gmane.comp.apache.uima.general

Multiple References to an Array

John David Osborne (Campus — 2013-06-19T20:14:52

Does anybody know what the underlying reason that this WARNING is generated?

WARNING: Warning: multiple references to an array.  Reference identity will not be preserved in XMI.
6/19/13 2:22:12 PM - 11: org.apache.uima.cas.impl.XmiCasSerializer$XmiCasDocSerializer.reportWarning(211):

Specifically, how do I figure out which references to which array and why is this a problem? (I actually don't care about generating the XMI, but I think when I deploy an AS service it automatically tries to write and or instantiate some XMI).

 -John

UIMA-AS Broker Trouble - InvalidDestinationException

John David Osborne (Campus — 2013-06-19T20:11:20

Hello!

Has anybody out there had the UIMA version of ActiveMQ cause them any trouble? I'm running into some difficulty with stability and I am considering replacing the broker entirely (not really desirable) and running document collections the old fashioned (non-AS) way.

I can initialize and run the service but it will sporadically generate the type of error message shown below. I have been treating the whole AS component as a black box up to this point, so I don't have much insight into temporary queues. Based on a quick web search, it certainly isn't obvious to me what the problem is.

Stack trace is below in case anybody can help,

I am running UIMA-AS 2.4 java version which uses the 2.4.1 version of ActiveMQ. I'm using java 1.7.0_21 on CentOS 6.3 64b bit.

 -John


javax.jms.InvalidDestinationException: Cannot publish to a deleted Destination: temp-queue://ID:sakura-38798-1371245690142-0:1:1
        at org.apache.activemq.ActiveMQSession.send(ActiveMQSession.java:1696)
        at org.apache.activemq.A

AW: Processing a Text Collection more than once?

Oliver Ferschke — 2013-06-17T20:54:16

I can really recommend the DKPro Lab that Richard suggested!
--
-------------------------------------------------------------------
Oliver Ferschke, M.A.
Doctoral Researcher
Ubiquitous Knowledge Processing Lab (UKP-TU DA)
FB 20 Computer Science Department
Technische Universität Darmstadt
Hochschulstr. 10, D-64289 Darmstadt, Germany
phone [+49] (0)6151 16-6227, fax -5455, room S2/02/B111
ferschke-UK+NJqpvEemuRZdhCRBl6YQuADTiUCJX< at >public.gmane.org
www.ukp.tu-darmstadt.de
Web Research at TU Darmstadt (WeRC) www.werc.tu-darmstadt.de
-------------------------------------------------------------------

________________________________________
Von: Richard Eckart de Castilho [richard.eckart-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org]
Gesendet: Montag, 17. Juni 2013 21:36
An: user-HHKbSdsD6WQPKjDvHGQMeg< at >public.gmane.org
Betreff: Re: Processing a Text Collection more than once?

Hi Susanne,

there are two options in UIMA:

1) you write your own reader which repeatedly outputs the same data
2) you write a flow controller

Re: Java objectes living outside and inside of a pipeline

Richard Eckart de Castilho — 2013-06-19T12:07:27

UIMA doesn't like using objects in a pipeline that it did not
instantiate itself.

There are ways though, e.g. the uimaFIT 
SimpleNamedResourceManager described here

http://uimafit.googlecode.com/svn/tags/uimafit-parent-1.4.0/apidocs/org/uimafit/util/SimpleNamedResourceManager.html
http://markmail.org/message/qcnupdgabemyinec

Alternatively, you could use a static or ThreadLocal variable.

AW: UIMA 2.4.0 - AnnotationIndex.Subiterator

2013-06-19T11:08:41

Hello David,

that works perfectly well.

Thank you,
Armin  

-----Ursprüngliche Nachricht-----
Von: David Garcia Narbona [mailto:david.garcian-/6OuRI5q/5Wypjl6hRHSJR2eb7JE58TQ< at >public.gmane.org] 
Gesendet: Mittwoch, 19. Juni 2013 13:01
An: user-HHKbSdsD6WQPKjDvHGQMeg< at >public.gmane.org
Betreff: Re: UIMA 2.4.0 - AnnotationIndex.Subiterator

Sorry, I meant:

AnnotationIndex<AnnotationFS> indexB = cas.getAnnotatinIndex(typeB); ...

FSIterator<AnnotationFS> itB = indexB.subiterator(annotA);



David

El 19/06/2013 12:53, David Garcia Narbona escribió:

Re: UIMA 2.4.0 - AnnotationIndex.Subiterator

David Garcia Narbona — 2013-06-19T11:01:02

Sorry, I meant:

AnnotationIndex<AnnotationFS> indexB = cas.getAnnotatinIndex(typeB);
...

