from:"JIRA"

Improve Maven build
---

 Key: UIMA-1755
 URL: https://issues.apache.org/jira/browse/UIMA-1755
 Project: UIMA
  Issue Type: Task
  Components: Build, Packaging and Test
Affects Versions: 2.3
Reporter: Marshall Schor
Assignee: Marshall Schor


Do this work in a branch (mavenAlign), because it is extensive and may take 
some time to get it working the way people want it to work.

Improve the maven build with the goal of making it more aligned with the maven 
way, being simpler, and following Apache conventions.

Subtasks will track individual parts of this.

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[jira] Created: (UIMA-1756) Maven-align: POM work

Maven-align: POM work
-

 Key: UIMA-1756
 URL: https://issues.apache.org/jira/browse/UIMA-1756
 Project: UIMA
  Issue Type: Sub-task
  Components: Build, Packaging and Test
Reporter: Marshall Schor
Assignee: Marshall Schor


1) eliminate need for any individual project checkout to depend on another 
project being checked out simultaneously.  This includes: 
* switching to docbkx maven plugin instead of our own docbook tooling
* using maven-remote-resources plugin for including common, shared things, 
rather than referring to other projects
* use POM dependencies from the repositories

2) make POMs inherit from Apache master POM.

3)  separate *parent* poms from *aggregation* poms.

4) make POMs inherit from Apache common POM

5) make parent poms separately releasable, using the apache/maven convention 
for version numbering (single digit).

6) position aggregator poms in the conventional position (not flat structure) 
to enable some plugins (assembly and release) to function better.

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[jira] Created: (UIMA-1757) use docbkx to create docbooks in place of current docbook tools project

use docbkx to create docbooks in place of current docbook tools project
---

 Key: UIMA-1757
 URL: https://issues.apache.org/jira/browse/UIMA-1757
 Project: UIMA
  Issue Type: Sub-task
Reporter: Marshall Schor
Assignee: Marshall Schor


1) align target dir structures with the way docbkx conventionally does this

2) update docbooks to 4.4 from 4.5 DTD (4.5 not in maven repo, 5.0 is, but may 
require more changes)

3) write parent pom for docbkx

4) change poms doing docbook to add docbkx in the pre-site phase

5) figure out olink database strategy - this should probably be remote 
resources, pulled in via maven dependencies (i.e., when a docbook links to 
another one, it has a dependency on that other docbook's olink database).

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[jira] Created: (UIMA-1758) remove dependency on checked-out other projects

remove dependency on checked-out other projects
---

 Key: UIMA-1758
 URL: https://issues.apache.org/jira/browse/UIMA-1758
 Project: UIMA
  Issue Type: Sub-task
Reporter: Marshall Schor
Assignee: Marshall Schor


use maven-remote-resources plugin for including common, shared things, rather 
than referring to other checked-out projects


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[jira] Updated: (UIMA-1756) Maven-align: POM work


 [ 
https://issues.apache.org/jira/browse/UIMA-1756?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor updated UIMA-1756:
-

Description: 
1) eliminate need for any individual project checkout to depend on another 
project being checked out simultaneously.  This includes: 
* switching to docbkx maven plugin instead of our own docbook tooling (see 
other subtask)
* using maven-remote-resources plugin for including common, shared things, 
rather than referring to other projects (see other subtask)
* use POM dependencies from the repositories

2) make POMs inherit from Apache master POM.

3)  separate *parent* poms from *aggregation* poms.

4) make POMs inherit from Apache common POM

5) make parent poms separately releasable, using the apache/maven convention 
for version numbering (single digit).

6) position aggregator poms in the conventional position (not flat structure) 
to enable some plugins (assembly and release) to function better.

  was:
1) eliminate need for any individual project checkout to depend on another 
project being checked out simultaneously.  This includes: 
* switching to docbkx maven plugin instead of our own docbook tooling
* using maven-remote-resources plugin for including common, shared things, 
rather than referring to other projects
* use POM dependencies from the repositories

2) make POMs inherit from Apache master POM.

3)  separate *parent* poms from *aggregation* poms.

4) make POMs inherit from Apache common POM

5) make parent poms separately releasable, using the apache/maven convention 
for version numbering (single digit).

6) position aggregator poms in the conventional position (not flat structure) 
to enable some plugins (assembly and release) to function better.


 Maven-align: POM work
 -

 Key: UIMA-1756
 URL: https://issues.apache.org/jira/browse/UIMA-1756
 Project: UIMA
  Issue Type: Sub-task
  Components: Build, Packaging and Test
Reporter: Marshall Schor
Assignee: Marshall Schor

 1) eliminate need for any individual project checkout to depend on another 
 project being checked out simultaneously.  This includes: 
 * switching to docbkx maven plugin instead of our own docbook tooling (see 
 other subtask)
 * using maven-remote-resources plugin for including common, shared things, 
 rather than referring to other projects (see other subtask)
 * use POM dependencies from the repositories
 2) make POMs inherit from Apache master POM.
 3)  separate *parent* poms from *aggregation* poms.
 4) make POMs inherit from Apache common POM
 5) make parent poms separately releasable, using the apache/maven convention 
 for version numbering (single digit).
 6) position aggregator poms in the conventional position (not flat structure) 
 to enable some plugins (assembly and release) to function better.

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[jira] Created: (UIMA-1759) make project versioning more conventional

make project versioning more conventional
-

 Key: UIMA-1759
 URL: https://issues.apache.org/jira/browse/UIMA-1759
 Project: UIMA
  Issue Type: Sub-task
  Components: Build, Packaging and Test
Reporter: Marshall Schor
Assignee: Marshall Schor


1) make aggregator poms distinct from parent poms

2) aggregator poms to specify which version(s) of modules they are including 
(some may not change release to release)

3) Eliminate the use of properties in values for versions  (these cause warning 
messages when used with maven 3 - saying this support will not work in the 
future)

4) align project versioning with the way the maven release  plugin works.

5) make parent poms separately releasable, using the apache/maven convention 
for version numbering of these kinds of artifacts (e.g., simple number, 
starting with 1).

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[jira] Resolved: (UIMA-1740) Mock integration tests on AlchemyAPI Annotator

2010-04-02 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1740?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili resolved UIMA-1740.
---

Resolution: Fixed

Mocked tests added, thanks to Simone Tripodi for suggestions on how to handle 
URLConnections for non-Http ones

 Mock integration tests on AlchemyAPI Annotator 
 ---

 Key: UIMA-1740
 URL: https://issues.apache.org/jira/browse/UIMA-1740
 Project: UIMA
  Issue Type: Bug
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Since previously the API key was already put inside the AE descriptor and now 
 it's been removed, the URL call should be mocked to avoid tests' failure due 
 to HTTP 403

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[jira] Closed: (UIMA-1740) Mock integration tests on AlchemyAPI Annotator

2010-04-02 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1740?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili closed UIMA-1740.
-


 Mock integration tests on AlchemyAPI Annotator 
 ---

 Key: UIMA-1740
 URL: https://issues.apache.org/jira/browse/UIMA-1740
 Project: UIMA
  Issue Type: Bug
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Since previously the API key was already put inside the AE descriptor and now 
 it's been removed, the URL call should be mocked to avoid tests' failure due 
 to HTTP 403

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[jira] Commented: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-04-01 Thread Tommaso Teofili (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1747?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12852309#action_12852309
 ] 

Tommaso Teofili commented on UIMA-1747:
---

Hi Greg, it seems to me you're right in regards of the Type string so the patch 
should be fixing the issue.

I am wondering about the need of the line:
Type markupType = 
cas.getTypeSystem().getType(org.apache.uima.tika.MarkupAnnotation)
since it seems it is never used, so we may choose to remove it.

In regards of Exception now that the package name is fixed, it's something it 
should happen only when that FS is not defined inside the TypeSystem.
So for example we may choose to create an UnknownTypeException like the one 
inside the ConceptMapper
https://svn.apache.org/repos/asf/incubator/uima/sandbox/trunk/ConceptMapper/src/main/java/org/apache/uima/conceptMapper/support/tokens/UnknownTypeException.java
but extending RuntimeException so that we should not change method signature to 
declare throwing exception.
What do you think?

 TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
 --

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker
 Attachments: UIMA-1747-patch.txt


 I get the following NPE.
 java.lang.NullPointerException
   at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
   at 
 org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
   at 
 org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
   at 
 org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Issue Comment Edited: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-04-01 Thread Greg Holmberg (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1747?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12848027#action_12848027
 ] 

Greg Holmberg edited comment on UIMA-1747 at 4/1/10 6:21 PM:
-

This is due to this line, 147 in MarkupHandler.java, returning null:

Type attributeType = 
cas.getTypeSystem().getType(org.apache.uima.AttributeFS);

The problem is that the class name string is incorrect.  It should be 
org.apache.uima.tika.AttributeFS.  Same for the line above, but that variable 
is never used, so it doesn't matter.


  was (Author: holmberg):
This is due to this line, 147 in MarkupHandler.java, returning null:

Type attributeType = 
cas.getTypeSystem().getType(org.apache.uima.AttributeFS);

The problem is that the class name string is incorrect.  It should be 
org.apache.tika.uima.AttributeFS.  Same for the line above, but that variable 
is never used, so it doesn't matter.

  
 TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
 --

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker
 Attachments: UIMA-1747-patch.txt


 I get the following NPE.
 java.lang.NullPointerException
   at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
   at 
 org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
   at 
 org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
   at 
 org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Commented: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-04-01 Thread Greg Holmberg (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1747?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12852496#action_12852496
 ] 

Greg Holmberg commented on UIMA-1747:
-

Hi Tommaso.  Regarding what is the correct exception to throw, I looked at the 
callers code (TIKAWrapper.populateCASfromURL), and it throws CASException, so 
MarkupHandler.populateCAS could throw that also without any changes to 
MarkupHandler.

