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Posted to dev@ctakes.apache.org by shahid ashraf <sh...@trialx.com> on 2017/02/10 19:49:42 UTC
CAS Pool
Hi
I was able to create the caspool using the descriptor approach, but
instead of getting ctakes blocked which was happening without caspool when
multiple threads are ran.
Currently i am getting following error:
Feb 10, 2017 8:44:06 PM
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
callAnalysisComponentProcess(430)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:310)
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:396)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at
org.apache.uima.analysis_engine.impl.MultiprocessingAnalysisEngine_impl.process(MultiprocessingAnalysisEngine_impl.java:199)
at
org.apache.ctakes.web.client.servlet.DemoServlet.doPost(DemoServlet.java:135)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:501)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
at
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at
org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
at
org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982)
at
org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at
org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
at
org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:667)
at
org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
at
org.apache.ctakes.lvg.ae.LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
at
org.apache.ctakes.lvg.ae.LvgAnnotator.annotateRange(LvgAnnotator.java:342)
at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:307)
... 35 more
Caused by: java.lang.NullPointerException
--
with Regards
Shahid Ashraf
Re: CAS Pool
Posted by Andrey Kurdumov <ka...@googlemail.com>.
That's sad.
I could try take a look tomorrow, but no promises. Since I expect that
issue was fixed in LVG, probably something else is going on here.
2017-02-13 17:16 GMT+06:00 shahid ashraf <sh...@trialx.com>:
> Hi All
>
>
> After updating to LVG 2017. It seems i am still getting the same error on
> multiple threads
>
> 13 Feb 2017 16:26:43 INFO LvgAnnotator - process(JCas)
>
> Feb 13, 2017 4:26:43 PM org.apache.uima.analysis_engin
> e.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(430)
>
> SEVERE: Exception occurred
>
> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:310)
>
> at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(
> JCasAnnotator_ImplBase.java:48)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
> _impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
> _impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateC
> asIterator.processUntilNextOutputCas(ASB_impl.java:570)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateC
> asIterator.<init>(ASB_impl.java:412)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(AS
> B_impl.java:344)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine
> _impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
>
> at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(
> AnalysisEngineImplBase.java:269)
>
> at org.apache.uima.analysis_engine.impl.MultiprocessingAnalysis
> Engine_impl.process(MultiprocessingAnalysisEngine_impl.java:199)
>
> at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(Demo
> Servlet.java:134)
>
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
>
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
>
> at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
>
> at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHan
> dler.java:501)
>
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(Scoped
> Handler.java:137)
>
> at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHa
> ndler.java:557)
>
> at org.eclipse.jetty.server.session.SessionHandler.doHandle(Ses
> sionHandler.java:231)
>
> at org.eclipse.jetty.server.handler.ContextHandler.doHandle(Con
> textHandler.java:1086)
>
> at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHand
> ler.java:428)
>
> at org.eclipse.jetty.server.session.SessionHandler.doScope(Sess
> ionHandler.java:193)
>
> at org.eclipse.jetty.server.handler.ContextHandler.doScope(Cont
> extHandler.java:1020)
>
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(Scoped
> Handler.java:135)
>
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(Handl
> erWrapper.java:116)
>
> at org.eclipse.jetty.server.Server.handle(Server.java:370)
>
> at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(
> AbstractHttpConnection.java:494)
>
> at org.eclipse.jetty.server.AbstractHttpConnection.content(Abst
> ractHttpConnection.java:982)
>
> at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(
> AbstractHttpConnection.java:1043)
>
> at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
>
> at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
>
> at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHtt
> pConnection.java:82)
>
> at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(Select
> ChannelEndPoint.java:667)
>
> at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectC
> hannelEndPoint.java:52)
>
> at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(Queued
> ThreadPool.java:608)
>
> at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedT
> hreadPool.java:543)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.setCanonicalForm(LvgAn
> notator.java:372)
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.annotateRange(LvgAnnot
> ator.java:342)
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:307)
>
> ... 35 more
>
> Caused by: java.lang.NullPointerException
>
>
> Feb 13, 2017 4:26:43 PM org.apache.uima.analysis_engin
> e.impl.AggregateAnalysisEngine_impl processAndOutputNewCASes(273)
>
> SEVERE: Exception occurred
>
> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:310)
>
> at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(
> JCasAnnotator_ImplBase.java:48)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
> _impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
> _impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateC
> asIterator.processUntilNextOutputCas(ASB_impl.java:570)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateC
> asIterator.<init>(ASB_impl.java:412)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(AS
> B_impl.java:344)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine
> _impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
>
> at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(
> AnalysisEngineImplBase.java:269)
>
> at org.apache.uima.analysis_engine.impl.MultiprocessingAnalysis
> Engine_impl.process(MultiprocessingAnalysisEngine_impl.java:199)
>
> at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(Demo
> Servlet.java:134)
>
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
>
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
>
> at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
>
> at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHan
> dler.java:501)
>
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(Scoped
> Handler.java:137)
>
> at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHa
> ndler.java:557)
>
> at org.eclipse.jetty.server.session.SessionHandler.doHandle(Ses
> sionHandler.java:231)
>
> at org.eclipse.jetty.server.handler.ContextHandler.doHandle(Con
> textHandler.java:1086)
>
> at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHand
> ler.java:428)
>
> at org.eclipse.jetty.server.session.SessionHandler.doScope(Sess
> ionHandler.java:193)
>
> at org.eclipse.jetty.server.handler.ContextHandler.doScope(Cont
> extHandler.java:1020)
>
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(Scoped
> Handler.java:135)
>
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(Handl
> erWrapper.java:116)
>
> at org.eclipse.jetty.server.Server.handle(Server.java:370)
>
> at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(
> AbstractHttpConnection.java:494)
>
> at org.eclipse.jetty.server.AbstractHttpConnection.content(Abst
> ractHttpConnection.java:982)
>
> at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(
> AbstractHttpConnection.java:1043)
>
> at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
>
> at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
>
> at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHtt
> pConnection.java:82)
>
> at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(Select
> ChannelEndPoint.java:667)
>
> at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectC
> hannelEndPoint.java:52)
>
> at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(Queued
> ThreadPool.java:608)
>
> at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedT
> hreadPool.java:543)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.setCanonicalForm(LvgAn
> notator.java:372)
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.annotateRange(LvgAnnot
> ator.java:342)
>
> at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:307)
>
> ... 35 more
>
> Caused by: java.lang.NullPointerException
>
> On Sun, Feb 12, 2017 at 12:45 PM, Andrey Kurdumov <kant2002@googlemail.com
> > wrote:
>
>> Hi Shahid,
>> This is related to CTAKES-151 (
>> https://issues.apache.org/jira/browse/CTAKES-151) where mentioned that
>> LVG
>> has bad multithreaded behavior.
>> You could either try update LVG or place some locking around calls to
>> MutateToString which probably affect performance.
>>
>> 2017-02-12 12:21 GMT+06:00 shahid ashraf <sh...@trialx.com>:
>>
>> > Hi Sean
>> >
>> >
>> > I found the line which is causing the null pointer exception in the
>> > ctakes-LVG..
>> > its
>> > *String[] output = out.split("\\|");*
>> >
>> > *but issue seems *
>> >
>> > String out = lvgCmd.MutateToString(word);
>> >
>> > returns null
>> >
>> > This only happens when running the LVG via CAS pool.
>> >
>> > It seems it has been patched here ...
>> >
>> > https://github.com/meikeric/ytex/blob/master/workspace/
>> > ctakes-patches/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java
>> > .
>> >
>> > My Question is why this happens in CAS pool (where each CAS has its own
>> > resource.)
>> >
>> > and seems it happens on even ... normal words ... but when testing these
>> > words one by one on same code String out = lvgCmd.MutateToString(word);
>> it
>> > returns back the canonical form
>> >
>> >
>> > Here is the log when
>> >
>> > String out = lvgCmd.MutateToString(word) *FAILS*
>> >
>> > WARN LvgAnnotator - mutateToString returned null for: anemia
>> >
>> > 12 Feb 2017 11:20:32 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > remained
>> >
>> > 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > course
>> >
>> > 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > profile.
>> >
>> > 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > a
>> >
>> > 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > pre-specified
>> >
>> > 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > these
>> >
>> > 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > inhibitors
>> >
>> > 12 Feb 2017 11:20:22 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > Many
>> >
>> > 12 Feb 2017 11:20:20 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > if
>> >
>> > 12 Feb 2017 11:20:15 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > third
>> >
>> > 12 Feb 2017 11:20:12 WARN LvgAnnotator - mutateToString returned null
>> for:
>> > Prolonged
>> >
>> > When trying these on same code ... but single thread ... we are getting
>> > results from LVG...
