date:20151119

RE: TermConsumers

2015-11-19 Thread Finan, Sean

Holy cattle, it worked ?!?

I don't know of a specific xcas reader offhand ... have you tried running with 
the xmi reader?  Some of the reads laying around will handle both.

-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu] 
Sent: Thursday, November 19, 2015 6:48 PM
To: dev@ctakes.apache.org
Subject: RE: TermConsumers

Sean,

I tested this, the Annotator itself works, great. The only change I had to do 
when writing the Annotator class with the code below is to provide generics in:

static private final Collection 
EVENT_CLASSES = Arrays.asList(
MedicationMention.class, DiseaseDisorderMention.class,
SignSymptomMention.class, LabMention.class, ProcedureMention.class 
);

At least on a small example XMI CAS I see the behavior is as expected for the 
IdentifiedAnnotations.

However, for my usecase, I have XCAS files, not XMI CAS files. I can use 
XCasWriterCasConsumer to write the CAS files, but I cannot find any XCAS 
Collection Reader to initially read them in. 

Is such a reader available?

Regards,
Tomasz



From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Thursday, November 19, 2015 4:03 PM
To: dev@ctakes.apache.org
Subject: RE: TermConsumers

Hi Tomasz,

I don't know that anybody has done this.  However, you could try running a 
pipeline with items in ctakes-core:
XmiCollectionReaderCtakes   to read your existing cas xmi files in directory
-- custom refiner AE below --   to remove unwanted umls annotations
XmiWriterCasConsumerCtakes  to write the new cas xmi files


The refiner AE would basically do what the PrecisionTermConsumer of the fast 
lookup does, but over a pre-populated cas.  This is mostly cut and paste from 
other code with a little bit of lookompiling  - I haven't tested it at all!  If 
you do give it a run-through and it works then let me know and I'll clean it up 
and check into sandbox.


static private final Collection 
EVENT_CLASSES = Arrays.asList(
 MedicationMention.class, DiseaseDisorderMention.class,
 SignSymptomMention.class, LabMention.class, ProcedureMention.class );
   // Don't forget AnatomicalSiteMention.class and generic EntityMention.class!

static private final Function createTextSpan
 = annotation -> new DefaultTextSpan( annotation.getBegin(), 
annotation.getEnd() );

static private final Function 
returnSelf = annotation -> annotation;

   @Override
   public void process( final JCas jcas ) throws AnalysisEngineProcessException 
{
  LOGGER.info( "Starting processing" );
  for ( Class eventClass : EVENT_CLASSES ) {
 refineForClass( jcas, eventClass );
  }
  final Collection anatomicals = JCasUtil.select( 
jcas, AnatomicalSiteMention.class );
  final Collection entityMentions = new ArrayList<>( 
JCasUtil.select( jcas, EntityMention.class ) );
  entityMentions.removeAll( anatomicals );
  refineForAnnotations( jcas, anatomicals );
  refineForAnnotations( jcas, entityMentions );
  LOGGER.info( "Finished processing" );
   }

   static private  void refineForClass( final 
JCas jcas,
final 
Class eventClass ) {
  refineForAnnotations( jcas, JCasUtil.select( jcas, eventClass ) );
   }

   static private  void refineForAnnotations( 
final JCas jcas,
  
final Collection annotations ) {
  final Map annotationTextSpans
= annotations.stream().collect( Collectors.toMap( createTextSpan, 
returnSelf ) );
  final Collection unwantedSpans = getUnwantedSpans( 
annotationTextSpans.keySet() );
  unwantedSpans.stream().map( annotationTextSpans::get ).forEach( t -> 
t.removeFromIndexes( jcas ) );
   }

   static private Collection getUnwantedSpans( final 
Collection originalTextSpans ) {
  final List textSpans = new ArrayList<>( originalTextSpans );
  final Collection discardSpans = new HashSet<>();
  final int count = textSpans.size();
  for ( int i = 0; i < count; i++ ) {
 final TextSpan spanKeyI = textSpans.get( i );
 for ( int j = i + 1; j < count; j++ ) {
final TextSpan spanKeyJ = textSpans.get( j );
if ( (spanKeyJ.getBegin() <= spanKeyI.getBegin() && 
spanKeyJ.getEnd() > spanKeyI.getEnd())
 || (spanKeyJ.getBegin() < spanKeyI.getBegin() && 
spanKeyJ.getEnd() >= spanKeyI.getEnd()) ) {
   // J contains I, discard less precise concepts for span I and 
move on to next span I
   discardSpans.add( spanKeyI );
   break;
}
if ( ((spanKeyI.getBegin() <= spanKeyJ.getBegin() && 
spanKeyI.getEnd() > spanKeyJ.getEnd())
  || (spanKeyI.getBegin() < spanKeyJ.getBegin() && 
spanKeyI.getEnd() >=