I'm not sure what the consequences of changing the signature of this method is. 
 Is it a real, documented public contract, or is it merely a method marked 
public and the only caller affected would be TIKAWrapper?  If the latter, 
then I wouldn't worry about keeping a stable signature.

If it would affect many callers other than TIKAWrapper, then throwing 
RuntimeException or something derived from it makes sense.

 TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
 --

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker
 Attachments: UIMA-1747-patch.txt


 I get the following NPE.
 java.lang.NullPointerException
   at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
   at 
 org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
   at 
 org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
   at 
 org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Issue Comment Edited: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-04-01 Thread Greg Holmberg (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1747?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12852496#action_12852496
 ] 

Greg Holmberg edited comment on UIMA-1747 at 4/1/10 6:35 PM:
-

Hi Tommaso.  Regarding what is the correct exception to throw, I looked at the 
callers code (TIKAWrapper.populateCASfromURL), and it throws CASException, so 
MarkupHandler.populateCAS could throw that also without any changes to 
MarkupHandler.

I'm not sure what the consequences of changing the signature of this method 
are.  Is it a real, documented public contract, or is it merely a method marked 
public and the only caller affected would be TIKAWrapper?  If the latter, 
then I wouldn't worry about keeping a stable signature.

If it would affect many callers other than TIKAWrapper, then throwing 
RuntimeException or something derived from it makes sense.

  was (Author: holmberg):
Hi Tommaso.  Regarding what is the correct exception to throw, I looked at 
the callers code (TIKAWrapper.populateCASfromURL), and it throws CASException, 
so MarkupHandler.populateCAS could throw that also without any changes to 
MarkupHandler.

I'm not sure what the consequences of changing the signature of this method is. 
 Is it a real, documented public contract, or is it merely a method marked 
public and the only caller affected would be TIKAWrapper?  If the latter, 
then I wouldn't worry about keeping a stable signature.

If it would affect many callers other than TIKAWrapper, then throwing 
RuntimeException or something derived from it makes sense.
  
 TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
 --

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker
 Attachments: UIMA-1747-patch.txt


 I get the following NPE.
 java.lang.NullPointerException
   at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
   at 
 org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
   at 
 org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
   at 
 org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Created: (UIMA-1754) Incorrect description of getCAS() method in UIMA AS documentation

2010-03-31 Thread Jerry Cwiklik (JIRA)

Incorrect description of getCAS() method in UIMA AS documentation
-

 Key: UIMA-1754
 URL: https://issues.apache.org/jira/browse/UIMA-1754
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik


Chapter 4.2 The UimaAsynchronousEngine Interface describes UIMA AS client 
interface. Its description of getCAS() tells the reader to call reset() or 
release() on the CAS before calling getCAS() again. This is wrong when the 
client application uses an async style of sending CASes using sendCAS() method. 
When using async calls, the framework actually releases a CAS *after* the 
user's listener callback completes. The code calls release() if the user 
callback is *not* provided. The only time when the user's code must call 
release() or reset() is when the *synchronous* calls are made via 
sendAndReceive(). In this style of invocation, the framework does not call 
release() nor reset() and it *is* user's responsibility to do so. 

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[jira] Commented: (UIMA-1754) Incorrect description of getCAS() method in UIMA AS documentation

2010-03-31 Thread Jerry Cwiklik (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1754?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12851985#action_12851985
 ] 

Jerry Cwiklik commented on UIMA-1754:
-

Modified description of getCAS() to read:

CAS getCAS(): Requests a new CAS instance from the CAS pool. This method
blocks until a free instance of CAS is available in the CAS pool. Applications 
that
use synchronous sendAndReceive() and getCAS() need to call CAS.reset()
before reusing the CAS, or CAS.release() to return it to the Cas pool. 
Applications
that use asychronous sendCAS() and getCAS() must not call CAS.release() nor
CAS.reset(). The UIMA AS client releases each CAS at the end of processing. If
a callback listener object is registered with UIMA AS client, the CAS.release() 
is
called after a call to the callback listener entityProcessComplete() completes.



 Incorrect description of getCAS() method in UIMA AS documentation
 -

 Key: UIMA-1754
 URL: https://issues.apache.org/jira/browse/UIMA-1754
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik

 Chapter 4.2 The UimaAsynchronousEngine Interface describes UIMA AS client 
 interface. Its description of getCAS() tells the reader to call reset() or 
 release() on the CAS before calling getCAS() again. This is wrong when the 
 client application uses an async style of sending CASes using sendCAS() 
 method. When using async calls, the framework actually releases a CAS *after* 
 the user's listener callback completes. The code calls release() if the user 
 callback is *not* provided. The only time when the user's code must call 
 release() or reset() is when the *synchronous* calls are made via 
 sendAndReceive(). In this style of invocation, the framework does not call 
 release() nor reset() and it *is* user's responsibility to do so. 

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[jira] Created: (UIMA-1753) XmiCasSerializer passes null for an attribute's URI and localName

2010-03-30 Thread Greg Holmberg (JIRA)

XmiCasSerializer passes null for an attribute's URI and localName
-

 Key: UIMA-1753
 URL: https://issues.apache.org/jira/browse/UIMA-1753
 Project: UIMA
  Issue Type: Bug
  Components: Core Java Framework
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Minor


XmiCasSerializer.XmiCasDocSerializer has this method: 

 private void addAttribute(AttributesImpl attrs, String attrName, String 
attrValue) { 
 attrs.addAttribute(null, null, attrName, cdataType, attrValue); 
 } 

This causes a NullPointerException in some ContentHandlers (such as those for 
EXI from Siemens and AgileDelta).

The JavaDoc says to pass an empty String for these parameters when you don't 
have a good value for them.

So the line should be changed to:

attrs.addAttribute(, , attrName, cdataType, attrValue); 

I tested that change with the AgileDelta ContentHandler, and it no longer threw 
any exceptions.



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[jira] Closed: (UIMA-1726) Long GC causes UIMA AS service to loose broker connection and marks the client as dead

[
https://issues.apache.org/jira/browse/UIMA-1726?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Jerry Cwiklik closed UIMA-1726.
---

Resolution: Fixed
Fix Version/s: 2.3AS

Removed DoNotProcess list as means of tracking disconnected clients. To detect
dead clients and to optimize processing, the code checks for existence of a
temp reply queue in the broker's JMX MBeanServer registry. If the temp queue
exists, the message is processed. If the queue lookup fails, the message is
dropped. A temp reply queue exists in the same broker that manages service
input queue. The code creates a connection to a JMX MBeanServer on initial
request message and caches it for subsequent lookups. If the broker is
configured to not use jmx, the optimization is not performed and every message
is processed. Such requests fail when a reply is attempted and the temp queue
doesnt exists due to client termination. The code supports: tcp, http, as well
as failover in the broker url.
The default jmx port used for creating connection to broker's MBeanServer is
1099. To override this, add this property: -Dactivemq.broker.jmx.port=XXX to
the service startup command

Long GC causes UIMA AS service to loose broker connection and marks the
client as dead
--

Key: UIMA-1726
URL: https://issues.apache.org/jira/browse/UIMA-1726
Project: UIMA
Issue Type: Bug
Components: Async Scaleout
Reporter: Jerry Cwiklik
Assignee: Jerry Cwiklik
Fix For: 2.3AS

When the JVMs GC takes a long time, the UIMA AS fails to validate the broker
connection and proceeds to close it as if the broker died. It seems that the
long GC freezes the jvm and prevents the low level socket pinging to work
correctly. This pinging is a mechanism by which the low level AMQ code relies
upon to detect a broker failure. In this case, the broker is actually fine.
The side effect of the above is that the UIMA AS service falsely adds the
client to the DoNotProcess list. This is an optimization that was recently
added that prevents wasting processing cycles while handling CASes that are
known to have come from clients that had gone away. Each CAS origin is
checked against that list and if there is a match the CAS is thrown away. It
seems that we need a better mechanism to detect broker failure.

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[jira] Created: (UIMA-1751) Fix NPE while looking up MessageProducer

Fix NPE while looking up MessageProducer


 Key: UIMA-1751
 URL: https://issues.apache.org/jira/browse/UIMA-1751
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik


ActiveMQMessageSender throws NPE in getMessageProducer() sometimes when the 
UIMA AS client is stopping. A race condition seems to be the cause. A thread 
doing a send tries to dereference engine object after the engine was forced to 
stop.  

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[jira] Closed: (UIMA-1751) Fix NPE while looking up MessageProducer


 [ 
https://issues.apache.org/jira/browse/UIMA-1751?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jerry Cwiklik closed UIMA-1751.
---

Resolution: Fixed

Modified getMessageProducer() in ActiveMQMessageSender to check the state of 
the engine before returning the Producer. 

 Fix NPE while looking up MessageProducer
 

 Key: UIMA-1751
 URL: https://issues.apache.org/jira/browse/UIMA-1751
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik

 ActiveMQMessageSender throws NPE in getMessageProducer() sometimes when the 
 UIMA AS client is stopping. A race condition seems to be the cause. A thread 
 doing a send tries to dereference engine object after the engine was forced 
 to stop.  

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[jira] Created: (UIMA-1752) Fisheye for Repository

Fisheye for Repository
--

 Key: UIMA-1752
 URL: https://issues.apache.org/jira/browse/UIMA-1752
 Project: UIMA
  Issue Type: New Feature
  Components: Website
Reporter: Brandon Fish


Setup a Fisheye source code search and browser for the repository.

This would be useful to new people to the project for locating classes, example 
code and packages. It is free for open source projects and ActiveMQ has one 
setup already.

