burn Lewis (JIRA)]

Burn Lewis created UIMA-5589:


 Summary: DUCC may preempt too many shares in some cases
 Key: UIMA-5589
 URL: https://issues.apache.org/jira/browse/UIMA-5589
 Project: UIMA
  Issue Type: Bug
  Components: DUCC
Reporter: Burn Lewis
Priority: Minor
 Fix For: future-DUCC


When preempting work for a new job the "shrinkBy" method evicts shares with the 
least investment from jobs with an excess of resources.  Later during 
defragmentation in takeFromTheRich it gives shares to a needy job by taking 
from the richest user in the required nodepool.  This can result in excessive 
preemption, double what is necessary, and the shares evicted by shrinkBy may 
not be in the node pool of the needy job, and may not free up enough contiguous 
space.  Perhaps the defrag step should adjust the evicted list for the rich 
jobs to be those in the nodepools of the needy job. 



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Re: testing uv3 with dk-pro?

[Richard Eckart de Castilho]

The fix in UIMA-5586 resolves various unit test failures in DKPro Core
when building against UIMAv3.

However, I still get the an NPE during deserialization in some cases when JCas
is used and when a custom document annotation class is used. I
have moved this to a separate issue:

https://issues.apache.org/jira/browse/UIMA-5588

Best,

-- Richard

> On 25.09.2017, at 19:18, Marshall Schor  wrote:
> 
> this is now fixed; additional testing much appreciated!  -Marshall

[jira] [Updated] (UIMA-5588) uv3: NPE during deserialization under certain circumstances

[Richard Eckart de Castilho (JIRA)]

 [ 
https://issues.apache.org/jira/browse/UIMA-5588?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Richard Eckart de Castilho updated UIMA-5588:
-
Description: 
This was previously thought to be covered by UIMA-5586 - however, the problem 
remains after the order of the deserialization had been fixed in UIMA-5586.

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}

Mind this is a minimal code for reproduction. The same happens when 
deserializing within the context of an initialized AnalysisEngine.

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:
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}

Mind this is a minimal code for reproduction. The same happens when 
deserializing within the context of an initialized AnalysisEngine.

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

[jira] [Created] (UIMA-5588) uv3: NPE during deserialization under certain circumstances

[Richard Eckart de Castilho (JIRA)]

Richard Eckart de Castilho created UIMA-5588:


 Summary: uv3: NPE during deserialization under certain 
circumstances
 Key: UIMA-5588
 URL: https://issues.apache.org/jira/browse/UIMA-5588
 Project: UIMA
  Issue Type: Bug
  Components: Core Java Framework
Affects Versions: 3.0.0SDK-beta
Reporter: Richard Eckart de Castilho


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}

Mind this is a minimal code for reproduction. The same happens when 
deserializing within the context of an initialized AnalysisEngine.

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}




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[jira] [Commented] (UIMA-5562) UIMA AS fails with HttpConnector

[John (JIRA)]

[ 
https://issues.apache.org/jira/browse/UIMA-5562?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16180539#comment-16180539
 ] 

John commented on UIMA-5562:


Problem is caused by this bug in AMQ. As this is fixed in master it will be 
part of AMQ 5.16.

> UIMA AS fails with HttpConnector
> 
>
> Key: UIMA-5562
> URL: https://issues.apache.org/jira/browse/UIMA-5562
> Project: UIMA
>  Issue Type: Bug
>  Components: Async Scaleout
>Affects Versions: 2.9.0AS
> Environment: Windows 7 and Linux
>Reporter: John
>Priority: Blocker
> Attachments: myTestScenario.bat
>
>
> Hi,
> if I try to use UIMA AS with ActiveMQ http-connector, which is provided in 
> default configuration, I do get a timeout.
> Steps to reproduce:
> # Unzip http://www-eu.apache.org/dist/uima/uima-as-2.9.0/uima-as-2.9.0-bin.zip
> # Set InputDirectory in 
> {{apache-uima-2.9.0/examples/descriptors/collection_reader/FileSystemCollectionReader.xml}}
>  to correct absolute path 
> # Copy attached Batch-File into directory
> # Start it, wait and press 3 times Enter
> If I set BROKER_URL to tcp://localhost:61616 in the Batch-Script, the 
> documents are processed successfully.
> With value http://localhost:8080 I get the following exception.
> {code}
> Error on getMeta call to remote service:
> org.apache.uima.aae.error.UimaASMetaRequestTimeout: UIMA AS Client Timed Out 
> Waiting For GetMeta Reply From a Service On Queue:MeetingDetectorTaeQueue
> at 
> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngineCommon_impl.notifyOnTimout(BaseUIMAAsynchronousEngineCommon_impl.java:2350)
> at 
> org.apache.uima.adapter.jms.client.ClientServiceDelegate.handleError(ClientServiceDelegate.java:192)
> at org.apache.uima.aae.delegate.Delegate$2.run(Delegate.java:839)
> at java.util.TimerThread.mainLoop(Timer.java:555)
> at java.util.TimerThread.run(Timer.java:505)
> Terminating Client...
> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngine_impl.stop() - 
> Stop
> ping UIMA-AS Client
> javax.jms.JMSException: A consumer is consuming from the temporary destination
> at 
> org.apache.activemq.ActiveMQConnection.deleteTempDestination(ActiveMQConnection.java:2061)
> at 
> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngine_impl.stopConnection(BaseUIMAAsynchronousEngine_impl.java:324)
> at 
> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngine_impl.stop(BaseUIMAAsynchronousEngine_impl.java:345)
> at 
> org.apache.uima.examples.as.RunRemoteAsyncAE$StatusCallbackListenerImpl.stop(RunRemoteAsyncAE.java:367)
> at 
> org.apache.uima.examples.as.RunRemoteAsyncAE$StatusCallbackListenerImpl.initializationComplete(RunRemoteAsyncAE.java:360)
> at 
> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngineCommon_impl.notifyListeners(BaseUIMAAsynchronousEngineCommon_impl.java:1220)
> at 
> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngineCommon_impl.notifyOnTimout(BaseUIMAAsynchronousEngineCommon_impl.java:2351)
> at 
> org.apache.uima.adapter.jms.client.ClientServiceDelegate.handleError(ClientServiceDelegate.java:192)
> at org.apache.uima.aae.delegate.Delegate$2.run(Delegate.java:839)
> at java.util.TimerThread.mainLoop(Timer.java:555)
> at java.util.TimerThread.run(Timer.java:505)
> {code}



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