RE: TermConsumers

2015-11-19 Thread Tomasz Oliwa

Sean,

I tested this, the Annotator itself works, great. The only change I had to do 
when writing the Annotator class with the code below is to provide generics in:

static private final Collection 
EVENT_CLASSES = Arrays.asList(
MedicationMention.class, DiseaseDisorderMention.class,
SignSymptomMention.class, LabMention.class, ProcedureMention.class 
);

At least on a small example XMI CAS I see the behavior is as expected for the 
IdentifiedAnnotations.

However, for my usecase, I have XCAS files, not XMI CAS files. I can use 
XCasWriterCasConsumer to write the CAS files, but I cannot find any XCAS 
Collection Reader to initially read them in. 

Is such a reader available?

Regards,
Tomasz



From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Thursday, November 19, 2015 4:03 PM
To: dev@ctakes.apache.org
Subject: RE: TermConsumers

Hi Tomasz,

I don't know that anybody has done this.  However, you could try running a 
pipeline with items in ctakes-core:
XmiCollectionReaderCtakes   to read your existing cas xmi files in directory
-- custom refiner AE below --   to remove unwanted umls annotations
XmiWriterCasConsumerCtakes  to write the new cas xmi files


The refiner AE would basically do what the PrecisionTermConsumer of the fast 
lookup does, but over a pre-populated cas.  This is mostly cut and paste from 
other code with a little bit of lookompiling  - I haven't tested it at all!  If 
you do give it a run-through and it works then let me know and I'll clean it up 
and check into sandbox.


static private final Collection 
EVENT_CLASSES = Arrays.asList(
 MedicationMention.class, DiseaseDisorderMention.class,
 SignSymptomMention.class, LabMention.class, ProcedureMention.class );
   // Don't forget AnatomicalSiteMention.class and generic EntityMention.class!

static private final Function createTextSpan
 = annotation -> new DefaultTextSpan( annotation.getBegin(), 
annotation.getEnd() );

static private final Function 
returnSelf = annotation -> annotation;

   @Override
   public void process( final JCas jcas ) throws AnalysisEngineProcessException 
{
  LOGGER.info( "Starting processing" );
  for ( Class eventClass : EVENT_CLASSES ) {
 refineForClass( jcas, eventClass );
  }
  final Collection anatomicals = JCasUtil.select( 
jcas, AnatomicalSiteMention.class );
  final Collection entityMentions = new ArrayList<>( 
JCasUtil.select( jcas, EntityMention.class ) );
  entityMentions.removeAll( anatomicals );
  refineForAnnotations( jcas, anatomicals );
  refineForAnnotations( jcas, entityMentions );
  LOGGER.info( "Finished processing" );
   }

   static private  void refineForClass( final 
JCas jcas,
final 
Class eventClass ) {
  refineForAnnotations( jcas, JCasUtil.select( jcas, eventClass ) );
   }

   static private  void refineForAnnotations( 
final JCas jcas,
  
final Collection annotations ) {
  final Map annotationTextSpans
= annotations.stream().collect( Collectors.toMap( createTextSpan, 
returnSelf ) );
  final Collection unwantedSpans = getUnwantedSpans( 
annotationTextSpans.keySet() );
  unwantedSpans.stream().map( annotationTextSpans::get ).forEach( t -> 
t.removeFromIndexes( jcas ) );
   }

   static private Collection getUnwantedSpans( final 
Collection originalTextSpans ) {
  final List textSpans = new ArrayList<>( originalTextSpans );
  final Collection discardSpans = new HashSet<>();
  final int count = textSpans.size();
  for ( int i = 0; i < count; i++ ) {
 final TextSpan spanKeyI = textSpans.get( i );
 for ( int j = i + 1; j < count; j++ ) {
final TextSpan spanKeyJ = textSpans.get( j );
if ( (spanKeyJ.getBegin() <= spanKeyI.getBegin() && 
spanKeyJ.getEnd() > spanKeyI.getEnd())
 || (spanKeyJ.getBegin() < spanKeyI.getBegin() && 
spanKeyJ.getEnd() >= spanKeyI.getEnd()) ) {
   // J contains I, discard less precise concepts for span I and 
move on to next span I
   discardSpans.add( spanKeyI );
   break;
}
if ( ((spanKeyI.getBegin() <= spanKeyJ.getBegin() && 
spanKeyI.getEnd() > spanKeyJ.getEnd())
  || (spanKeyI.getBegin() < spanKeyJ.getBegin() && 
spanKeyI.getEnd() >= spanKeyJ.getEnd())) ) {
   // I contains J, discard less precise concepts for span J and 
move on to next span J
   discardSpans.add( spanKeyJ );
}
 }
  }
  return discardSpans;
   }


Good luck,
Sean


-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Thursday, November

Re: AggregatePlaintextFastUMLSProcessor.xml will not load

2015-11-19 Thread Arron Lacey

Hi Sean - I can't remember doing so, so that's probably the issue. Would 
you be able to provide to sourceforge url?