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - process(JCas)
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - annotate over full doc text
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > anemia|anemia|1|1|l+b|1|
>> >
>> > anemia|anemia|2|1|l+b|1|
>> >
>> > anemia|anemia|128|1|l+b|1|
>> >
>> > anemia|anemia|1024|1|l+b|1|
>> >
>> > anemia|anemion|128|512|l+b|1|
>> >
>> > anemia|anemium|128|512|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > placebo|placebo|1|1|l+b|1|
>> >
>> > placebo|placebo|2|1|l+b|1|
>> >
>> > placebo|placebo|128|1|l+b|1|
>> >
>> > placebo|placebo|1024|1|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > Prolonged|prolong|1024|1024|l+b|1|
>> >
>> > Prolonged|prolonge|1024|1024|l+b|1|
>> >
>> > Prolonged|prolonged|1|1|l+b|1|
>> >
>> > Prolonged|prolonged|2|1|l+b|1|
>> >
>> > Prolonged|prolonged|128|1|l+b|1|
>> >
>> > Prolonged|prolonged|1024|1|l+b|1|
>> >
>> > Prolonged|prolongeed|1024|1024|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > third|third|1|1|l+b|1|
>> >
>> > third|third|2|1|l+b|1|
>> >
>> > third|third|128|1|l+b|1|
>> >
>> > third|third|1024|1|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > inhibitors|inhibitor|128|512|l+b|1|
>> >
>> > inhibitors|inhibitor|1024|1024|l+b|1|
>> >
>> > inhibitors|inhibitors|1|1|l+b|1|
>> >
>> > inhibitors|inhibitors|2|1|l+b|1|
>> >
>> > inhibitors|inhibitors|128|1|l+b|1|
>> >
>> > inhibitors|inhibitors|1024|1|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > these|these|1|1|l+b|1|
>> >
>> > these|these|2|1|l+b|1|
>> >
>> > these|these|128|1|l+b|1|
>> >
>> > these|these|1024|1|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > pre-specified|pre-specifi|1024|1024|l+b|1|
>> >
>> > pre-specified|pre-specifie|1024|1024|l+b|1|
>> >
>> > pre-specified|pre-specified|1|1|l+b|1|
>> >
>> > pre-specified|pre-specified|2|1|l+b|1|
>> >
>> > pre-specified|pre-specified|128|1|l+b|1|
>> >
>> > pre-specified|pre-specified|1024|1|l+b|1|
>> >
>> > pre-specified|pre-specifieed|1024|1024|l+b|1|
>> >
>> > pre-specified|pre-specify|1024|1024|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > profile.|profile.|1|1|l+b|1|
>> >
>> > profile.|profile.|2|1|l+b|1|
>> >
>> > profile.|profile.|128|1|l+b|1|
>> >
>> > profile.|profile.|1024|1|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > course|course|1|1|l+b|1|
>> >
>> > course|course|2|1|l+b|1|
>> >
>> > course|course|128|1|l+b|1|
>> >
>> > course|course|1024|1|l+b|1|
>> >
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
>> > canonical form
>> >
>> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
>> > remained|remain|1024|1024|l+b|1|
>> >
>> > remained|remaine|1024|1024|l+b|1|
>> >
>> > remained|remained|1|1|l+b|1|
>> >
>> > remained|remained|2|1|l+b|1|
>> >
>> > remained|remained|128|1|l+b|1|
>> >
>> > remained|remained|1024|1|l+b|1|
>> >
>> > remained|remaineed|1024|1024|l+b|1|
>> >
>> >
>> >
>> >
>> > On Sat, Feb 11, 2017 at 2:51 AM, shahid ashraf <sh...@trialx.com>
>> wrote:
>> >
>> > > To add more it only happens when using caspool
>> > >
>> > > On Sat, Feb 11, 2017 at 2:48 AM, Finan, Sean <
>> > > Sean.Finan@childrens.harvard.edu> wrote:
>> > >
>> > >> Yes, thanks. I will try to look into this a little later.
>> > >>
>> > >>
>> > >>
>> > >> Sean
>> > >>
>> > >>
>> > >>
>> > >> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> > >> *Sent:* Friday, February 10, 2017 3:45 PM
>> > >> *To:* Finan, Sean
>> > >> *Subject:* Re: CAS Pool
>> > >>
>> > >>
>> > >>
>> > >> Are you looking for these lines
>> > >>
>> > >>
>> > >>
>> > >> 11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
>> > >> org/apache/ctakes/postagger/models/mayo-pos.zip
>> > >>
>> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - Loading NLM Norm
>> and
>> > >> Lvg with config file = /Users/shahid/projects/healthn
>> > >> lp/examples/ctakes-web-client/target/classes/org/apache/
>> > >> ctakes/lvg/data/config/lvg.properties
>> > >>
>> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - config file
>> > absolute
>> > >> path = /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
>> > >> target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
>> > >>
>> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cwd =
>> > >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
>> > >>
>> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
>> > >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
>> > >> target/classes/org/apache/ctakes/lvg/
>> > >>
>> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
>> > >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
>> > >>
>> > >> 11 Feb 2017 02:14:07 INFO DrugMentionAnnotator - Finite state
>> machines
>> > >> loaded.
>> > >>
>> > >>
>> > >>
>> > >> On Sat, Feb 11, 2017 at 2:01 AM, Finan, Sean <
>> > >> Sean.Finan@childrens.harvard.edu> wrote:
>> > >>
>> > >> Hi Shahid,
>> > >>
>> > >>
>> > >>
>> > >> Are you getting any log information from the lvg classes during
>> > >> initialization?
>> > >>
>> > >>
>> > >>
>> > >> Sean
>> > >>
>> > >>
>> > >>
>> > >> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> > >> *Sent:* Friday, February 10, 2017 2:50 PM
>> > >> *To:* dev@ctakes.apache.org; Finan, Sean
>> > >> *Subject:* CAS Pool
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> Hi
>> > >>
>> > >>
>> > >>
>> > >> I was able to create the caspool using the descriptor approach, but
>> > >> instead of getting ctakes blocked which was happening without caspool
>> > when
>> > >> multiple threads are ran.