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[jira] Commented: (UIMA-1752) Fisheye for Repository

2010-03-26 Thread Marshall Schor (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1752?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12850231#action_12850231
 ] 

Marshall Schor commented on UIMA-1752:
--

Do you know the process to do this?  Are there any downsides to doing it?

 Fisheye for Repository
 --

 Key: UIMA-1752
 URL: https://issues.apache.org/jira/browse/UIMA-1752
 Project: UIMA
  Issue Type: New Feature
  Components: Website
Reporter: Brandon Fish

 Setup a Fisheye source code search and browser for the repository.
 This would be useful to new people to the project for locating classes, 
 example code and packages. It is free for open source projects and ActiveMQ 
 has one setup already.

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[jira] Commented: (UIMA-1752) Fisheye for Repository


[ 
https://issues.apache.org/jira/browse/UIMA-1752?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12850245#action_12850245
 ] 

Brandon Fish commented on UIMA-1752:


The license  download can be found here:
http://www.atlassian.com/software/fisheye/pricing.jsp?type=opensource

Installation guides for Atlassian Products are well documented:
http://confluence.atlassian.com/display/FISHEYE/FishEye+Installation+Guide

I don't see any downsides, you just need a server. Installation is very quick. 
There may be some configuration required so Fisheye knows your projects' layout 
but this is easy as well.  Then you just wait for it to index your repository.

 Fisheye for Repository
 --

 Key: UIMA-1752
 URL: https://issues.apache.org/jira/browse/UIMA-1752
 Project: UIMA
  Issue Type: New Feature
  Components: Website
Reporter: Brandon Fish

 Setup a Fisheye source code search and browser for the repository.
 This would be useful to new people to the project for locating classes, 
 example code and packages. It is free for open source projects and ActiveMQ 
 has one setup already.

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[jira] Commented: (UIMA-1752) Fisheye for Repository


[ 
https://issues.apache.org/jira/browse/UIMA-1752?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12850261#action_12850261
 ] 

Brandon Fish commented on UIMA-1752:


I also noticed Atlassian is hosting for ActiveMQ: 
http://fisheye6.atlassian.com/browse/activemq

Maybe there is a possibility to do the same for UIMA. 

 Fisheye for Repository
 --

 Key: UIMA-1752
 URL: https://issues.apache.org/jira/browse/UIMA-1752
 Project: UIMA
  Issue Type: New Feature
  Components: Website
Reporter: Brandon Fish

 Setup a Fisheye source code search and browser for the repository.
 This would be useful to new people to the project for locating classes, 
 example code and packages. It is free for open source projects and ActiveMQ 
 has one setup already.

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[jira] Commented: (UIMA-1752) Fisheye for Repository

[
https://issues.apache.org/jira/browse/UIMA-1752?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12850270#action_12850270
]

Brandon Fish commented on UIMA-1752:

From http://fisheye6.atlassian.com/:

FishEye on Apache Projects

This FishEye instance is proudly brought to you by Atlassian and Contegix.

Please feel free to experiment with Crucible using the DEMO project. Ping
support if you would like a Crucible project for your project. We can set
default reviewers, restrict users who can create reviews, and other useful
things.

FishEye 6 contains Subversion repositories from Apache. Other hosted FishEye
repositories can be found:

* FishEye 1 SourceForge CVS repositories.
* FishEye 2 Miscellaneous repositories.
* FishEye 3 SourceForge Subversion repositories.
* FishEye 4 Java.net Subversion repositories.
* FishEye 5 Java.net CVS repositories.
* FishEye 6 Apache Subversion Repositories.

Adding an Apache Repo

Atlassian is now running a mirror of the Apache SVN repository which makes it a
simple matter for us to add an Apache project to this instance. If you would
like to have an Apache project listed here:

Create a support request at Atlassian Support(http://support.atlassian.com/) in
the FishEye project. Please use the Public Hosting component for your request.

Fisheye for Repository
--

Key: UIMA-1752
URL: https://issues.apache.org/jira/browse/UIMA-1752
Project: UIMA
Issue Type: New Feature
Components: Website
Reporter: Brandon Fish

Setup a Fisheye source code search and browser for the repository.
This would be useful to new people to the project for locating classes,
example code and packages. It is free for open source projects and ActiveMQ
has one setup already.

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[jira] Closed: (UIMA-1405) Uima AS not allowing deployment of more than one deployment descriptor in the same jvm


 [ 
https://issues.apache.org/jira/browse/UIMA-1405?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jerry Cwiklik closed UIMA-1405.
---

Resolution: Won't Fix

 Uima AS not allowing deployment of more than one deployment descriptor in the 
 same jvm
 --

 Key: UIMA-1405
 URL: https://issues.apache.org/jira/browse/UIMA-1405
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik
Assignee: Jerry Cwiklik
Priority: Minor

 Uima AS fails with ResourceInitializationException when one tries to deploy 
 more than one deployment descriptor using deployAsyncService script. The 
 problem is that components in generated spring context files are deployed 
 into a single Spring container. But each spring context files defines 
 singleton objects that are not meant to be used externally. An example of 
 such non-shared singleton would the InProcessCache. It is meant to be shared 
 by components defined in a single context file. There are few possibly 
 solutions here:
 1) modify dd2spring to assign unique names to spring beans to prevent sharing 
 across context files. 
 2) modify uima-as deployer to deploy each context file in a separate spring 
 container
 3) find a way to prevent spring from sharing singleton objects across context 
 files.

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[jira] Commented: (UIMA-1752) Fisheye for Repository

2010-03-26 Thread Marshall Schor (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1752?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12850423#action_12850423
 ] 

Marshall Schor commented on UIMA-1752:
--

looks like FishEye 6 has no incubator projects.  We've graduated, but are 
still waiting to get set up as a top level project.  I think it best to wait 
till that happens to move on this.

 Fisheye for Repository
 --

 Key: UIMA-1752
 URL: https://issues.apache.org/jira/browse/UIMA-1752
 Project: UIMA
  Issue Type: New Feature
  Components: Website
Reporter: Brandon Fish

 Setup a Fisheye source code search and browser for the repository.
 This would be useful to new people to the project for locating classes, 
 example code and packages. It is free for open source projects and ActiveMQ 
 has one setup already.

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[jira] Created: (UIMA-1750) Tutorial and Developers' Guides: setActionOnMaxError

2010-03-25 Thread Prokopis Prokopidis (JIRA)

Tutorial and Developers' Guides: setActionOnMaxError


 Key: UIMA-1750
 URL: https://issues.apache.org/jira/browse/UIMA-1750
 Project: UIMA
  Issue Type: Bug
  Components: Documentation
Reporter: Prokopis Prokopidis
Priority: Minor


In UIMA Tutorial and Developer's guide, section 3.3.2 Configuring a 
Collection Processing Engine Descriptor Programmatically, the example code 
contains a repetition of the setActionOnMaxError method call:

{code::borderStyle=solid}

//Continue, despite errors and skip bad Cas
personTitleProcessor.setActionOnMaxError(terminate);
...
//  Define and add CAS Consumer
CpeIntegratedCasProcessor consumerProcessor = 
CpeDescriptorFactory.produceCasProcessor(Printer);
consumerProcessor.setDescriptor([descriptor]);

//Define batch size
consumerProcessor.setBatchSize(100);

//Terminate CPE on max errors
personTitleProcessor.setActionOnMaxError(terminate);

{code}

The first instance seems wrongly commented, while the second wrongly placed.



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[jira] Created: (UIMA-1749) UIMA AS uses one instance of a Serializer object

2010-03-24 Thread Jerry Cwiklik (JIRA)

UIMA AS uses one instance of a Serializer object 
-

 Key: UIMA-1749
 URL: https://issues.apache.org/jira/browse/UIMA-1749
 Project: UIMA
  Issue Type: Improvement
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik


There is a single instance of a Deserializer object processing incoming CASes 
and also a single instance of a Serializer object processing outgoing CASes. 
This may bottleneck UIMA AS Service when handling large CASes and multiple 
threads are processing incoming and outgoing CASes. It would be more efficient 
to create and dedicate an instance of a Serializer/Deserializer to each 
processing thread so that multiple CASes cas be serialized/deserialized at the 
same time. 

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[jira] Closed: (UIMA-1749) UIMA AS uses one instance of a Serializer object

2010-03-24 Thread Jerry Cwiklik (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1749?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jerry Cwiklik closed UIMA-1749.
---

   Resolution: Fixed
Fix Version/s: 2.3AS

Added a cache object to create and cache an instance of a Serializer object for 
each thread processing remote CASes. The Serializer instance is cached using a 
thread id. This effectively dedicates a unique instance of Serializer to each 
thread processing a CAS allowing concurrency during serialization and 
deserialization of CASes. 

 UIMA AS uses one instance of a Serializer object 
 -

 Key: UIMA-1749
 URL: https://issues.apache.org/jira/browse/UIMA-1749
 Project: UIMA
  Issue Type: Improvement
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik
 Fix For: 2.3AS


 There is a single instance of a Deserializer object processing incoming CASes 
 and also a single instance of a Serializer object processing outgoing CASes. 
 This may bottleneck UIMA AS Service when handling large CASes and multiple 
 threads are processing incoming and outgoing CASes. It would be more 
 efficient to create and dedicate an instance of a Serializer/Deserializer to 
 each processing thread so that multiple CASes cas be serialized/deserialized 
 at the same time. 

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[jira] Created: (UIMA-1748) BSFAnnotator fails tests

2010-03-22 Thread Greg Holmberg (JIRA)

BSFAnnotator fails tests


 Key: UIMA-1748
 URL: https://issues.apache.org/jira/browse/UIMA-1748
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-BSFAnnotator
Affects Versions: 2.3
 Environment: Windows
Reporter: Greg Holmberg
Priority: Minor


All tests fail saying it can't locate files such as TEST.bsh.