Thanks for the quick reply by the way!

Arron.

*Arron Lacey
**Research Data Analyst/Research Assistant |
Dadansoddwr Data Ymchwil/Cynorthwyydd Ymchwil
*__


Data Science Building (Third Floor) | Yr Adeilad Gwyddor Data (Trydydd 
Llawr)


Swansea University Medical School | Ysgol Feddygaeth Prifysgol Abertawe

Singleton Park | Parc Singleton

SWANSEA SA2 8PP | ABERTAWE SA2 8PP

Wales, United Kingdom | Cymru, Y Deyrnas Unedig


*Phone | Ffôn*+44 (0) 1792 60 2023
*Email | Ebost*a.s.la...@swansea.ac.uk 

*www.farrinstitute.org 
*

*The University welcomes correspondence in Welsh and English | Mae'r 
Brifysgol yn croesawu gohebiaeth yn Gymraeg ac yn Saesneg.

*
Please don't print this e-mail unless you really need to. | Peidiwch ag 
argraffu'r e-bost hwn oni bai fod gwir angen gwneud hynny.


The contents of this email are confidential and for the intended 
recipient only. If you have received this
message in error, please inform the sender and delete the message. | Mae 
cynnwys yr ebost hwn yn gyfrinachol a dim ond y derbynnydd a fwriadwyd a 
ddylai ei ddarllen. Os derbynioch y neges mewn camgymeriad, rhowch wybod 
i'r anfonydd a dilëwch y neges.


Swansea University is a registered charity. No. 1138342 | Mae Prifysgol 
Abertawe yn elusen gofrestredig. Rhif. 1138342



On 19/11/15 22:08, Finan, Sean wrote:

Dictionary UmlsHsqlRareWord

AggregatePlaintextFastUMLSProcessor.xml will not load

2015-11-19 Thread Arron Lacey

Hi - I am trying to load AE "AggregatePlaintextFastUMLSProcessor.xml" 
but it will not load. Here I include my log file, bash output and 
runctakesCVD.sh. I am using version 3.2.2 (downloaded and installed today)


Any help would be appreciated thanks.

*** LOG FILE ***

19/11/15 21:46:37 - 13: 
org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: 
Initialization of annotator class 
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" 
failed.  (Descriptor: 
file:/home/arron/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization 
of annotator class 
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" 
failed.  (Descriptor: 
file:/home/arron/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)

at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at 
org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at 
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at 
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at 
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
at 
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at 
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at 
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at 
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)

at java.awt.Component.processMouseEvent(Component.java:6525)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6290)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatchEventImpl(Component.java:4881)
at java.awt.Container.dispatchEventImpl(Container.java:2292)
at java.awt.Component.dispatchEvent(Component.java:4703)
at 
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
at 
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
at java.awt.Container.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.java:2739)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746)
at java.awt.EventQueue.access$400(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:697)
at java.awt.EventQueue$3.run(EventQueue.java:691)
at java.security.AccessController.doPrivileged(Native Method)
at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)

at java.awt.EventQueue$4.run(EventQueue.java:719)
at java.awt.EventQueue$4.run(EventQueue.java:717)
at java.security.AccessController.doPrivileged(Native Method)
at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:716)
at

RE: Create next cTAKES release (3.2.3)?

2015-11-19 Thread Finan, Sean

Hi Pei, thanks for the link to our Jira dashboard.  From my 3 second 
run-through I would say that there remains a lot of outstanding work slated for 
the 3.2.3 release.  Below are the Blocker, Critical and Major items.  Some may 
actually have been or can be quickly resolved, but it looks like we may have 
more than a few bumps to 3.2.4 if we want to push out a release. 

I say in my bazaar way: release early, release often ... 
+1 for bumps and release ... *but first some comments in Jira on the state of 
all listed below...

Can anybody confirm that our only Blocker (dependencies not in maven central) 
is still a problem?  https://issues.apache.org/jira/browse/CTAKES-76  
Where do we stand on the related Critical 
https://issues.apache.org/jira/browse/CTAKES-138 ?

