Petr Baudis | 23 May 00:21 2015
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CasCopier breakages in uimaj-2.7.0

  Hi!

  I'm trying to bring uimaj-2.7.0 to my code, but I'm hitting some
trouble with my CasCopier code:

  * alreadyCopied(FeatureStructure fs) is gone without an obvious
    replacement; it seems to me that

	alreadyCopied(((FeatureStructureImpl) fs).getAddress())

    is the correct replacement after digging somewhat at CasCopier
    source code, but is that even really right?  I guess this
    is a bug as that interface was public...

  * Even with the fix above, my code, e.g.

	https://github.com/brmson/yodaqa/blob/master/src/main/java/cz/brmlab/yodaqa/analysis/passextract/PassFilter.java#L67

crashes with

	Caused by: java.util.ConcurrentModificationException
		at org.apache.uima.cas.impl.FSIndexRepositoryImpl$LeafPointerIterator.checkConcurrentModification(FSIndexRepositoryImpl.java:967)
		at org.apache.uima.cas.impl.FSIndexRepositoryImpl$LeafPointerIterator.ll_get(FSIndexRepositoryImpl.java:1002)
		at org.apache.uima.cas.impl.FSIndexRepositoryImpl$LeafPointerIterator.get(FSIndexRepositoryImpl.java:995)
		at org.apache.uima.cas.impl.FSIteratorWrapper.get(FSIteratorWrapper.java:53)
		at org.apache.uima.cas.impl.FSIteratorImplBase.next(FSIteratorImplBase.java:67)
		at org.apache.uima.cas.impl.FSIteratorImplBase.next(FSIteratorImplBase.java:33)
		at cz.brmlab.yodaqa.analysis.passextract.PassFilter.process(PassFilter.java:74)
		at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
		at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:385)
(Continue reading)

Mario Gazzo | 22 May 16:59 2015
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Injecting nested resources using UIMA fit

I have some trouble with initialising some nested resource with UIMA fit. I have followed the approach
described in the section “Resources implementing SharedResourceObject”. I just have a resource B
that uses resource A and a collection reader and a flow control that use both A and B but I get "mandatory
resource A not set on resource B” illegal state exception. I use the  <at> ExternalResource annotations to
get them injected and I used ExternalResourceFactory.bindExternalResource with A and B on the
collection reader and flow control descriptions when creating my aggregate. It works if B is not
dependent on A but as soon I add the dependency then it breaks. I also tried to explicitly use
ExternalResourceFactory.bindExternalResource on A to B but that caused null pointer exception in
ExternalResourceFactory when trying to bind to the collection reader right after.

I would appreciate any ideas about what I might be doing wrong.

Cheers
Mario
Lothar Diefenbaker | 22 May 15:36 2015
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Problem with Eclipse and UIMA

Hello Everyone,

 I recently become involved in a project with Apache UIMA. As I was totally
unfamiliar with it as I was to eclipse, so I started reading the
documentation from the very beginning and I try to follow the tutorials.
But a problem came up when I tried to configure Eclipse to work with UIMA.
I installed the UIMA plugins for eclipse from
http://www.apache.org/dist/uima/eclipse-update-site, I followed all the
steps in order to set it up, I added my UIMA_HOME to the Java Build Path in
Eclipse. I imported the uimaj-examples but I cannot run them, when I tried
to run any of the tools I get the Error: Could not find or load main class
org.apache.uima.tools.AnnotationViewerMain (for example this happens when I
tried to run the Annotation Viewer). I know this seems to be a path
problem, so I checked the build path of the project and it does includes
everything in my installation of UIMA, the lib is there with the jar of the
tools. My environment variables of %UIMA_HOME%, %JAVA_HOME% exist and they
hold as value the path of UIMA and JAVA respectively. I also included the
lib directory of uima to the %CLASSPATH%, and the bin and lib directories
of the uima to the %PATH%.

 I tried to make the tutorial of “My first Annotator”, I created the
project RoomNumberAnnotator and followed the tutorial step by step. But at
the end when I tried to test it with the UIMA CAS Visual Debugger again I
only got Error: Could not find or load main class
org.apache.uima.tools.cvd.CVD since I cannot run the SDK tools from
eclipse. I ran from the CVD from the console and it worked, and I loaded
the analysis engine of RoomNumberAnnotator and it worked. Nevertheless I
still cannot make it work from eclipse.