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[jira] Updated: (UIMA-1748) BSFAnnotator fails tests

2010-03-22 Thread Greg Holmberg (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1748?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Greg Holmberg updated UIMA-1748:


Attachment: UIMA-1748-patch.txt

This happens when the path to the source project includes spaces.  In my case, 
my workspace is in my home directory in Windows, which is under C:\Documents 
and Settings.

The problem is that the file URL is not decoded to translate %20 to a space.

I've attached a suggested fix for BSFAnnotator.java.


 BSFAnnotator fails tests
 

 Key: UIMA-1748
 URL: https://issues.apache.org/jira/browse/UIMA-1748
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-BSFAnnotator
Affects Versions: 2.3
 Environment: Windows
Reporter: Greg Holmberg
Priority: Minor
 Attachments: UIMA-1748-patch.txt


 All tests fail saying it can't locate files such as TEST.bsh.

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[jira] Commented: (UIMA-1748) BSFAnnotator fails tests

2010-03-22 Thread Greg Holmberg (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1748?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12848342#action_12848342
 ] 

Greg Holmberg commented on UIMA-1748:
-

Perhaps this would be better:

return new File(url.toURI());

 BSFAnnotator fails tests
 

 Key: UIMA-1748
 URL: https://issues.apache.org/jira/browse/UIMA-1748
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-BSFAnnotator
Affects Versions: 2.3
 Environment: Windows
Reporter: Greg Holmberg
Priority: Minor
 Attachments: UIMA-1748-patch.txt


 All tests fail saying it can't locate files such as TEST.bsh.

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[jira] Created: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-03-21 Thread Greg Holmberg (JIRA)

TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
--

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker


I get the following NPE.

java.lang.NullPointerException
at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
at 
org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
at 
org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
at 
org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
at 
org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
at 
org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Commented: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-03-21 Thread Greg Holmberg (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1747?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12848027#action_12848027
 ] 

Greg Holmberg commented on UIMA-1747:
-

This is due to this line, 147 in MarkupHandler.java, returning null:

Type attributeType = 
cas.getTypeSystem().getType(org.apache.uima.AttributeFS);

The problem is that the class name string is incorrect.  It should be 
org.apache.tika.uima.AttributeFS.  Same for the line above, but that variable 
is never used, so it doesn't matter.


 TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
 --

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker

 I get the following NPE.
 java.lang.NullPointerException
   at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
   at 
 org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
   at 
 org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
   at 
 org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Updated: (UIMA-1747) TikaAnnotator: null pointer exception in MarkupHandler.populateCAS

2010-03-21 Thread Greg Holmberg (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1747?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Greg Holmberg updated UIMA-1747:


Attachment: UIMA-1747-patch.txt

Suggested fix.  I'm not sure about the type of exception thrown.  The method 
doesn't declare that it throws any exceptions, so RuntimeException was all I 
could come up with.

 TikaAnnotator: null pointer exception in MarkupHandler.populateCAS
 --

 Key: UIMA-1747
 URL: https://issues.apache.org/jira/browse/UIMA-1747
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-TikaAnnotator
Affects Versions: 2.3
Reporter: Greg Holmberg
Priority: Blocker
 Attachments: UIMA-1747-patch.txt


 I get the following NPE.
 java.lang.NullPointerException
   at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:474)
   at 
 org.apache.uima.tika.MarkupHandler.populateCAS(MarkupHandler.java:168)
   at 
 org.apache.uima.tika.TIKAWrapper.populateCASfromURL(TIKAWrapper.java:105)
   at 
 org.apache.uima.tika.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:99)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.readNext(ArtifactProducer.java:494)
   at 
 org.apache.uima.collection.impl.cpm.engine.ArtifactProducer.run(ArtifactProducer.java:711)

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[jira] Updated: (UIMA-1746) Lock with org.apache.uima.utils.XmlInputSource (uimaj-core)

2010-03-18 Thread Baptiste Gaillard (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1746?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Baptiste Gaillard updated UIMA-1746:


Attachment: UIMA-1746-TEST.zip

Eclipse project with an unit test class to illustrate the bug. 

Just comment / uncomment line 77 in the org.apache.uima.util.XmlInputSourceTest 
class to see the problem. 


 Lock with org.apache.uima.utils.XmlInputSource (uimaj-core)
 ---

 Key: UIMA-1746
 URL: https://issues.apache.org/jira/browse/UIMA-1746
 Project: UIMA
  Issue Type: Bug
  Components: Core Java Framework
Affects Versions: 2.2.2, 2.3
 Environment: Tested on Windows, but should appear also on UNIX 
 platforms.
Reporter: Baptiste Gaillard
Priority: Minor
 Attachments: UIMA-1746-TEST.zip

   Original Estimate: 1h
  Remaining Estimate: 1h

 See: http://uima.markmail.org/thread/4h7ljnaz26v4jicl
 XmlInputSource.close() locks the JARs where a JARUrlConnection is used. 
 This bug is described in the SUN bug database: 
 http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4386865
 To fix that we only have to insert the following lines before each 
 'URL.openStream()' call: 
 URLConnection urlConnection = mURL.openConnection();
 if(urlConnection instanceof JarURLConnection) 
 {
 ((JarURLConnection) mURL.openConnection()).setDefaultUseCaches(false);
 }

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[jira] Updated: (UIMA-1746) Lock with org.apache.uima.utils.XmlInputSource (uimaj-core)

2010-03-18 Thread Baptiste Gaillard (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1746?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Baptiste Gaillard updated UIMA-1746:


Attachment: UIMA-1746.patch

Patch which fix the bug

 Lock with org.apache.uima.utils.XmlInputSource (uimaj-core)
 ---

 Key: UIMA-1746
 URL: https://issues.apache.org/jira/browse/UIMA-1746
 Project: UIMA
  Issue Type: Bug
  Components: Core Java Framework
Affects Versions: 2.2.2, 2.3
 Environment: Tested on Windows, but should appear also on UNIX 
 platforms.
Reporter: Baptiste Gaillard
Priority: Minor
 Attachments: UIMA-1746-TEST.zip, UIMA-1746.patch

   Original Estimate: 1h
  Remaining Estimate: 1h

 See: http://uima.markmail.org/thread/4h7ljnaz26v4jicl
 XmlInputSource.close() locks the JARs where a JARUrlConnection is used. 
 This bug is described in the SUN bug database: 
 http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4386865
 To fix that we only have to insert the following lines before each 
 'URL.openStream()' call: 
 URLConnection urlConnection = mURL.openConnection();
 if(urlConnection instanceof JarURLConnection) 
 {
 ((JarURLConnection) mURL.openConnection()).setDefaultUseCaches(false);
 }

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[jira] Created: (UIMA-1745) Wrong name in TextLanguageDetectionAEDescriptor

2010-03-17 Thread Tommaso Teofili (JIRA)

Wrong name in TextLanguageDetectionAEDescriptor
---

 Key: UIMA-1745
 URL: https://issues.apache.org/jira/browse/UIMA-1745
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Priority: Minor


name inside TextLanguageDetectionAEDescriptor.xml descriptor of 
AlchemyAPIAnnotator refers to TextCategorizationAEDescriptor

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[jira] Resolved: (UIMA-1745) Wrong name in TextLanguageDetectionAEDescriptor

2010-03-17 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1745?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili resolved UIMA-1745.
---

Resolution: Fixed

 Wrong name in TextLanguageDetectionAEDescriptor
 ---

 Key: UIMA-1745
 URL: https://issues.apache.org/jira/browse/UIMA-1745
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Priority: Minor

 name inside TextLanguageDetectionAEDescriptor.xml descriptor of 
 AlchemyAPIAnnotator refers to TextCategorizationAEDescriptor

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[jira] Closed: (UIMA-1745) Wrong name in TextLanguageDetectionAEDescriptor

2010-03-17 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1745?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili closed UIMA-1745.
-

Assignee: Tommaso Teofili

 Wrong name in TextLanguageDetectionAEDescriptor
 ---

 Key: UIMA-1745
 URL: https://issues.apache.org/jira/browse/UIMA-1745
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili
Priority: Minor

 name inside TextLanguageDetectionAEDescriptor.xml descriptor of 
 AlchemyAPIAnnotator refers to TextCategorizationAEDescriptor

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[jira] Resolved: (UIMA-1741) Add AlchmeyAPI Annotator documentation

2010-03-07 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1741?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili resolved UIMA-1741.
---

Resolution: Fixed

 Add AlchmeyAPI Annotator documentation
 --

 Key: UIMA-1741
 URL: https://issues.apache.org/jira/browse/UIMA-1741
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Generated documentation on features and use of AlchemyAPI Annotator must be 
 provided

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[jira] Commented: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox

2010-03-03 Thread Jukka Zitting (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12840665#action_12840665
 ] 

Jukka Zitting commented on UIMA-1733:
-

The IP clearance is now complete.

 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili
 Attachments: alchemy-annotator.zip


 Once the SGA has been recorded we can start importing the code

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[jira] Commented: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox

2010-02-26 Thread Jukka Zitting (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12838889#action_12838889
 ] 

Jukka Zitting commented on UIMA-1733:
-

I've filed the IP clearance record and requested lazy consensus on 
gene...@incubator. The process should be complete in three days unless anything 
unexpected comes up.