Our other Critical item is PTB tokenizer breaking on apostrophes: 
https://issues.apache.org/jira/browse/CTAKES-74

A Major bug is FractionFSM incorrectly handling dashed ranges: 
https://issues.apache.org/jira/browse/CTAKES-341  Britt, it looks like you 
might have a fix ready?

Another Major bug is for ytex UMLS.hbm.template.xml ... 
https://issues.apache.org/jira/browse/CTAKES-302 Vijay it looks like you have a 
fix started?

Major bug for Missing Modifiers 
https://issues.apache.org/jira/browse/CTAKES-213 ... Steve indicates that this 
will require a lot of work.  Should we bump it or has somebody been making 
progress?

A Major bug in Medication Strength parsing has sat since our original 
incubation, so I'm just guessing that it hasn't been touched and will be 
bumped.  https://issues.apache.org/jira/browse/CTAKES-178

Major bug SimpleSegmentWithTags ... 5 char names ... has also been around 
single the continents were formed.
https://issues.apache.org/jira/browse/CTAKES-155  I'd say a bump seems ok 
except that there is an NPE ...

There is a patch posted for our good old blues brothers boys band "URI not 
hierarchical" on the old dictionary lookup 
https://issues.apache.org/jira/browse/CTAKES-388  Can anybody volunteer to test 
and commit?  I think that this is basically the same problem relayed in 
https://issues.apache.org/jira/browse/CTAKES-320
 

We have two placeholders for 3.2.3 additions.  They should probably be added 
and (widely) tested asap or bumped to the next release.
New Sentence Detector https://issues.apache.org/jira/browse/CTAKES-380
ISO Time Normalizer https://issues.apache.org/jira/browse/CTAKES-379

Has anybody started to tackle clean up / ?removal? of xml descriptors?  Tagged 
as Major improvement.  https://issues.apache.org/jira/browse/CTAKES-328
This is related to https://issues.apache.org/jira/browse/CTAKES-295 - for which 
Tim Miller has done a lot of great work, but is still incomplete.  Do others 
have checkins awaitin'?
A related Major Improvement is updating/fixing the relation extractor xml: 
https://issues.apache.org/jira/browse/CTAKES-172


Another Major improvement is an lvg update.  Do we have time to play with this 
or should we bump it? https://issues.apache.org/jira/browse/CTAKES-388  Related 
to https://issues.apache.org/jira/browse/CTAKES-122


Pei or Jay, are you ready to check in a working BigTop integration?
https://issues.apache.org/jira/browse/CTAKES-314



-Original Message-
From: Pei Chen [mailto:chen...@apache.org] 
Sent: Wednesday, November 18, 2015 10:02 PM
To: dev@ctakes.apache.org
Subject: Create next cTAKES release (3.2.3)?

Hi Folks,
It looks like there have been a lot of progress in Jira's.  What do folks think 
of preparing a cut for the next release- would be nice to get one more out 
before holidays/end of the year?
I'll be happy to volunteer to be RM again.

Full list of Jira items slated for 3.2.3:
https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES_fixforversion_12328718_-3FselectedTab-3Dcom.atlassian.jira.jira-2Dprojects-2Dplugin-3Aversion-2Dissues-2Dpanel=BQIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=_7ouzO0-tjeIkyk9Gs02WBejxjOgYQstemelRj8yHcY=Bb9i6bbeLKK1UiJCVzZZPIkgQpmbHNsYJbEBDhsaBA4=
 

--Pei

Re: Create next cTAKES release (3.2.3)?

2015-11-19 Thread Pei Chen

A lot of the Jira's haven't been bumped into 3.2.4 yet.  This is to
get everyone to start looking and update their Jira's and if they
don't think they'll get a chance to work on it, I suggest to bump it
to the next release...  And if someone would like something to be
included in this release, please create a Jira and assign it to 3.2.3.