>> > >>
>> > >> Currently i am getting following error:
>> > >>
>> > >>
>> > >>
>> > >> Feb 10, 2017 8:44:06 PM org.apache.uima.analysis_engin
>> > >> e.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(4
>> 30)
>> > >>
>> > >> SEVERE: Exception occurred
>> > >>
>> > >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>> > >>
>> > >> at org.apache.ctakes.lvg.ae
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
>> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
>> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
>> d4f7d4gTao&m=
>> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
>> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> > >> .LvgAnnotator.process(LvgAnnotator.java:310)
>> > >>
>> > >> at org.apache.uima.analysis_component.JCasAnnotator_
>> > ImplBase.
>> > >> process(JCasAnnotator_ImplBase.java:48)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentPro
>> > >> cess(PrimitiveAnalysisEngine_impl.java:396)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes
>> > >> (PrimitiveAnalysisEngine_impl.java:314)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOut
>> > >> putCas(ASB_impl.java:570)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
>> > >>
>> > >> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
>> > process(
>> > >> ASB_impl.java:344)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes
>> > >> (AggregateAnalysisEngine_impl.java:265)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase
>> .java:269)
>> > >>
>> > >> at org.apache.uima.analysis_engin
>> > >> e.impl.MultiprocessingAnalysisEngine_impl.process(Multiproce
>> > >> ssingAnalysisEngine_impl.java:199)
>> > >>
>> > >> at org.apache.ctakes.web.client.s
>> > >> ervlet.DemoServlet.doPost(DemoServlet.java:135)
>> > >>
>> > >> at javax.servlet.http.HttpServlet
>> > >> .service(HttpServlet.java:755)
>> > >>
>> > >> at javax.servlet.http.HttpServlet
>> > >> .service(HttpServlet.java:848)
>> > >>
>> > >> at org.eclipse.jetty.servlet.Serv
>> > >> letHolder.handle(ServletHolder.java:684)
>> > >>
>> > >> at org.eclipse.jetty.servlet.Serv
>> > >> letHandler.doHandle(ServletHandler.java:501)
>> > >>
>> > >> at org.eclipse.jetty.server.handl
>> > >> er.ScopedHandler.handle(ScopedHandler.java:137)
>> > >>
>> > >> at org.eclipse.jetty.security.Sec
>> > >> urityHandler.handle(SecurityHandler.java:557)
>> > >>
>> > >> at org.eclipse.jetty.server.session.SessionHandler.
>> > doHandle(
>> > >> SessionHandler.java:231)
>> > >>
>> > >> at org.eclipse.jetty.server.handler.ContextHandler.
>> > doHandle(
>> > >> ContextHandler.java:1086)
>> > >>
>> > >> at org.eclipse.jetty.servlet.Serv
>> > >> letHandler.doScope(ServletHandler.java:428)
>> > >>
>> > >> at org.eclipse.jetty.server.sessi
>> on.SessionHandler.doScope(
>> > >> SessionHandler.java:193)
>> > >>
>> > >> at org.eclipse.jetty.server.handl
>> er.ContextHandler.doScope(
>> > >> ContextHandler.java:1020)
>> > >>
>> > >> at org.eclipse.jetty.server.handl
>> > >> er.ScopedHandler.handle(ScopedHandler.java:135)
>> > >>
>> > >> at org.eclipse.jetty.server.handl
>> > >> er.HandlerWrapper.handle(HandlerWrapper.java:116)
>> > >>
>> > >> at org.eclipse.jetty.server.Serve
>> r.handle(Server.java:370)
>> > >>
>> > >> at org.eclipse.jetty.server.Abstr
>> > >> actHttpConnection.handleRequest(AbstractHttpConnection.java:494)
>> > >>
>> > >> at org.eclipse.jetty.server.Abstr
>> > >> actHttpConnection.content(AbstractHttpConnection.java:982)
>> > >>
>> > >> at org.eclipse.jetty.server.Abstr
>> > >> actHttpConnection$RequestHandler.content(AbstractHttpConnect
>> > >> ion.java:1043)
>> > >>
>> > >> at org.eclipse.jetty.http.HttpPar
>> > >> ser.parseNext(HttpParser.java:865)
>> > >>
>> > >> at org.eclipse.jetty.http.HttpPar
>> > >> ser.parseAvailable(HttpParser.java:240)
>> > >>
>> > >> at org.eclipse.jetty.server.Async
>> > >> HttpConnection.handle(AsyncHttpConnection.java:82)
>> > >>
>> > >> at org.eclipse.jetty.io.nio.Selec
>> > >> tChannelEndPoint.handle(SelectChannelEndPoint.java:667)
>> > >>
>> > >> at org.eclipse.jetty.io.nio.Selec
>> > >> tChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
>> > >>
>> > >> at org.eclipse.jetty.util.thread.
>> > >> QueuedThreadPool.runJob(QueuedThreadPool.java:608)
>> > >>
>> > >> at org.eclipse.jetty.util.thread.
>> > >> QueuedThreadPool$3.run(QueuedThreadPool.java:543)
>> > >>
>> > >> at java.lang.Thread.run(Thread.java:745)
>> > >>
>> > >> Caused by: org.apache.uima.analysis_engine.