 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili
 Attachments: alchemy-annotator.zip


 Once the SGA has been recorded we can start importing the code

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[jira] Created: (UIMA-1744) Remove generated local path commenti inside AlchemyAPI Annotator FeatureStructures

2010-02-24 Thread Tommaso Teofili (JIRA)

Remove generated local path commenti inside AlchemyAPI Annotator 
FeatureStructures
--

 Key: UIMA-1744
 URL: https://issues.apache.org/jira/browse/UIMA-1744
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili
Priority: Trivial


remove /** ... /Users/... */ comments inside FeatureStructures generated by 
JCasGen inside AlchemyAPI Annotator

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[jira] Updated: (UIMA-1744) Remove generated local path comments inside AlchemyAPI Annotator FeatureStructures

2010-02-24 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1744?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili updated UIMA-1744:
--

Summary: Remove generated local path comments inside AlchemyAPI Annotator 
FeatureStructures  (was: Remove generated local path commenti inside AlchemyAPI 
Annotator FeatureStructures)

 Remove generated local path comments inside AlchemyAPI Annotator 
 FeatureStructures
 --

 Key: UIMA-1744
 URL: https://issues.apache.org/jira/browse/UIMA-1744
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili
Priority: Trivial

 remove /** ... /Users/... */ comments inside FeatureStructures generated by 
 JCasGen inside AlchemyAPI Annotator

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[jira] Closed: (UIMA-1739) Modification of FormPanel's getCaptionFromName method

2010-02-23 Thread Marshall Schor (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1739?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor closed UIMA-1739.


   Resolution: Fixed
Fix Version/s: 2.3.1
 Assignee: Marshall Schor

applied the patch

 Modification of FormPanel's  getCaptionFromName method
 --

 Key: UIMA-1739
 URL: https://issues.apache.org/jira/browse/UIMA-1739
 Project: UIMA
  Issue Type: Improvement
  Components: Tools
Affects Versions: 2.3C
Reporter: Jérôme Rocheteau
Assignee: Marshall Schor
Priority: Trivial
 Fix For: 2.3.1

 Attachments: FormPanel Patch.txt


 I'll suggest to change the current if-then condition « if (c  'A'  c  
 'Z') » to that one « if (c = 'A'  c = 'Z') » found in 
 org.apache.uima.tools.util.gui.FormPanel.getCaptionFromName(String name).

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[jira] Updated: (UIMA-1739) Modification of FormPanel's getCaptionFromName method

2010-02-23 Thread Marshall Schor (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1739?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor updated UIMA-1739:
-

Affects Version/s: (was: 2.3C)
   2.3

 Modification of FormPanel's  getCaptionFromName method
 --

 Key: UIMA-1739
 URL: https://issues.apache.org/jira/browse/UIMA-1739
 Project: UIMA
  Issue Type: Improvement
  Components: Tools
Affects Versions: 2.3
Reporter: Jérôme Rocheteau
Assignee: Marshall Schor
Priority: Trivial
 Fix For: 2.3.1

 Attachments: FormPanel Patch.txt


 I'll suggest to change the current if-then condition « if (c  'A'  c  
 'Z') » to that one « if (c = 'A'  c = 'Z') » found in 
 org.apache.uima.tools.util.gui.FormPanel.getCaptionFromName(String name).

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[jira] Updated: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox

2010-02-20 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili updated UIMA-1733:
--

Attachment: alchemy-annotator.zip

the code donated (in its pre import version)

 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili
 Attachments: alchemy-annotator.zip


 Once the SGA has been recorded we can start importing the code

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[jira] Closed: (UIMA-1743) UIMA AS aggregate may hang when one of its primitive delgates fails during initialization

2010-02-19 Thread Jerry Cwiklik (JIRA)

[
https://issues.apache.org/jira/browse/UIMA-1743?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Jerry Cwiklik closed UIMA-1743.
---

Resolution: Fixed

Modified initializeAnalysisEngine() to destroy AE and return if a service was
stopped while initializing AE in the core's produceAnalysisEngine() method.
Modified postInitialize() to spin a cleanup thread and mark service as
initialized only if the service is not stopped.

UIMA AS aggregate may hang when one of its primitive delgates fails during
initialization
-

Key: UIMA-1743
URL: https://issues.apache.org/jira/browse/UIMA-1743
Project: UIMA
Issue Type: Bug
Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik
Assignee: Jerry Cwiklik

There is a race condition in UIMA AS that may lead to a hang while trying to
stop an aggregate service with multiple primitive delegates. If one of the
delegates fails during initialization and the DD says to terminate, the
aggregate sends STOP event to each delegate to force clean shutdown. When a
primitive is instantiating AE via produceAnalysisEngine() call and the STOP
comes on another thread, the state of the service is changed to stopped. When
the AE is finally initialized and produceAnalysisEngine() returns, the code
does not check for service status and proceeds to call postInitialize() which
spins a cleanup thread and marks the service as initialized successfully.
There are two problems:
1) Primitive service doesnt check if it has been stopped after
produceAnalysisEngine() returns
2) In postInitialize(), the primitive service always starts a cleanup thread
no matter what the status of the service is. This cleanup thread is never
stopped and leads to a hang.

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[jira] Closed: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox

2010-02-18 Thread Tommaso Teofili (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili closed UIMA-1733.
-


 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Once the SGA has been recorded we can start importing the code

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[jira] Commented: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox


[ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12834679#action_12834679
 ] 

Tommaso Teofili commented on UIMA-1733:
---

SGA has been recorded, so we can start importing the code

 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Once the SGA has been recorded we can start importing the code

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[jira] Resolved: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox


 [ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Tommaso Teofili resolved UIMA-1733.
---

Resolution: Fixed

Code import completed

 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Once the SGA has been recorded we can start importing the code

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[jira] Created: (UIMA-1740) Mock integration tests on AlchemyAPI Annotator

Mock integration tests on AlchemyAPI Annotator 
---

 Key: UIMA-1740
 URL: https://issues.apache.org/jira/browse/UIMA-1740
 Project: UIMA
  Issue Type: Bug
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili


Since previously the API key was already put inside the AE descriptor and now 
it's been removed, the URL call should be mocked to avoid tests' failure due to 
HTTP 403

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[jira] Created: (UIMA-1741) Add AlchmeyAPI Annotator documentation

Add AlchmeyAPI Annotator documentation
--

 Key: UIMA-1741
 URL: https://issues.apache.org/jira/browse/UIMA-1741
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili


Generated documentation on features and use of AlchemyAPI Annotator must be 
provided

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[jira] Created: (UIMA-1742) UIMA AS Aggregate not exposing number of consumer threads on its delegate's reply queues

2010-02-17 Thread Jerry Cwiklik (JIRA)

UIMA AS Aggregate not exposing number of consumer threads on its delegate's 
reply queues


 Key: UIMA-1742
 URL: https://issues.apache.org/jira/browse/UIMA-1742
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik
Assignee: Jerry Cwiklik
Priority: Minor


UIMA AS Spring listener uses a single thread per delegate to handle replies. If 
a deployment descriptor is configured to process replies using multiple 
threads, the UIMA AS creates a concurrent listener with a thread pool to which 
the single-threaded Spring listener delegates all reply messages. This logic 
was added to assure that the parent CAS is always processed ahead of its 
children. The problem is that a JMX console shows a single JMS Consumer on a 
reply queue. This is correct, but the number of threads in the concurrent 
listener should be shown in the UIMA AS MBeans.

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[jira] Created: (UIMA-1738) Adding a JTextArea in MetaDataPanel for larger text fields

2010-02-16 Thread JIRA

Adding a JTextArea in MetaDataPanel for larger text fields
--

 Key: UIMA-1738
 URL: https://issues.apache.org/jira/browse/UIMA-1738
 Project: UIMA
  Issue Type: New Feature
  Components: Tools
Affects Versions: 2.3
Reporter: Jérôme Rocheteau
Priority: Minor


I'll suggest to add the Swing component JTextArea into MetaDataPanel in order 
to set parameters that need large text fiedls.

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[jira] Updated: (UIMA-1738) Adding a JTextArea in MetaDataPanel for larger text fields

2010-02-16 Thread JIRA


 [ 
https://issues.apache.org/jira/browse/UIMA-1738?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jérôme Rocheteau updated UIMA-1738:
---

Attachment: MetaDataPanel and ConfigField Patch.txt

I provide this patch for the MetaDataPanel and ConfigField classes that enables 
JTextArea into MetaDataPanel.

 Adding a JTextArea in MetaDataPanel for larger text fields
 --

 Key: UIMA-1738
 URL: https://issues.apache.org/jira/browse/UIMA-1738
 Project: UIMA
  Issue Type: New Feature
  Components: Tools
Affects Versions: 2.3
Reporter: Jérôme Rocheteau
Priority: Minor
 Attachments: MetaDataPanel and ConfigField Patch.txt

   Original Estimate: 0.25h
  Remaining Estimate: 0.25h

 I'll suggest to add the Swing component JTextArea into MetaDataPanel in order 
 to set parameters that need large text fiedls.

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[jira] Created: (UIMA-1739) Modification of FormPanel's getCaptionFromName method

2010-02-16 Thread JIRA

Modification of FormPanel's  getCaptionFromName method
--

 Key: UIMA-1739
 URL: https://issues.apache.org/jira/browse/UIMA-1739
 Project: UIMA
  Issue Type: Improvement
  Components: Tools
Affects Versions: 2.3C
Reporter: Jérôme Rocheteau
Priority: Trivial


I'll suggest to change the current if-then condition « if (c  'A'  c  'Z') 
» to that one « if (c = 'A'  c = 'Z') » found in 
org.apache.uima.tools.util.gui.FormPanel.getCaptionFromName(String name).

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[jira] Reopened: (UIMA-1553) Add prospective search AE to Lucas

2010-02-16 Thread Marshall Schor (JIRA)


 [ 
https://issues.apache.org/jira/browse/UIMA-1553?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor reopened UIMA-1553:
--


reopening - seems that the calls to new IOException on line 134 and 136 use a 
form of this constructor that is only available on Java 6, not Java 5.