 I looked for information about this and I didn't find much, which makes me
(Continue reading)

William Colen | 20 May 21:45 2015
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Error using RUTA from Java

Hello,

We have a Main RUTA script that imports a few children scripts, as follows:

PACKAGE cogroo.ruta;
> TYPESYSTEM BaseTypeSystem;
> IMPORT opennlp.uima.Token FROM TypeSystem AS cgToken;
> IMPORT opennlp.uima.Sentence FROM TypeSystem AS cgSentence;
> SCRIPT Crase;
> SCRIPT Base;
> Document{-> CALL(Base)};
> Document{-> CALL(Crase)};

All the scripts are in the root of the classpath.

We are trying to call it from Java, using the following code:

TypeSystemDescription tsd =
> TypeSystemDescriptionFactory.createTypeSystemDescription("MainTypeSystem"
> );
> URL url = Resources.getResource("Main.ruta");
> String scriptText = Resources.toString(url, Charsets.UTF_8);
> AnalysisEngineDescription aeDes =
> Ruta.createAnalysisEngineDescription(scriptText, tsd);
> AnalysisEngine ae = UIMAFramework.produceAnalysisEngine(aeDes);

 The error we are getting:

org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator
> processing failed.
(Continue reading)

Petr Baudis | 20 May 03:27 2015
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Multi-threaded UIMA ParallelStep

  Hi!

  I'm looking into ways to run a part of my pipeline multi-threaded:

                .-> Multip0 -> A1 -> Multip1 -> A2 ->.
  reader -> A0 <                                      > CASmerger
                `-> Multip2 -> A3 ------------> A2 ->'
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                ParallelStep is generated for each branch
		in a custom flow controller

Basically, I need a way to tell UIMA to run each ParallelStep (which
normally just denotes the CAS flow) truly in parallel.  I have two
constraints:

  (i) I'm using UIMAfit heavily, and multiple CAS multipliers and
mergers (even within the parallel branches).  So I can't use CPE.

  (ii) I need multi-threading, not separate processes.  (I have just
a meager 24G RAM (sigh) and one Java process with all the linguistic
models and stuff loaded takes 3GB RAM.  So I really need to load these
resources to memory only once.)

  I looked into UIMA-AS, including Richard's helpful DKpro-lab code
sample, but I can't figure out how to make it reasonably work with
a *complex* UIMAfit pipeline that spans many branches and many
analysis engines - it seems to me that I would need some centralized
places where to specify it, and basically completely rewrite my pipeline
building code (to the worse, in my impression).

(Continue reading)

Satya Nand Kanodia | 18 May 08:39 2015

DUCC Services keep stopping

Hi,

I am using DUCC service with UIMA-AS client to process Documents. I am 
facing one problem. DUCC service , I am using, keeps  stopping itself.  
I get one message "stopped+alert". I have enabled autostart in service 
configuration but it doesn't auto start.

I am unable to find the reason of it. Can you tell me where to start 
looking for it and how to make sure it stays alive every time.

--

-- 
Thanks and Regards,
Satya Nand Kanodia

Diego Buoro | 15 May 20:53 2015
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Accessing a string array child tag in UIMA-RUTA

Hello, guys!
How is everyone doing? Hope everything is fine.

I have just posted in stackoverflow this question <
http://stackoverflow.com/questions/30266328/how-to-access-a-string-array-child-tag-in-uima-ruta>.
I am having trouble to access a string array child tag using the UIMA-RUTA
technology. Please, can someone have a quick look at my problem?

Thanks in advance!
Armando Stellato | 14 May 12:02 2015
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ANN: CODA 1.1.2 released

Dear all,

*** apologies for cross-posting ***

A new release of CODA is out there!

CODA 1.1.2 jar bundles are available on Maven and a running demo can be
downloaded by following instructions at:

 <http://art.uniroma2.it/coda/downloads>
http://art.uniroma2.it/coda/downloads 

----

For those new to CODA.