>> > AnalysisEngineProcessException
>> > >>
>> > >> at org.apache.ctakes.lvg.ae
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
>> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
>> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
>> d4f7d4gTao&m=
>> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
>> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> > >> .LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
>> > >>
>> > >> at org.apache.ctakes.lvg.ae
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
>> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
>> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
>> d4f7d4gTao&m=
>> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
>> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> > >> .LvgAnnotator.annotateRange(LvgAnnotator.java:342)
>> > >>
>> > >> at org.apache.ctakes.lvg.ae
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
>> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
>> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
>> d4f7d4gTao&m=
>> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
>> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> > >> .LvgAnnotator.process(LvgAnnotator.java:307)
>> > >>
>> > >> ... 35 more
>> > >>
>> > >> Caused by: java.lang.NullPointerException
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >>
>> > >> with Regards
>> > >>
>> > >> Shahid Ashraf
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >>
>> > >> with Regards
>> > >>
>> > >> Shahid Ashraf
>> > >>
>> > >
>> > >
>> > >
>> > > --
>> > > with Regards
>> > > Shahid Ashraf
>> > >
>> >
>> >
>> >
>> > --
>> > with Regards
>> > Shahid Ashraf
>> >
>>
>
>
>
> --
> with Regards
> Shahid Ashraf
>
Re: CAS Pool
Posted by shahid ashraf <sh...@trialx.com>.
Hi All
After updating to LVG 2017. It seems i am still getting the same error on
multiple threads
13 Feb 2017 16:26:43 INFO LvgAnnotator - process(JCas)
Feb 13, 2017 4:26:43 PM
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
callAnalysisComponentProcess(430)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:310)
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:396)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.
processUntilNextOutputCas(ASB_impl.java:570)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
AggregateCasIterator.<init>(ASB_impl.java:412)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(
ASB_impl.java:344)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(
AnalysisEngineImplBase.java:269)
at org.apache.uima.analysis_engine.impl.MultiprocessingAnalysisEngine_
impl.process(MultiprocessingAnalysisEngine_impl.java:199)
at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(Dem
oServlet.java:134)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:501
)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(S
copedHandler.java:137)
at org.eclipse.jetty.security.SecurityHandler.handle(Securit
yHandler.java:557)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(
SessionHandler.java:231)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(
ContextHandler.java:1086)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428)
at org.eclipse.jetty.server.session.SessionHandler.doScope(
SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(
ContextHandler.java:1020)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(S
copedHandler.java:135)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(
HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(
AbstractHttpConnection.java:494)
at org.eclipse.jetty.server.AbstractHttpConnection.content(
AbstractHttpConnection.java:982)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(
AbstractHttpConnection.java:1043)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at org.eclipse.jetty.server.AsyncHttpConnection.handle(Asy
ncHttpConnection.java:82)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(S
electChannelEndPoint.java:667)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(Se
lectChannelEndPoint.java:52)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(Queued
ThreadPool.java:608)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedT
hreadPool.java:543)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae.LvgAnnotator.setCanonicalForm(
LvgAnnotator.java:372)
at org.apache.ctakes.lvg.ae.LvgAnnotator.annotateRange(LvgAnnotator.java:342
)
at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:307)
... 35 more
Caused by: java.lang.NullPointerException
Feb 13, 2017 4:26:43 PM
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
processAndOutputNewCASes(273)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:310)
at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(
JCasAnnotator_ImplBase.java:48)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.
processUntilNextOutputCas(ASB_impl.java:570)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
AggregateCasIterator.<init>(ASB_impl.java:412)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(
ASB_impl.java:344)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(
AnalysisEngineImplBase.java:269)
at org.apache.uima.analysis_engine.impl.MultiprocessingAnalysisEngine_
impl.process(MultiprocessingAnalysisEngine_impl.java:199)
at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(Dem
oServlet.java:134)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:501
)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(S
copedHandler.java:137)
at org.eclipse.jetty.security.SecurityHandler.handle(Securit
yHandler.java:557)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(
SessionHandler.java:231)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(
ContextHandler.java:1086)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428)
at org.eclipse.jetty.server.session.SessionHandler.doScope(
SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(
ContextHandler.java:1020)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(S
copedHandler.java:135)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(
HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(
AbstractHttpConnection.java:494)
at org.eclipse.jetty.server.AbstractHttpConnection.content(
AbstractHttpConnection.java:982)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(
AbstractHttpConnection.java:1043)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at org.eclipse.jetty.server.AsyncHttpConnection.handle(Asy
ncHttpConnection.java:82)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(S
electChannelEndPoint.java:667)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(Se
lectChannelEndPoint.java:52)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(Queued
ThreadPool.java:608)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedT
hreadPool.java:543)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae.LvgAnnotator.setCanonicalForm(
LvgAnnotator.java:372)
at org.apache.ctakes.lvg.ae.LvgAnnotator.annotateRange(LvgAnnotator.java:342
)
at org.apache.ctakes.lvg.ae.LvgAnnotator.process(LvgAnnotator.java:307)
... 35 more
Caused by: java.lang.NullPointerException
On Sun, Feb 12, 2017 at 12:45 PM, Andrey Kurdumov <ka...@googlemail.com>
wrote:
> Hi Shahid,
> This is related to CTAKES-151 (
> https://issues.apache.org/jira/browse/CTAKES-151) where mentioned that LVG
> has bad multithreaded behavior.