 Add prospective search AE to Lucas
 --

 Key: UIMA-1553
 URL: https://issues.apache.org/jira/browse/UIMA-1553
 Project: UIMA
  Issue Type: Improvement
  Components: Sandbox-Lucas
Affects Versions: 2.3S
Reporter: Jörn Kottmann
Assignee: Jörn Kottmann

 Prospective search is a search method where the search query is given first
 and then searched against a stream of text, e.g. a xml feed.
 Lucene supports prospective search via their MemoryIndex
 http://lucene.apache.org/java/2_4_1/api/contrib-memory/org/apache/lucene/index/memory/MemoryIndex.html
 which is a fast one document in memory index.
 To add prospective search support to Lucas a new AE should be implemented,
 which uses a resource interface to fetch the search queries either from
 a user implemented object or from a resource file.
 The search results should be written to the CAS to be available for further
 processing by user implemented AEs.
 The new AE should share the code which is used to build the Index with the
 LuceneCASIndexer.

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[jira] Closed: (UIMA-1553) Add prospective search AE to Lucas

2010-02-16 Thread JIRA


 [ 
https://issues.apache.org/jira/browse/UIMA-1553?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jörn Kottmann closed UIMA-1553.
---

Resolution: Fixed

Replaced the call to IOException(String, Throwable) with IOException(String).

 Add prospective search AE to Lucas
 --

 Key: UIMA-1553
 URL: https://issues.apache.org/jira/browse/UIMA-1553
 Project: UIMA
  Issue Type: Improvement
  Components: Sandbox-Lucas
Affects Versions: 2.3S
Reporter: Jörn Kottmann
Assignee: Jörn Kottmann

 Prospective search is a search method where the search query is given first
 and then searched against a stream of text, e.g. a xml feed.
 Lucene supports prospective search via their MemoryIndex
 http://lucene.apache.org/java/2_4_1/api/contrib-memory/org/apache/lucene/index/memory/MemoryIndex.html
 which is a fast one document in memory index.
 To add prospective search support to Lucas a new AE should be implemented,
 which uses a resource interface to fetch the search queries either from
 a user implemented object or from a resource file.
 The search results should be written to the CAS to be available for further
 processing by user implemented AEs.
 The new AE should share the code which is used to build the Index with the
 LuceneCASIndexer.

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[jira] Created: (UIMA-1736) Tutorial example - no match between text and code in 1.3.1

2010-02-11 Thread Erwan Moreau (JIRA)

Tutorial example - no match between text and code in 1.3.1
--

 Key: UIMA-1736
 URL: https://issues.apache.org/jira/browse/UIMA-1736
 Project: UIMA
  Issue Type: Bug
  Components: Documentation
Reporter: Erwan Moreau
Priority: Minor


In UIMA Tutorial and Developer's guide, section 1.3.1 Combining annotators, 
there are references to sentences and words ouptuts for the TutorialDateTime 
annotator:

- for a TutorialDateTime annotator. This annotator detects dates and times (and 
also sentences and words)
- In this case, for example, we have decided to suppress the Word and Sentence 
annotations that are produced by the TutorialDateTime annotator.
- You should see that RoomNumbers, Dates, and Times are all shown but that 
Words and Sentences are not

But the source code provided (annotator and descriptor) does not deal with 
words/sentences.

It seems that either the text or the code should be modified in order to make 
them consistent.

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[jira] Created: (UIMA-1737) BSF Annotator reports errors on user scripts with line numbers starting from zero

2010-02-11 Thread Pablo Duboue (JIRA)

BSF Annotator reports errors on user scripts with line numbers starting from 
zero
-

 Key: UIMA-1737
 URL: https://issues.apache.org/jira/browse/UIMA-1737
 Project: UIMA
  Issue Type: Bug
  Components: Sandbox-BSFAnnotator
Affects Versions: 2.3
Reporter: Pablo Duboue
Priority: Minor


In BSFAnnotator in trunk, replace

engine.exec(scriptFileName, 0, 0, script);

to

engine.exec(scriptFileName, 1, 0, script);

to indicate that script is located starting in line 1 of scriptFileName.

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[jira] Commented: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox

2010-02-10 Thread Tommaso Teofili (JIRA)


[ 
https://issues.apache.org/jira/browse/UIMA-1733?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12832088#action_12832088
 ] 

Tommaso Teofili commented on UIMA-1733:
---

SGA has been sent

 Import AlchemyAPI Annotator code inside the Sandbox
 ---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili

 Once the SGA has been recorded we can start importing the code

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[jira] Assigned: (UIMA-1735) Javadoc Link on Website is Broken


 [ 
https://issues.apache.org/jira/browse/UIMA-1735?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor reassigned UIMA-1735:


Assignee: Marshall Schor

 Javadoc Link on Website is Broken
 -

 Key: UIMA-1735
 URL: https://issues.apache.org/jira/browse/UIMA-1735
 Project: UIMA
  Issue Type: Bug
  Components: Website
Reporter: Adam Lally
Assignee: Marshall Schor

 The Javadoc Online link from 
 http://incubator.apache.org/uima/documentation.html seems to be broken.  
 It points at: 
 http://incubator.apache.org/uima/downloads/releaseDocs/2.3.0-incubating/docs/api/index.html,
  but I get a 404 Not Found error for that URL.

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[jira] Updated: (UIMA-927) Provide a way to drain Dead Letter Queue


 [ 
https://issues.apache.org/jira/browse/UIMA-927?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor updated UIMA-927:


Fix Version/s: (was: 2.3AS)

 Provide a way to drain Dead Letter Queue 
 -

 Key: UIMA-927
 URL: https://issues.apache.org/jira/browse/UIMA-927
 Project: UIMA
  Issue Type: Improvement
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jerry Cwiklik
Priority: Minor

 ActiveMQ currently doesnt evict expried messages from the Dead Letter Queue. 
 This can potentially lead to Out Of Memory situation as by default the broker 
 keeps all messages in memory. One possible strategy is to modify ActiveMQ 
 broker configuration to spool messages from the DLQ to disk when memory is 
 tight. Other strategy may involve creating a custom DLQ Consumer to drain 
 messages.

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[jira] Updated: (UIMA-1559) lucas.xsd exists 3 times in different places


 [ 
https://issues.apache.org/jira/browse/UIMA-1559?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor updated UIMA-1559:
-

Fix Version/s: (was: 2.3S)

 lucas.xsd exists 3 times in different places
 

 Key: UIMA-1559
 URL: https://issues.apache.org/jira/browse/UIMA-1559
 Project: UIMA
  Issue Type: Improvement
  Components: Sandbox-Lucas
Affects Versions: 2.3S
Reporter: Jörn Kottmann
Assignee: Rico Landefeld

 lucas.xsd exists three times in different places:
 desc/
 src/main/resources (seems to be the current version)
 src/test/resorces
 Can it be deleted from desc and src/test/resources ?

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[jira] Closed: (UIMA-1735) Javadoc Link on Website is Broken


 [ 
https://issues.apache.org/jira/browse/UIMA-1735?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor closed UIMA-1735.


   Resolution: Fixed
Fix Version/s: 2.3
   2.3AS

missing Javadocs added to website.  The documentation page was updated to have 
2 links - one for the uimaj sdk and the other for uima-as javadocs.

 Javadoc Link on Website is Broken
 -

 Key: UIMA-1735
 URL: https://issues.apache.org/jira/browse/UIMA-1735
 Project: UIMA
  Issue Type: Bug
  Components: Website
Reporter: Adam Lally
Assignee: Marshall Schor
 Fix For: 2.3AS, 2.3


 The Javadoc Online link from 
 http://incubator.apache.org/uima/documentation.html seems to be broken.  
 It points at: 
 http://incubator.apache.org/uima/downloads/releaseDocs/2.3.0-incubating/docs/api/index.html,
  but I get a 404 Not Found error for that URL.

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[jira] Created: (UIMA-1734) UIMA-AS Deployment Descriptor doesn't work with Eclipse 3.4.2

2010-02-04 Thread Tong Fin (JIRA)

UIMA-AS Deployment Descriptor doesn't work with Eclipse 3.4.2
-

 Key: UIMA-1734
 URL: https://issues.apache.org/jira/browse/UIMA-1734
 Project: UIMA
  Issue Type: Bug
  Components: Eclipse plugins
Affects Versions: 2.3
Reporter: Tong Fin
Assignee: Tong Fin


There is a problem when running DDE in Eclipse 3.4.2:

3.4.2 Linux - fail
3.4.2 Windows - fail
3.5.1 Linux OK
3.5.1 Windows OK
3.3.2 Windows OK

Look like there are some images used by the form are missing.
These images are belong to some plugins that might not be the same for Eclipse 
3.4.2 and 3.5.x.


 Stack Trace ---
eclipse.buildId=M20090211-1700
java.version=1.6.0_16
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Command-line arguments:  -os win32 -ws win32 -arch x86 -clean

!ENTRY org.eclipse.ui.workbench.texteditor 4 0 2010-02-04 09:07:23.657
!MESSAGE The 
'org.eclipse.wst.jsdt.web.ui.internal.hyperlink.script.JSPJavaHyperlinkDetector'
 extension from plug-in 'org.eclipse.wst.jsdt.web.ui' to the 
'org.eclipse.ui.workbench.texteditor.hyperlinkDetectors' extension point will 
be ignored because it contains invalid attributes.

!ENTRY org.eclipse.ui.workbench.texteditor 4 0 2010-02-04 09:07:23.657
!MESSAGE The 
'org.eclipse.wst.jsdt.web.ui.internal.hyperlink.script.event.JSPJavaHyperlinkDetector'
 extension from plug-in 'org.eclipse.wst.jsdt.web.ui' to the 
'org.eclipse.ui.workbench.texteditor.hyperlinkDetectors' extension point will 
be ignored because it contains invalid attributes.