--Pei


On Thu, Nov 19, 2015 at 11:09 AM, Finan, Sean
 wrote:
> Hi Pei, thanks for the link to our Jira dashboard.  From my 3 second 
> run-through I would say that there remains a lot of outstanding work slated 
> for the 3.2.3 release.  Below are the Blocker, Critical and Major items.  
> Some may actually have been or can be quickly resolved, but it looks like we 
> may have more than a few bumps to 3.2.4 if we want to push out a release.
>
> I say in my bazaar way: release early, release often ...
> +1 for bumps and release ... *but first some comments in Jira on the state of 
> all listed below...
>
> Can anybody confirm that our only Blocker (dependencies not in maven central) 
> is still a problem?  https://issues.apache.org/jira/browse/CTAKES-76
> Where do we stand on the related Critical 
> https://issues.apache.org/jira/browse/CTAKES-138 ?
>
> Our other Critical item is PTB tokenizer breaking on apostrophes: 
> https://issues.apache.org/jira/browse/CTAKES-74
>
> A Major bug is FractionFSM incorrectly handling dashed ranges: 
> https://issues.apache.org/jira/browse/CTAKES-341  Britt, it looks like you 
> might have a fix ready?
>
> Another Major bug is for ytex UMLS.hbm.template.xml ... 
> https://issues.apache.org/jira/browse/CTAKES-302 Vijay it looks like you have 
> a fix started?
>
> Major bug for Missing Modifiers 
> https://issues.apache.org/jira/browse/CTAKES-213 ... Steve indicates that 
> this will require a lot of work.  Should we bump it or has somebody been 
> making progress?
>
> A Major bug in Medication Strength parsing has sat since our original 
> incubation, so I'm just guessing that it hasn't been touched and will be 
> bumped.  https://issues.apache.org/jira/browse/CTAKES-178
>
> Major bug SimpleSegmentWithTags ... 5 char names ... has also been around 
> single the continents were formed.
> https://issues.apache.org/jira/browse/CTAKES-155  I'd say a bump seems ok 
> except that there is an NPE ...
>
> There is a patch posted for our good old blues brothers boys band "URI not 
> hierarchical" on the old dictionary lookup 
> https://issues.apache.org/jira/browse/CTAKES-388  Can anybody volunteer to 
> test and commit?  I think that this is basically the same problem relayed in 
> https://issues.apache.org/jira/browse/CTAKES-320
>
>
> We have two placeholders for 3.2.3 additions.  They should probably be added 
> and (widely) tested asap or bumped to the next release.
> New Sentence Detector https://issues.apache.org/jira/browse/CTAKES-380
> ISO Time Normalizer https://issues.apache.org/jira/browse/CTAKES-379
>
> Has anybody started to tackle clean up / ?removal? of xml descriptors?  
> Tagged as Major improvement.  https://issues.apache.org/jira/browse/CTAKES-328
> This is related to https://issues.apache.org/jira/browse/CTAKES-295 - for 
> which Tim Miller has done a lot of great work, but is still incomplete.  Do 
> others have checkins awaitin'?
> A related Major Improvement is updating/fixing the relation extractor xml: 
> https://issues.apache.org/jira/browse/CTAKES-172
>
>
> Another Major improvement is an lvg update.  Do we have time to play with 
> this or should we bump it? https://issues.apache.org/jira/browse/CTAKES-388  
> Related to https://issues.apache.org/jira/browse/CTAKES-122
>
>
> Pei or Jay, are you ready to check in a working BigTop integration?
> https://issues.apache.org/jira/browse/CTAKES-314
>
>
>
> -Original Message-
> From: Pei Chen [mailto:chen...@apache.org]
> Sent: Wednesday, November 18, 2015 10:02 PM
> To: dev@ctakes.apache.org
> Subject: Create next cTAKES release (3.2.3)?
>
> Hi Folks,
> It looks like there have been a lot of progress in Jira's.  What do folks 
> think of preparing a cut for the next release- would be nice to get one more 
> out before holidays/end of the year?
> I'll be happy to volunteer to be RM again.
>
> Full list of Jira items slated for 3.2.3:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES_fixforversion_12328718_-3FselectedTab-3Dcom.atlassian.jira.jira-2Dprojects-2Dplugin-3Aversion-2Dissues-2Dpanel=BQIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=_7ouzO0-tjeIkyk9Gs02WBejxjOgYQstemelRj8yHcY=Bb9i6bbeLKK1UiJCVzZZPIkgQpmbHNsYJbEBDhsaBA4=
>
> --Pei

TermConsumers

2015-11-19 Thread Tomasz Oliwa

Hi,

How can I run a different TermConsumer on already generated CAS files?

I have CAS files created by the AggregatePlaintextFastUMLSProcessor with the 
DefaultTermConsumer set in cTakesHsql.xml. 

Now I would like to apply the PrecisionTermConsumer on these CAS files without 
having to do the whole annotation process again. The IdentifiedAnnotations are 
all there, it is only a matter of removing them according to the TermConsumers 
logic.

Is there a way to create a passthrough Processor that simply reads the CAS, 
applies a different TermConsumer and writes it to disk? 

Or is there a different way to go on about this?

Thanks for any help,
Tomasz

RE: TermConsumers

RE: TermConsumers

Re: AggregatePlaintextFastUMLSProcessor.xml will not load

AggregatePlaintextFastUMLSProcessor.xml will not load

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Re: Create next cTAKES release (3.2.3)?

TermConsumers

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