> You could either try update LVG or place some locking around calls to
> MutateToString which probably affect performance.
>
> 2017-02-12 12:21 GMT+06:00 shahid ashraf <sh...@trialx.com>:
>
> > Hi Sean
> >
> >
> > I found the line which is causing the null pointer exception in the
> > ctakes-LVG..
> > its
> > *String[] output = out.split("\\|");*
> >
> > *but issue seems *
> >
> > String out = lvgCmd.MutateToString(word);
> >
> > returns null
> >
> > This only happens when running the LVG via CAS pool.
> >
> > It seems it has been patched here ...
> >
> > https://github.com/meikeric/ytex/blob/master/workspace/
> > ctakes-patches/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java
> > .
> >
> > My Question is why this happens in CAS pool (where each CAS has its own
> > resource.)
> >
> > and seems it happens on even ... normal words ... but when testing these
> > words one by one on same code String out = lvgCmd.MutateToString(word);
> it
> > returns back the canonical form
> >
> >
> > Here is the log when
> >
> > String out = lvgCmd.MutateToString(word) *FAILS*
> >
> > WARN LvgAnnotator - mutateToString returned null for: anemia
> >
> > 12 Feb 2017 11:20:32 WARN LvgAnnotator - mutateToString returned null
> for:
> > remained
> >
> > 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null
> for:
> > course
> >
> > 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null
> for:
> > profile.
> >
> > 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null
> for:
> > a
> >
> > 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null
> for:
> > pre-specified
> >
> > 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null
> for:
> > these
> >
> > 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null
> for:
> > inhibitors
> >
> > 12 Feb 2017 11:20:22 WARN LvgAnnotator - mutateToString returned null
> for:
> > Many
> >
> > 12 Feb 2017 11:20:20 WARN LvgAnnotator - mutateToString returned null
> for:
> > if
> >
> > 12 Feb 2017 11:20:15 WARN LvgAnnotator - mutateToString returned null
> for:
> > third
> >
> > 12 Feb 2017 11:20:12 WARN LvgAnnotator - mutateToString returned null
> for:
> > Prolonged
> >
> > When trying these on same code ... but single thread ... we are getting
> > results from LVG...
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - process(JCas)
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - annotate over full doc text
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > anemia|anemia|1|1|l+b|1|
> >
> > anemia|anemia|2|1|l+b|1|
> >
> > anemia|anemia|128|1|l+b|1|
> >
> > anemia|anemia|1024|1|l+b|1|
> >
> > anemia|anemion|128|512|l+b|1|
> >
> > anemia|anemium|128|512|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > placebo|placebo|1|1|l+b|1|
> >
> > placebo|placebo|2|1|l+b|1|
> >
> > placebo|placebo|128|1|l+b|1|
> >
> > placebo|placebo|1024|1|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > Prolonged|prolong|1024|1024|l+b|1|
> >
> > Prolonged|prolonge|1024|1024|l+b|1|
> >
> > Prolonged|prolonged|1|1|l+b|1|
> >
> > Prolonged|prolonged|2|1|l+b|1|
> >
> > Prolonged|prolonged|128|1|l+b|1|
> >
> > Prolonged|prolonged|1024|1|l+b|1|
> >
> > Prolonged|prolongeed|1024|1024|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > third|third|1|1|l+b|1|
> >
> > third|third|2|1|l+b|1|
> >
> > third|third|128|1|l+b|1|
> >
> > third|third|1024|1|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > inhibitors|inhibitor|128|512|l+b|1|
> >
> > inhibitors|inhibitor|1024|1024|l+b|1|
> >
> > inhibitors|inhibitors|1|1|l+b|1|
> >
> > inhibitors|inhibitors|2|1|l+b|1|
> >
> > inhibitors|inhibitors|128|1|l+b|1|
> >
> > inhibitors|inhibitors|1024|1|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > these|these|1|1|l+b|1|
> >
> > these|these|2|1|l+b|1|
> >
> > these|these|128|1|l+b|1|
> >
> > these|these|1024|1|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > pre-specified|pre-specifi|1024|1024|l+b|1|
> >
> > pre-specified|pre-specifie|1024|1024|l+b|1|
> >
> > pre-specified|pre-specified|1|1|l+b|1|
> >
> > pre-specified|pre-specified|2|1|l+b|1|
> >
> > pre-specified|pre-specified|128|1|l+b|1|
> >
> > pre-specified|pre-specified|1024|1|l+b|1|
> >
> > pre-specified|pre-specifieed|1024|1024|l+b|1|
> >
> > pre-specified|pre-specify|1024|1024|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > profile.|profile.|1|1|l+b|1|
> >
> > profile.|profile.|2|1|l+b|1|
> >
> > profile.|profile.|128|1|l+b|1|
> >
> > profile.|profile.|1024|1|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > course|course|1|1|l+b|1|
> >
> > course|course|2|1|l+b|1|
> >
> > course|course|128|1|l+b|1|
> >
> > course|course|1024|1|l+b|1|
> >
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> > canonical form
> >
> > 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> > remained|remain|1024|1024|l+b|1|
> >
> > remained|remaine|1024|1024|l+b|1|
> >
> > remained|remained|1|1|l+b|1|
> >
> > remained|remained|2|1|l+b|1|
> >
> > remained|remained|128|1|l+b|1|
> >
> > remained|remained|1024|1|l+b|1|
> >
> > remained|remaineed|1024|1024|l+b|1|
> >
> >
> >
> >
> > On Sat, Feb 11, 2017 at 2:51 AM, shahid ashraf <sh...@trialx.com>
> wrote:
> >
> > > To add more it only happens when using caspool
> > >
> > > On Sat, Feb 11, 2017 at 2:48 AM, Finan, Sean <
> > > Sean.Finan@childrens.harvard.edu> wrote:
> > >
> > >> Yes, thanks. I will try to look into this a little later.
