Re: ConcurrentModificationException with CasDumpWriter

[Gary Underwood]

You might want to consider using UIMA 3.0.0-alpha02 that fixes that error. My 
understanding is the issue existed previously, but no exception was thrown when 
it happened. I think it started getting thrown around 2.7

Gary Underwood
gunderw...@clinacuity.com



> On Jun 30, 2017, at 11:17 AM, Kaeshammer, Miriam  
> wrote:
> 
> Hi,
> 
> I get a java.util.ConcurrentModificationException (see below) when using the 
> CasDumpWriter in the following way:
> 
> import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine;
> import org.apache.uima.UIMAException;
> import org.apache.uima.analysis_engine.AnalysisEngine;
> import org.apache.uima.fit.component.CasDumpWriter;
> import org.apache.uima.fit.factory.JCasFactory;
> import org.apache.uima.jcas.JCas;
> import org.junit.Test;
> 
> public class CasDumpWriterTest {
> 
>@Test
>public final void testDump() throws UIMAException {
> 
>// Set up the CAS
>JCas jcas = JCasFactory.createJCas();
>JCas view = jcas.createView("testview");
>view.setDocumentText("test");
> 
>AnalysisEngine dump = createEngine(CasDumpWriter.class, //
>CasDumpWriter.PARAM_OUTPUT_FILE, "target/cas-dump.txt");
> 
>dump.process(jcas);
> 
>}
> }
> 
> Is there anything I am doing wrong? How can I use the CasDumpWriter without 
> causing this exception? I am using UIMA 2.9.0 and uimafit 2.2.0, but the same 
> also happens with 2.3.0. This definitely worked with earlier version of UIMA.
> 
> If this is not the write channel to ask this question, please let me know.
> 
> Thank you!
> Best regards, Miriam
> 
> 
> Output:
> 
> Jun 30, 2017 5:12:31 PM 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl 
> callAnalysisComponentProcess(430)
> SEVERE: Exception occurred
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator 
> processing failed.
>at 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:412)
>at 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
>at 
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
>at 
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:284)
>at 
> com.sap.gs.hlt.mt.pipelines.de.nmt.CasDumpWriterTest.testDump(CasDumpWriterTest.java:25)
>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>at java.lang.reflect.Method.invoke(Method.java:497)
>at 
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
>at 
> org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
>at 
> org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
>at 
> org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
>at 
> org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
>at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
>at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
>at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
>at 
> org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
>at 
> org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
>at 
> org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
>at 
> org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
>at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
>at 
> org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:50)
>at 
> org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:459)
>at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:675)
>at 
> org.eclipse.

Re: What is the status of the CVD viewer?

[Gary Underwood]

I use the free ETUDE-viewer (https://github.com/Clinacuity/etude-viewer 
<https://github.com/Clinacuity/etude-viewer>) for viewing documents. I’m biased 
as it was developed by the company I work for. It is primarily for comparison 
between system and reference documents, but it can also be used as a viewer by 
loading the same document as both.
Gary Underwood
gunderw...@clinacuity.com



> On May 1, 2019, at 6:29 AM, Rune Stilling  wrote:
> 
> Hi
> 
> I just got the CAS Editor up and running. It seems that this tool is more 
> actively being developed. Is that so?
> 
> /Rune
> 
>> Den 8. okt. 2018 kl. 17.48 skrev Marshall Schor :
>> 
>> One alternative that may be useful is the DocumentAnalyzer. 
>> https://uima.apache.org/d/uimaj-current/tools.html#ugr.tools.doc_analyzer
>> 
>> Patches welcome :-)
>> 
>> -Marshall
>> 
>> On 10/8/2018 11:27 AM, Rune Stilling wrote:
>>> Hi list
>>> 
>>> We are using the CVD-viewer to view rather complex annotation document but 
>>> have stumbled upon some problems.
>>> 
>>> First of all scrolling in the bottom left annotation pane is possible on a 
>>> Mac. The scroll bar simply never shows up and moving the cursor downwards 
>>> doesn’t move the contents. This makes the viewer very limited in use.
>>> 
>>> Secondly I really miss a search function in the text view especially, so 
>>> that it would be possible to look up specific words. 
>>> 
>>> Is the tool still actively being developed at all? Aren’t people using it, 
>>> and if not, then how do they analyze their results? Just by looking the 
>>> cas.xmi file or?
>>> 
>>> Best,
>>> Rune
> 

Re: Visualize analysis results in web demo

[Gary Underwood]

My company developed an open source viewer and evaluator: 
https://github.com/Clinacuity/etude-viewer
It handles WebAnno and UIMA Xml files (others too I think and more coming). 
With configuration files it will score them (true/false positives and 
negatives, recall, precision F1, etc.). You can then view the results with 
TP/FP/FN highlighted in reference and system documents with annotations 
highlighted by types. It can compare based on type of annotation and features 
within it (I think only boolean for now, still being developed). If you aren’t 
comparing to a reference standard you can compare it with itself to just view 
annotations.
Gary Undrewood
gunderw...@clinacuity.com

> On Jun 18, 2019, at 9:49 AM, Kameron Cole  wrote:
> 
> There are the UIMA tools - like the CPE - which let you see the annotations 
> visually.
> 
> Then, if you have access, you can use IBM Watson Explorer, Analytical 
> Components
> 
> https://www-01.ibm.com/support/docview.wss?uid=ibm10732169 
>  
> 
> 
> 
> Regards,
> Kameron Cole
> Watson Explorer Support
> Analytical Components
> IBM Watson and Cloud Platform
> 
> 
> Phone: 1-305-389-8512 | Fax: 1-845-491-4052
> E-mail: kameronc...@us.ibm.com 
> Find me on:      
>  and within IBM on:   
>    
>   
>  
> 
> 1751 SW 11th Terrace
> Miami, FL 33135
> United States
> 
> 
> 
> "Zesch, Torsten" ---06/17/2019 01:17:38 PM---Hi, I want to visualize the 
> results of an analysis in a web application.
> 
> From: "Zesch, Torsten" 
> To: "user@uima.apache.org" 
> Date: 06/17/2019 01:17 PM
> Subject: [EXTERNAL] Visualize analysis results in web demo
> 
> 
> 
> 
> Hi,
> 
> I want to visualize the results of an analysis in a web application.
> (input document, press button, certain types of results are shown and 
> highlighted in the text)
> 
> Is there something available that I could use as a starting point?
> 
> Thanks,
> Torsten
> 
> 
> 
> 

Deserialization of Annotation containing Map

[gary underwood]

Hello all,
I have made a subclass of Annotation that contains a user defined Map object of 
String to Boolean. The class implements UimaSerializable.

It overrides _save_to_cas_data() which is called by XmiCasSerializer.serialize. 
It follows documentation from user guides for storing the keys and values of 
the Map as StringArray and BooleanArray respectively.  Stepping through the 
code it does run and the resulting xml file has the proper data in it from the 
map.

It also overrides _init_from_cas_data(). However, stepping through the code 
when usingXmiCasSerializer.deserialize, the method is never called and 
deserialization doesn’t work.

I do not know why _init_from_cas_data() is not called or how to make it get 
called during deserialization.

Thanks,
Gary
Clinacuity, Inc.

Re: Changes to CPE <-> UIMA Versioning

[Gary Underwood]

I would consider this a minor change as well.
Gary Underwood

> On Jan 21, 2022, at 4:20 PM, Zesch, Torsten  wrote:
> 
> 
> 
>2) Would anybody like to express their opinion on UIMA versioning?
> 
> TZ: I would consider this a minor change so we could stay on UIMA v3.
> 
> -Torsten
>