!ENTRY org.eclipse.ui 4 0 2010-02-04 09:07:46.388
!MESSAGE Unable to create editor ID taeconfigurator.editors.MultiPageEditor: An 
unexpected exception was thrown.
!STACK 0
java.lang.NullPointerException
   at 
org.eclipse.ui.internal.forms.widgets.FormImages$ImageIdentifier.hashCode(FormImages.java:69)
   at 
org.eclipse.ui.internal.forms.widgets.FormImages$ComplexImageIdentifier.hashCode(FormImages.java:138)
   at java.util.HashMap.get(HashMap.java:300)
   at 
org.eclipse.ui.internal.forms.widgets.FormImages.getGradient(FormImages.java:187)
   at 
org.eclipse.ui.internal.forms.widgets.FormHeading.updateGradientImage(FormHeading.java:868)
   at 
org.eclipse.ui.internal.forms.widgets.FormHeading.setTextBackground(FormHeading.java:718)
   at org.eclipse.ui.forms.widgets.Form.setTextBackground(Form.java:315)
   at 
org.apache.uima.dde.internal.page.OverviewPage.createFormContent(OverviewPage.java:375)
   at org.eclipse.ui.forms.editor.FormPage$1.run(FormPage.java:151)
   at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
   at org.eclipse.ui.forms.editor.FormPage.createPartControl(FormPage.java:149)
   at org.eclipse.ui.forms.editor.FormEditor.pageChange(FormEditor.java:488)
   at 
org.apache.uima.taeconfigurator.editors.MultiPageEditor.pageChangeSuper(MultiPageEditor.java:615)
   at 
org.apache.uima.dde.internal.DeploymentDescriptorEditor.pageChangeForCurrentEditor(DeploymentDescriptorEditor.java:308)
   at 
org.apache.uima.taeconfigurator.editors.MultiPageEditor.pageChange(MultiPageEditor.java:1118)
   at 
org.eclipse.ui.part.MultiPageEditorPart.setActivePage(MultiPageEditorPart.java:973)
   at org.eclipse.ui.forms.editor.FormEditor.setActivePage(FormEditor.java:623)
   at 
org.eclipse.ui.part.MultiPageEditorPart.createPartControl(MultiPageEditorPart.java:314)
   at 
org.eclipse.ui.internal.EditorReference.createPartHelper(EditorReference.java:661)
   at 
org.eclipse.ui.internal.EditorReference.createPart(EditorReference.java:428)
   at 
org.eclipse.ui.internal.WorkbenchPartReference.getPart(WorkbenchPartReference.java:594)
   at 
org.eclipse.ui.internal.EditorReference.getEditor(EditorReference.java:266)
   at 
org.eclipse.ui.internal.WorkbenchPage.busyOpenEditorBatched(WorkbenchPage.java:2820)
   at 
org.eclipse.ui.internal.WorkbenchPage.busyOpenEditor(WorkbenchPage.java:2729)
   at org.eclipse.ui.internal.WorkbenchPage.access$11(WorkbenchPage.java:2721)
   at org.eclipse.ui.internal.WorkbenchPage$10.run(WorkbenchPage.java:2673)
   at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
   at org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:2668)
   at org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:2652)
   at org.eclipse.ui.actions.OpenWithMenu.openEditor(OpenWithMenu.java:337)
   at org.eclipse.ui.actions.OpenWithMenu.access$0(OpenWithMenu.java:325)
   at org.eclipse.ui.actions.OpenWithMenu$2.handleEvent(OpenWithMenu.java:187)
   at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
   at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1003)
   at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3823)
   at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3422)
   at org.eclipse.ui.internal.Workbench.runEventLoop

[jira] Created: (UIMA-1735) Javadoc Link on Website is Broken

2010-02-04 Thread Adam Lally (JIRA)

Javadoc Link on Website is Broken
-

 Key: UIMA-1735
 URL: https://issues.apache.org/jira/browse/UIMA-1735
 Project: UIMA
  Issue Type: Bug
  Components: Website
Reporter: Adam Lally


The Javadoc Online link from 
http://incubator.apache.org/uima/documentation.html seems to be broken.  

It points at: 
http://incubator.apache.org/uima/downloads/releaseDocs/2.3.0-incubating/docs/api/index.html,
 but I get a 404 Not Found error for that URL.

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[jira] Created: (UIMA-1732) CPM setAnalysisEngine throws IndexOutOfBounds

2010-02-03 Thread Marshall Schor (JIRA)

CPM setAnalysisEngine throws IndexOutOfBounds
-

 Key: UIMA-1732
 URL: https://issues.apache.org/jira/browse/UIMA-1732
 Project: UIMA
  Issue Type: Bug
  Components: Collection Processing
Affects Versions: 2.3
Reporter: Marshall Schor
Assignee: Jerry Cwiklik
Priority: Minor


A user tried to do several calls to aCPM.setAnalysisEngine(xxx).  This method 
is set up to remove a previous AE if it exists, replacing it with the new one.

See http://markmail.org/message/3s2w7hxb24l3czky
There are several issues:

The method CPMEngine removeCasProcessor(int aCasProcessorIndex) has a bad 
bounds test, need to change
{noformat}
if (aCasProcessorIndex  0 || aCasProcessorIndex  annotatorList.size())  to
if (aCasProcessorIndex  0 || aCasProcessorIndex = annotatorList.size())
{noformat} 

The CPMEngine class uses two different collections to represent lists of 
analysis engines:
*  casprocessorList (an array - includes AEs and Cas Consumers)
* annotatorList (a linked list, not sure if it has both AEs and Cas Consumers)

The CPMImpl setAnalysisEngine seems to have set something which shows up in the 
array from getCasProcessors call, while the annotatorList is not updated and 
remains empty.

This method:
{noformat}
  public void removeCasProcessor(CasProcessor aCasProcessor) { 
cpEngine.removeCasProcessor(0);
  }
{noformat}
 
ignores its argument, and removes the 0'th CasProcessor.  This seems wrong, 
given the Javadoc.

The Javadoc for setAnalysisEngine's javadoc should emphasize that this is a 
convenience method for the common case of supporting a single AE. If it is 
called multiple times, it will replace the first AE (if it exists) .  The 
Javadocs should be expanded to say if you want to add multiple AEs to a pipe 
line, to not use this method, but use addCasProcessor instead. 

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[jira] Created: (UIMA-1733) Import AlchemyAPI Annotator code inside the Sandbox

2010-02-03 Thread Tommaso Teofili (JIRA)

Import AlchemyAPI Annotator code inside the Sandbox
---

 Key: UIMA-1733
 URL: https://issues.apache.org/jira/browse/UIMA-1733
 Project: UIMA
  Issue Type: Task
  Components: Sandbox
Reporter: Tommaso Teofili
Assignee: Tommaso Teofili


Once the SGA has been recorded we can start importing the code

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[jira] Commented: (UIMA-1728) UIMA AS Service logs falsely Stopping Collocated Delegate Cas Multiplier message

2010-02-01 Thread JIRA


[ 
https://issues.apache.org/jira/browse/UIMA-1728?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12828078#action_12828078
 ] 

Jörn Kottmann commented on UIMA-1728:
-

Jerry:

What is happening in your scenario
is the following:

1) CM receives input CAS C1
2) The CM generates a new CAS C2
3) C2 is sent to Delegate Service D1
4) D1 throws exception on C2
5) Aggregate receives exception from D1 and sends STOP message to CM asking
it to stop producing
new CASes from C1. This message is not sent to stop the CM!
6) CM returns C1 to the Aggregate
7) Aggregate determines that C1 has been marked as failed ( because of C2
failure)
8) Aggregate returns C1 marked as failed to the client

The confusion is the message that the aggregate logs: Stopping Collocated
Delegate Cas Multiplier:
It should say something like, Sending Request to CM to Stop Generating New
CASes from CAS id: xxx


 UIMA AS Service logs falsely Stopping Collocated Delegate Cas Multiplier 
 message
 

 Key: UIMA-1728
 URL: https://issues.apache.org/jira/browse/UIMA-1728
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jörn Kottmann
Priority: Minor
 Attachments: test.zip


 The service has one CM which creates for every CAS one new CAS and a dummy AE 
 which throws an exception on every second CAS.
 It looks like that for each exception thrown from the AE.process method the 
 stopping collocated delegate CM message is printed
 and logged:
  Instance Hashcode:28681226 Controller:TestAAE Stopping Collocated 
  Delegate Cas Multiplier:TestCM
 and
 1/25/10 1:14:51 PM - 13: 
 org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.stopCasMultiplier:
  INFO: Controller: TestAAE Stopping Collocated Delegate Cas Multiplier: 
 TestAAE
 The problem might relate to the hang issue reported here:
 http://markmail.org/message/5dr5r3yyha4kbtlb

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[jira] Commented: (UIMA-1728) UIMA AS Service logs falsely Stopping Collocated Delegate Cas Multiplier message

2010-02-01 Thread JIRA


[ 
https://issues.apache.org/jira/browse/UIMA-1728?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12828090#action_12828090
 ] 

Jörn Kottmann commented on UIMA-1728:
-

The message is also logged to the console, but the exception from the process 
method is not logged to the console.  
The message should not be logged to the console, or together with the exception.

