Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

2019-01-17 Thread Sana Riaz 
Hi Sean.
Sorry for bothering you again. I tried applying the above patches. I am
getting following error after changing the typesystem as mentioned in
https://issues.apache.org/jira/browse/CTAKES-500

 org.springframework.beans.BeanInstantiationException: Failed to
instantiate [com.canehealth.spring.ctakes.service.CtakesService]:
Constructor threw e
xception; nested exception is org.apache.uima.cas.CASRuntimeException: CAS
type system doesn''t match JCas Type definition for type "{0}".
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:182)
at
org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1228)
... 30 more
Caused by: org.apache.uima.cas.CASRuntimeException: CAS type system
doesn''t match JCas Type definition for type "{0}".
at org.apache.uima.jcas.impl.JCasImpl.logAndThrow(JCasImpl.java:493)
at
org.apache.uima.jcas.impl.JCasImpl.makeInstanceOf_Type(JCasImpl.java:1036)
at
org.apache.uima.jcas.impl.JCasImpl.instantiateJCas_Types(JCasImpl.java:714)
at org.apache.uima.jcas.impl.JCasImpl.(JCasImpl.java:545)
at org.apache.uima.jcas.impl.JCasImpl.getJCas(JCasImpl.java:785)
at org.apache.uima.cas.impl.CASImpl.getJCas(CASImpl.java:3105)
at org.apache.uima.jcas.impl.JCasImpl.(JCasImpl.java:528)
at org.apache.uima.jcas.impl.JCasImpl.getJCas(JCasImpl.java:785)
at org.apache.uima.cas.impl.CASImpl.getJCas(CASImpl.java:3105)
at
com.canehealth.spring.ctakes.service.CtakesService.(CtakesService.java:85)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:170)
... 32 more
Caused by: java.lang.reflect.InvocationTargetException
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at
org.apache.uima.jcas.impl.JCasImpl.makeInstanceOf_Type(JCasImpl.java:1017)
... 45 more
Caused by: java.lang.Error: Unresolved compilation problem:
The method addGeneratorForType(TypeImpl, FSGenerator) is
undefined for the type FSClassRegistry

at
org.apache.ctakes.typesystem.type.textspan.SectionHeading_Type.(SectionHeading_Type.java:83)
... 50 more




*CAS type system doesn''t match JCas Type definition for type "{0}".*i
understand that this error occured due to new typedescription
"SectionHeading" but I couldnt find what this error means or how to solve
it. It would be very kind if you'd help me through this.

Warm Regards,

Sana Riaz


On Mon, Jan 14, 2019 at 8:05 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> Maybe this would help?
> http://maven.apache.org/plugins/maven-patch-plugin/
>
> 
> From: Sana Riaz 
> Sent: Monday, January 14, 2019 4:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA
> document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
>
> Hi Sean,
> Thanks for your reply. Can you please help me how can I apply these patches
> to my current project. I have added ctakes libraries as jar files through
> maven dependencies. how would i update those jar files with these changes.
> Currently, I have tried using maven-plugin as following but it didnt change
> anything.
>
> 
> > org.apache.maven.plugins
> > maven-patch-plugin
> > 1.2
> > 
> > 
> > 
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_secure_attachment_12916325_CTAKES-2D500.patch=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=gPZ5JJ-v0kMpDC-vOJTwHP3Ygmn5Ayabo1Rt2xwetpM=Ec0ElrVtO9JsYMvjj46U0V07C6KOBvt3Hstk82MR-Og=
> > 
> > 
> > 
> > 
> > 
> > patch
> > process-sources
> > 
> > apply
> > 
> > 
> > 
> > 
>
>
>
>
> Warm Regards,
>
> Sana Riaz
>
>
> On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Thanks Tim.
> > There is a patch in the jira item, but I don't know if it was ever
> applied
> > (checked in).
> > Does anybody know?
> >
> > 
> > From: Miller, Timothy 
> > Sent: Friday, January 11, 2019 11:32 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA
> >

Re: uima-as examples

2019-01-17 Thread Peter Abramowitsch 
I used a completely different approach that allows parallel but not async
processing.  Multiple [analysis engine+cas] pair objects pre-instantiated
into into a threadsafe pool running behind a web service interface. We can
fully saturate a single ctakes server process using multiple client
processes talking to that API each working synchronously and arriving at an
overall speed of 10-15 6K notes per second on a single server process.

I haven't used AS but it looks as if that middleware could have too many
moving parts for our needs.  They would generate many wakeups and context
switches adding undesired latency as a request makes its way to the
server.   I'm assuming that in AS, the broker and the MQ are separate
processes and not just in-process subsystems to the ctakes server process.
Is that right?

On Thu, Jan 17, 2019 at 4:09 PM Greg Silverman  wrote:

> Anyone out there developed a pipeline using UIMA-AS, as opposed to the
> CPE/CPM file reader?
>
> Thanks in advance!
>
> Greg--
>
> --
> Greg M. Silverman
> Senior Systems Developer
> NLP/IE 
> Cardiovascular Informatics 
> University of Minnesota
> g...@umn.edu
>
>  ›  evaluate-it.org  ‹
>

uima-as examples

2019-01-17 Thread Greg Silverman 
Anyone out there developed a pipeline using UIMA-AS, as opposed to the
CPE/CPM file reader?

Thanks in advance!

Greg--

-- 
Greg M. Silverman
Senior Systems Developer
NLP/IE 
Cardiovascular Informatics 
University of Minnesota
g...@umn.edu

 ›  evaluate-it.org  ‹