FSIterator<AnnotationFS> itB = indexB.subiterator(annotA);



David

El 19/06/2013 12:53, David Garcia Narbona escribió:

AW: uimafit - configuration parameter used twice

2013-06-19T10:59:54

Hi Richard,

I'm using uimafit's Resource_Impl, now. It is even easer to use than Initializable.

Thanks for all your fast help,
Armin

-----Ursprüngliche Nachricht-----
Von: Richard Eckart de Castilho [mailto:richard.eckart-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org] 
Gesendet: Freitag, 14. Juni 2013 09:40
An: user-HHKbSdsD6WQPKjDvHGQMeg< at >public.gmane.org
Betreff: Re: uimafit - configuration parameter used twice

Hi Armin,

the Initalizable-concept code relies on having unique parameter names across all involved components. For that reason, ClearTK uses fully qualified parameter names in the form "my.package.ClassName.parameter" (or similar). This code was developed when uimaFIT didn't have support for external resources yet.

Today, I would suggest to use external resources instead, which allow to scope the parameters directly to the resources [1].

We are starting to use external resources more today in DKPro Core, not only for accessing data, but for general implementations of a "strategy design pattern". S

Re: UIMA 2.4.0 - AnnotationIndex.Subiterator

David Garcia Narbona — 2013-06-19T10:53:44

Hi,

it should be:

FSIterator<AnnotationFS> itB = indexA.subiterator(annotB);


David

El 19/06/2013 12:47, Armin.Wegner-w0Tf80GBFXAb1SvskN2V4Q< at >public.gmane.org escribió:

Java objectes living outside and inside of a pipeline

2013-06-19T10:51:24

Hi,

I'd like to use java objectes in a pipeline which are constructed before the pipeline is run and which are still there, after the pipeline has finished its job. Is this even possible?

Cheers,
Armin

UIMA 2.4.0 - AnnotationIndex.Subiterator

2013-06-19T10:47:42

Hi,

Using this code

AnnotationIndex<AnnotationFS> indexA = cas.getAnnotatinIndex(typeA);
FSIterator<AnnotationFS> itA = indexA.iterator();

// outer loop
while (itA.hasNext()) {
        AnnotationFS annotA = itA.next();
        FSIterator<AnnotationFS> itB = indexA.subiterator(annotA);

        // inner loop
        while (itB.hasNext()) {
                AnnotationFS annotB = itB.next();
                // do something
        }
}

the inner loop is never run. There are annotations covered by annotA. Have I done something wrong?

Cheers,
Armin

Call for papers: 3rd UIMA< at >GSCL Workshop - 2013

Peter Klügl — 2013-06-19T07:39:49

====================================================


Second Call for Papers (Submission deadline: July, 12)
Workshop: Unstructured Information Management Architecture (UIMA)
3rd UIMA< at >GSCL Workshop


September 23, 2013
Darmstadt, Germany


Further Information:
http://bit.ly/123EYSv


====================================================


In recent years, the Unstructured Information Management Architecture
(UIMA) framework has been proposed as a middleware platform which offers
integration by design through common type systems and
standardized communication methods for components analysing streams
of unstructured information, such as natural language. The UIMA
framework offers a solid processing infrastructure that allows
developers to concentrate on the implementation of the actual
analytics components. An increasing number of members of the NLP
community thus have adopted UIMA as a platform facilitating the
creation of reusable NLP components that can be assembled to address
different NLP tasks depending

Re: Pythonnator Build Error

Bhavani Iyer — 2013-06-18T14:03:21

Hi
The pythonnator has been tested with Python 2.7 and swig 1.3.29.
You could either use these versions or try to fix the generated
uima_wrap.cxx to work with your versions.

Regards,
Bhavani


On Tue, Jun 11, 2013 at 2:28 PM, Bill Scuba <billscuba-PkbjNfxxIARBDgjK7y7TUQ< at >public.gmane.org> wrote:

AW: Processing a Text Collection Several Times?

Neumann, Susanne — 2013-06-18T09:12:34

Thanks for your immediate reply. I will have a look at the flow controller. It seems to be what I am looking for and I'll consider the other options as well. 
And sorry for double posting. I posted the question last week and thought that sending failed. 
________________________________________
Von: Marshall Schor [msa-DzKsKX1/Fv4AvxtiuMwx3w< at >public.gmane.org]
Gesendet: Montag, 17. Juni 2013 21:30
An: user-HHKbSdsD6WQPKjDvHGQMeg< at >public.gmane.org
Betreff: Re: Processing a Text Collection Several Times?

Hi,

Here are a couple of thoughts.

1) you can write a custom flow controller.  See
http://uima.apache.org/d/uimaj-2.4.0/tutorials_and_users_guides.html#ugr.tug.fc

This would allow you to redirect CASes back from the end of the pipeline into
the front (or anywhere else you wanted), any number of times.