CODA (Computer-aided Ontology Development Architecture) is an architecture
and an associated Java framework for the RDF <http://www.w3.org/RDF/>
triplification of UIMA <http://uima.apache.org/>  results from analysis of
unstructured content.

The purpose of CODA is to support the entire process embracing data
extraction and transformation, identity resolution up to feeding semantic
repositories with knowledge extracted from unstructured content. The
motivation behind CODA lies in the large effort and design issues required
for developing RDF compliant knowledge acquisition systems on top of
well-established content analytics frameworks such as UIMA
<http://uima.apache.org/>  and GATE <https://gate.ac.uk/> . Therefore, CODA
extends UIMA with facilities and a powerful language - PEARL
<http://art.uniroma2.it/coda/documentation/pearl.jsf>  - for projection and
(Continue reading)

Satya Nand Kanodia | 14 May 06:46 2015

DUCC_MON Authentication

Hi,

While  installing DUCC cluster on two machines I purposefully installed 
duccling  in the shared directory to see what happens.
Everything worked fine. Even the test job successfully executed. problem 
came when I tried to login DUCC-MON, I could not login. It says "failure 
code:-1, reason:pam_authenticate failed : Authentication failure".  I 
would like to mention that while creating user ducc I created it without 
password and and after installing DUCC I gave it password. I am able to 
ssh on this user with updated password from other system.

But I am unable to login in DUCC-MON with this password . I am able to 
login in DUCC-MON with another user that was created a long before DUCC 
installation but when I hover mouse pointer to terminate button it says 
you have to be administrator to terminate it(that's okay).

After that I created another user for testing , executed 
ducc_post_install, start_ducc. Now when I tried to login with new user 
It didn't let me log in. It says " failure code:-1, 
reason:pam_authenticate failed : Authentication failure"

I want to know Why It didn't work. How does ducc_ling work. what happend 
when some one installs ducc_ling in shared directory(I thought it would 
be cool as I had to install it once, I know there is one line in 
DUCC_DOCUMENTATION that says never do it) and the last How does DUCC_ 
MON authentication work.

--

-- 
Thanks and Regards,
Satya Nand Kanodia
(Continue reading)

Sylvain Surcin | 30 Apr 17:40 2015

UIMAFit and UIMA-AS deployment

Hello,

I'm trying to see if I can adapt our UIMA-AS architecture to UIMAFit.

And I'm wondering how to actually do it from the main level where I have a
class

UimaAsynchronousEngine myEngine = new BaseUIMAAsynchronousEngine_impl();
myEngine.addStatusCallbackListener(myListener);
myEngine.deploy(myAsDeploymentDescriptorFile, applicationContext);

The AS deployment descriptor file has a section
<topDescriptor>
  <import location="./MyAggregateChain.xml"/>
</topDescriptor>

Now, if I want to be smart and use UIMAFit's AggregateBuilder, how do I
reconciliate that with the deployment descriptor file?

Is there a way to do that entirely from within the Java code?
Or do I have to use UIMAFit to generate the aggregate descriptor file from
the AnalysisEngine built by the AggregateBuilder?

Thanks for your help,

[+] Add me to your address book
<https://ws.writethat.name/kwaga-bin/titan/WEB/me.pl/5075409511380703595/i>

Sylvain SURCIN, Ph.D.
*KWAGA*
(Continue reading)

Renaud Richardet | 28 Apr 16:36 2015
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Ruta syntax simplifications?

Hello,

I have been using Ruta a lot lately, and it has made me much more
productive. Thanks to all the people that contributed to it!

I have been thinking about two small syntax simplifications and was
wondering if they would make sense:

A) Types declarations (2.5.1)

// Types with features may add a parent type in their declarations.

// *If no parent type is specified, Annotation is used as the implied
default parent type. *

// before

DECLARE Annotation MyAnnotation(STRING myFeature);

// after

DECLARE MyAnnotation(STRING myFeature);

B) Matching condition

// The matching condition of the rule element refers to the complete
document,

// or more specific to the annotation of the type “DocumentAnnotation”,
which covers the whole document.
(Continue reading)


Gmane