 UIMA AS Service logs falsely Stopping Collocated Delegate Cas Multiplier 
 message
 

 Key: UIMA-1728
 URL: https://issues.apache.org/jira/browse/UIMA-1728
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jörn Kottmann
Priority: Minor
 Attachments: test.zip


 The service has one CM which creates for every CAS one new CAS and a dummy AE 
 which throws an exception on every second CAS.
 It looks like that for each exception thrown from the AE.process method the 
 stopping collocated delegate CM message is printed
 and logged:
  Instance Hashcode:28681226 Controller:TestAAE Stopping Collocated 
  Delegate Cas Multiplier:TestCM
 and
 1/25/10 1:14:51 PM - 13: 
 org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.stopCasMultiplier:
  INFO: Controller: TestAAE Stopping Collocated Delegate Cas Multiplier: 
 TestAAE
 The problem might relate to the hang issue reported here:
 http://markmail.org/message/5dr5r3yyha4kbtlb

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[jira] Commented: (UIMA-1731) ResourceInitializationExceptions thrown by a deployed aggregate are only partially logged


[ 
https://issues.apache.org/jira/browse/UIMA-1731?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=12828217#action_12828217
 ] 

Jerry Cwiklik commented on UIMA-1731:
-

I checked the code and discovered that the problem described here is due to a 
wrong style of logging. In many places, while logging WARNING messages using 
these keys: 

UIMAEE_exception__WARNING
UIMAJMS_exception__WARNING

the UIMA AS code uses something like this:

UIMAFramework.getLogger(CLASS_NAME).logrb(Level.WARNING, getClass().getName(),
takeAction, UIMAEE_Constants.JMS_LOG_RESOURCE_BUNDLE,
UIMAEE_exception__WARNING, new Object[] { e });

The above does not log the whole stack trace hiding a real cause. Change code 
to use this instead:

UIMAFramework.getLogger(CLASS_NAME).logrb(Level.WARNING, getClass().getName(),
takeAction, UIMAEE_Constants.JMS_LOG_RESOURCE_BUNDLE,
UIMAEE_exception__WARNING, e);

The above is better than just using 

log(Level level, String aMessage, Throwable thrown);

since it identifies a method where the failure is detected.


 ResourceInitializationExceptions thrown by a deployed aggregate are only 
 partially logged
 -

 Key: UIMA-1731
 URL: https://issues.apache.org/jira/browse/UIMA-1731
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Reporter: Burn Lewis
Priority: Minor
 Fix For: 2.3AS


 When the XcasCollectionReader fails to init because its input directory is 
 missing it reports the cause when run in core UIMA, i.e.
 Caused by: org.apache.uima.resource.ResourceInitializationException: 
 Initialization of annotator class com.ibm.nlp.readers.XcasCollectionReader 
 failed.  (Descriptor: 
 file:/.automount/hlthome01/a/hlthome01/homes/hlthome01.3/burn/workspace/factotem/desc/pipe/readers/XcasCollectionReader.xml)
 Caused by: org.apache.uima.resource.ResourceInitializationException: Invalid 
 value for parameter InputDirectory in component null -- directory 
 xmidata does not exist.
 but when deployed under UIMA-AS this detailed exception is missing ... all we 
 get is the higher-level cause, e.g.
 1/30/10 10:56:15 PM - 3: 
 org.apache.uima.aae.controller.PrimitiveAnalysisEngineController_impl.initializeAnalysisEngine:
  WARNING: org.apache.uima.resource.ResourceInitializationException: 
 Initialization of annotator class com.ibm.nlp.readers.XcasCollectionReader 
 failed.  (Descriptor: 
 file:/u/burn/workspace/factotem/desc/pipe/readers/XcasCollectionReader.xml)
 Also, the detailed message lists the component as null ... the collection 
 reader follows the example code and reports the error with:
   throw new ResourceInitializationException(
   ResourceConfigurationException.DIRECTORY_NOT_FOUND,
   new Object[] { PARAM_INPUTDIR, this.getMetaData().getName(), 
 directory.getPath() });
 How should we retrieve the component name?

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[jira] Closed: (UIMA-1731) ResourceInitializationExceptions thrown by a deployed aggregate are only partially logged

[
https://issues.apache.org/jira/browse/UIMA-1731?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Jerry Cwiklik closed UIMA-1731.
---

Resolution: Fixed
Assignee: Jerry Cwiklik

Modified UIMA AS code to log the entire stack trace when logging exceptions.
Also, added additional messages identifying service name in which an exception
occurs.

ResourceInitializationExceptions thrown by a deployed aggregate are only
partially logged
-

Key: UIMA-1731
URL: https://issues.apache.org/jira/browse/UIMA-1731
Project: UIMA
Issue Type: Bug
Components: Async Scaleout
Reporter: Burn Lewis
Assignee: Jerry Cwiklik
Priority: Minor
Fix For: 2.3AS

When the XcasCollectionReader fails to init because its input directory is
missing it reports the cause when run in core UIMA, i.e.
Caused by: org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class com.ibm.nlp.readers.XcasCollectionReader
failed. (Descriptor:
file:/.automount/hlthome01/a/hlthome01/homes/hlthome01.3/burn/workspace/factotem/desc/pipe/readers/XcasCollectionReader.xml)
Caused by: org.apache.uima.resource.ResourceInitializationException: Invalid
value for parameter InputDirectory in component null -- directory
xmidata does not exist.
but when deployed under UIMA-AS this detailed exception is missing ... all we
get is the higher-level cause, e.g.
1/30/10 10:56:15 PM - 3:
org.apache.uima.aae.controller.PrimitiveAnalysisEngineController_impl.initializeAnalysisEngine:
WARNING: org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class com.ibm.nlp.readers.XcasCollectionReader
failed. (Descriptor:
file:/u/burn/workspace/factotem/desc/pipe/readers/XcasCollectionReader.xml)
Also, the detailed message lists the component as null ... the collection
reader follows the example code and reports the error with:
throw new ResourceInitializationException(
ResourceConfigurationException.DIRECTORY_NOT_FOUND,
new Object[] { PARAM_INPUTDIR, this.getMetaData().getName(),
directory.getPath() });
How should we retrieve the component name?

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[jira] Closed: (UIMA-1728) UIMA AS Service logs falsely Stopping Collocated Delegate Cas Multiplier message


 [ 
https://issues.apache.org/jira/browse/UIMA-1728?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jerry Cwiklik closed UIMA-1728.
---

Resolution: Fixed
  Assignee: Jerry Cwiklik

Modified log message when sending a request to CM to stop producing CASes from 
an input CAS. Removed logging to stdout.

 UIMA AS Service logs falsely Stopping Collocated Delegate Cas Multiplier 
 message
 

 Key: UIMA-1728
 URL: https://issues.apache.org/jira/browse/UIMA-1728
 Project: UIMA
  Issue Type: Bug
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jörn Kottmann
Assignee: Jerry Cwiklik
Priority: Minor
 Attachments: test.zip


 The service has one CM which creates for every CAS one new CAS and a dummy AE 
 which throws an exception on every second CAS.
 It looks like that for each exception thrown from the AE.process method the 
 stopping collocated delegate CM message is printed
 and logged:
  Instance Hashcode:28681226 Controller:TestAAE Stopping Collocated 
  Delegate Cas Multiplier:TestCM
 and
 1/25/10 1:14:51 PM - 13: 
 org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.stopCasMultiplier:
  INFO: Controller: TestAAE Stopping Collocated Delegate Cas Multiplier: 
 TestAAE
 The problem might relate to the hang issue reported here:
 http://markmail.org/message/5dr5r3yyha4kbtlb

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[jira] Closed: (UIMA-1667) UIMA AS should also log the ActiveMQ version on startup


 [ 
https://issues.apache.org/jira/browse/UIMA-1667?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jerry Cwiklik closed UIMA-1667.
---

Resolution: Fixed
  Assignee: Jerry Cwiklik

The best thing I can log is the value of environment variable ACTIVEMQ_HOME. 
This is set in runUIMAClass scripts when launching a UIMA AS service. Below is 
an example of what is now logged upon UIMA AS service startup:
+--
   Starting UIMA AS Service - PID:6708
+--
+ Service Name:Room Number Annotator
+ Service Queue Name:RoomNumberAnnotatorQueue
+ Service Start Time:01 Feb 2010 15:06:37
+ UIMA AS Version:2.3.0
+ UIMA Core Version:2.3.0
b+ JMS Provider 
Home:c:\uima\releases\2.3.0\apache-uima\apache-activemq-4.1.1/b
+ OS Name:Windows XP
+ OS Version:5.1
+ OS Architecture:x86
+ OS CPU Count:2
+ JVM Vendor:Sun Microsystems Inc.
+ JVM Name:Java HotSpot(TM) Client VM
+ JMS Provider Home:c:\uima\releases\2.3.0-09\apache-uima\apache-activemq-4.1.1
+ JVM Version:1.6.0_02-b05
+ JVM Input Args:[-DVNS_HOST=localhost, -DVNS_PORT=9000, -Duima.home=c:\uima\rel


 UIMA AS should also log the ActiveMQ version on startup
 ---

 Key: UIMA-1667
 URL: https://issues.apache.org/jira/browse/UIMA-1667
 Project: UIMA
  Issue Type: Improvement
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jörn Kottmann
Assignee: Jerry Cwiklik
Priority: Trivial

 UIMA AS should also log the ActiveMQ version on startup.

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[jira] Reopened: (UIMA-1667) UIMA AS should also log the ActiveMQ version on startup


 [ 
https://issues.apache.org/jira/browse/UIMA-1667?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Jerry Cwiklik reopened UIMA-1667:
-


Reopening to remove redundant logging of JMS Provider Home Dir. Two of these 
are being logged. 

 UIMA AS should also log the ActiveMQ version on startup
 ---

 Key: UIMA-1667
 URL: https://issues.apache.org/jira/browse/UIMA-1667
 Project: UIMA
  Issue Type: Improvement
  Components: Async Scaleout
Affects Versions: 2.3AS
Reporter: Jörn Kottmann
Assignee: Jerry Cwiklik
Priority: Trivial

 UIMA AS should also log the ActiveMQ version on startup.

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[jira] Closed: (UIMA-1667) UIMA AS should also log the ActiveMQ version on startup