> > >>
> > >>
> > >>
> > >> Sean
> > >>
> > >>
> > >>
> > >> *From:* shahid ashraf [mailto:shahid@trialx.com]
> > >> *Sent:* Friday, February 10, 2017 3:45 PM
> > >> *To:* Finan, Sean
> > >> *Subject:* Re: CAS Pool
> > >>
> > >>
> > >>
> > >> Are you looking for these lines
> > >>
> > >>
> > >>
> > >> 11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
> > >> org/apache/ctakes/postagger/models/mayo-pos.zip
> > >>
> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - Loading NLM Norm
> and
> > >> Lvg with config file = /Users/shahid/projects/healthn
> > >> lp/examples/ctakes-web-client/target/classes/org/apache/
> > >> ctakes/lvg/data/config/lvg.properties
> > >>
> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - config file
> > absolute
> > >> path = /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
> > >> target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
> > >>
> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cwd =
> > >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
> > >>
> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
> > >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
> > >> target/classes/org/apache/ctakes/lvg/
> > >>
> > >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
> > >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
> > >>
> > >> 11 Feb 2017 02:14:07 INFO DrugMentionAnnotator - Finite state
> machines
> > >> loaded.
> > >>
> > >>
> > >>
> > >> On Sat, Feb 11, 2017 at 2:01 AM, Finan, Sean <
> > >> Sean.Finan@childrens.harvard.edu> wrote:
> > >>
> > >> Hi Shahid,
> > >>
> > >>
> > >>
> > >> Are you getting any log information from the lvg classes during
> > >> initialization?
> > >>
> > >>
> > >>
> > >> Sean
> > >>
> > >>
> > >>
> > >> *From:* shahid ashraf [mailto:shahid@trialx.com]
> > >> *Sent:* Friday, February 10, 2017 2:50 PM
> > >> *To:* dev@ctakes.apache.org; Finan, Sean
> > >> *Subject:* CAS Pool
> > >>
> > >>
> > >>
> > >>
> > >> Hi
> > >>
> > >>
> > >>
> > >> I was able to create the caspool using the descriptor approach, but
> > >> instead of getting ctakes blocked which was happening without caspool
> > when
> > >> multiple threads are ran.
> > >>
> > >> Currently i am getting following error:
> > >>
> > >>
> > >>
> > >> Feb 10, 2017 8:44:06 PM org.apache.uima.analysis_engin
> > >> e.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(430)
> > >>
> > >> SEVERE: Exception occurred
> > >>
> > >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> > >>
> > >> at org.apache.ctakes.lvg.ae
> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
> d4f7d4gTao&m=
> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> > >> .LvgAnnotator.process(LvgAnnotator.java:310)
> > >>
> > >> at org.apache.uima.analysis_component.JCasAnnotator_
> > ImplBase.
> > >> process(JCasAnnotator_ImplBase.java:48)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentPro
> > >> cess(PrimitiveAnalysisEngine_impl.java:396)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes
> > >> (PrimitiveAnalysisEngine_impl.java:314)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOut
> > >> putCas(ASB_impl.java:570)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
> > >>
> > >> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> > process(
> > >> ASB_impl.java:344)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes
> > >> (AggregateAnalysisEngine_impl.java:265)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase
> .java:269)
> > >>
> > >> at org.apache.uima.analysis_engin
> > >> e.impl.MultiprocessingAnalysisEngine_impl.process(Multiproce
> > >> ssingAnalysisEngine_impl.java:199)
> > >>
> > >> at org.apache.ctakes.web.client.s
> > >> ervlet.DemoServlet.doPost(DemoServlet.java:135)
> > >>
> > >> at javax.servlet.http.HttpServlet
> > >> .service(HttpServlet.java:755)
> > >>
> > >> at javax.servlet.http.HttpServlet
> > >> .service(HttpServlet.java:848)
> > >>
> > >> at org.eclipse.jetty.servlet.Serv
> > >> letHolder.handle(ServletHolder.java:684)
> > >>
> > >> at org.eclipse.jetty.servlet.Serv
> > >> letHandler.doHandle(ServletHandler.java:501)
> > >>
> > >> at org.eclipse.jetty.server.handl
> > >> er.ScopedHandler.handle(ScopedHandler.java:137)
> > >>
> > >> at org.eclipse.jetty.security.Sec
> > >> urityHandler.handle(SecurityHandler.java:557)
> > >>
> > >> at org.eclipse.jetty.server.session.SessionHandler.