There are example flow controller implementations in the examples directory of
the distribution ( in src/main/java/org/apache/uima/examples/flow )

2) you could split the application as follows:

  a) a plain

Re: Processing a Text Collection more than once?

Richard Eckart de Castilho — 2013-06-17T19:36:29

Hi Susanne,

there are two options in UIMA:

1) you write your own reader which repeatedly outputs the same data
2) you write a flow controller which saves all data produced by the reader and re-runs all components again on it

However, I'd recommend we check offline if/how DKPro Lab could fit in with your scenario. It may even just be the easiest to run your pipeline in a loop using uimaFIT and XMI/binary CAS serialization to feed in the output of one run into the next one.

Cheers,

Re: Processing a Text Collection Several Times?

Marshall Schor — 2013-06-17T19:30:33

Hi,

Here are a couple of thoughts.

1) you can write a custom flow controller.  See
http://uima.apache.org/d/uimaj-2.4.0/tutorials_and_users_guides.html#ugr.tug.fc

This would allow you to redirect CASes back from the end of the pipeline into
the front (or anywhere else you wanted), any number of times.

There are example flow controller implementations in the examples directory of
the distribution ( in src/main/java/org/apache/uima/examples/flow )

2) you could split the application as follows:

  a) a plain Java app which sets up the UIMA pipeline, and then creates & sends
CASes through the pipe line, as many times as you want.  Being that this is
plain old Java code, you can use any/ all of Java's capabilities to control this.

HTH -Marshall

On 6/17/2013 9:12 AM, Susanne Neumann wrote:

Processing a Text Collection Several Times?

Susanne Neumann — 2013-06-17T13:12:50

Hi,

I want to implement a bootstrapping algorithm using UIMA, which requires processing a whole text collection several times. With each iteration, new evidence based on the results of the previous runs on all the documents is collected and applied. The number of iterations is determined at runtime.

I planned to write a bootstrapping AE, but I can't figure out how to iteratively process the collection with UIMA, because the process method processes the text collection only once.

As a workaround, I am considering to add the annotator several times to the pipeline. However, it depends on the order in which the documents are processed withing the pipeline to work as desired. In which order are documents being processed in a pipeline? Does each component process the whole text collection first before going to the next component, or is every document of the collection being processed by each component first? In the latter case, the workaround would not work. Another solution is, to run a whole Pipeline contain

Processing a Text Collection more than once?

Susanne Neumann — 2013-06-13T15:32:54

Hi,

is there a (good) way in UIMA to process the whole text collection more than once? The process method processes each document once for the whole collection. But I need to iterate several times over the whole collection.

The background is, that I want to implement a bootstrapping annotator using UIMA. One of the main characteristics of bootstrapping is, that the corpus is processed several times, collecting new rules, terms and evidence each time, based on the results of the previous turns. I planned to write a bootstrapping AE, but I can't figure out how to iteratively process the collection.

I am looking for any hints or tips about how to implement this with UIMA.

Thanks,
Susanne

Re: Uimafit source browser

Richard Eckart de Castilho — 2013-06-17T13:51:00

Why is that a problem?
What did you expect?
What do you want to do?

Uimafit source browser

2013-06-17T13:46:27

Hi,

the uimafit source browser at code.google shows only HTML source code.

Cheers,
Armin

Re: uimafit - configuration parameter used twice

Richard Eckart de Castilho — 2013-06-14T07:40:08

Hi Armin,

the Initalizable-concept code relies on having unique parameter names across all involved components. For that reason, ClearTK uses fully qualified parameter names in the form "my.package.ClassName.parameter" (or similar). This code was developed when uimaFIT didn't have support for external resources yet.

Today, I would suggest to use external resources instead, which allow to scope the parameters directly to the resources [1].

We are starting to use external resources more today in DKPro Core, not only for accessing data, but for general implementations of a "strategy design pattern". So that's what I would recommend instead of Initializable.

Apparently, the way that uimaFIT now makes it natural to work with external resources for different purposes, has the potential to take the idea of external resources to a completely new level. There is still some way to go here, both in the UIMA core as well as in uimaFIT.

Cheers,

uimafit - configuration parameter used twice

2013-06-14T06:45:45

Hi,

the following code uses a file namer class of class org.uimafit.factory.initializable.Initializable to create a CAS consumer.

aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(Writer.class, Writer.PARAM_OUTPUT_DIRECTORY_PATH, "output", Writer.PARAM_FILE_NAMER_CLASS_NAME, FileNamer.class.getName()));

Writer.PARAM_OUTPUT_DIRECTORY_PATH equals "outputDirectoryPath". FileNamer has a configuration parameter of the same name. So both parameter values are set to "output". That is not what I intended. Only the parameter for Writer should be set. The parameter of FileNamer should stay the default.

What is the best practice to deal with this?

Cheers,
Armin