> > doHandle(
> > >> SessionHandler.java:231)
> > >>
> > >> at org.eclipse.jetty.server.handler.ContextHandler.
> > doHandle(
> > >> ContextHandler.java:1086)
> > >>
> > >> at org.eclipse.jetty.servlet.Serv
> > >> letHandler.doScope(ServletHandler.java:428)
> > >>
> > >> at org.eclipse.jetty.server.sessi
> on.SessionHandler.doScope(
> > >> SessionHandler.java:193)
> > >>
> > >> at org.eclipse.jetty.server.handl
> er.ContextHandler.doScope(
> > >> ContextHandler.java:1020)
> > >>
> > >> at org.eclipse.jetty.server.handl
> > >> er.ScopedHandler.handle(ScopedHandler.java:135)
> > >>
> > >> at org.eclipse.jetty.server.handl
> > >> er.HandlerWrapper.handle(HandlerWrapper.java:116)
> > >>
> > >> at org.eclipse.jetty.server.Serve
> r.handle(Server.java:370)
> > >>
> > >> at org.eclipse.jetty.server.Abstr
> > >> actHttpConnection.handleRequest(AbstractHttpConnection.java:494)
> > >>
> > >> at org.eclipse.jetty.server.Abstr
> > >> actHttpConnection.content(AbstractHttpConnection.java:982)
> > >>
> > >> at org.eclipse.jetty.server.Abstr
> > >> actHttpConnection$RequestHandler.content(AbstractHttpConnect
> > >> ion.java:1043)
> > >>
> > >> at org.eclipse.jetty.http.HttpPar
> > >> ser.parseNext(HttpParser.java:865)
> > >>
> > >> at org.eclipse.jetty.http.HttpPar
> > >> ser.parseAvailable(HttpParser.java:240)
> > >>
> > >> at org.eclipse.jetty.server.Async
> > >> HttpConnection.handle(AsyncHttpConnection.java:82)
> > >>
> > >> at org.eclipse.jetty.io.nio.Selec
> > >> tChannelEndPoint.handle(SelectChannelEndPoint.java:667)
> > >>
> > >> at org.eclipse.jetty.io.nio.Selec
> > >> tChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
> > >>
> > >> at org.eclipse.jetty.util.thread.
> > >> QueuedThreadPool.runJob(QueuedThreadPool.java:608)
> > >>
> > >> at org.eclipse.jetty.util.thread.
> > >> QueuedThreadPool$3.run(QueuedThreadPool.java:543)
> > >>
> > >> at java.lang.Thread.run(Thread.java:745)
> > >>
> > >> Caused by: org.apache.uima.analysis_engine.
> > AnalysisEngineProcessException
> > >>
> > >> at org.apache.ctakes.lvg.ae
> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
> d4f7d4gTao&m=
> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> > >> .LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
> > >>
> > >> at org.apache.ctakes.lvg.ae
> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
> d4f7d4gTao&m=
> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> > >> .LvgAnnotator.annotateRange(LvgAnnotator.java:342)
> > >>
> > >> at org.apache.ctakes.lvg.ae
> > >> <https://urldefense.proofpoint.com/v2/url?u=http-
> > 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKG
> d4f7d4gTao&m=
> > ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> > mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> > >> .LvgAnnotator.process(LvgAnnotator.java:307)
> > >>
> > >> ... 35 more
> > >>
> > >> Caused by: java.lang.NullPointerException
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> --
> > >>
> > >> with Regards
> > >>
> > >> Shahid Ashraf
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> --
> > >>
> > >> with Regards
> > >>
> > >> Shahid Ashraf
> > >>
> > >
> > >
> > >
> > > --
> > > with Regards
> > > Shahid Ashraf
> > >
> >
> >
> >
> > --
> > with Regards
> > Shahid Ashraf
> >
>
--
with Regards
Shahid Ashraf
Re: CAS Pool
Posted by Andrey Kurdumov <ka...@googlemail.com>.
Hi Shahid,
This is related to CTAKES-151 (
https://issues.apache.org/jira/browse/CTAKES-151) where mentioned that LVG
has bad multithreaded behavior.
You could either try update LVG or place some locking around calls to
MutateToString which probably affect performance.
2017-02-12 12:21 GMT+06:00 shahid ashraf <sh...@trialx.com>:
> Hi Sean
>
>
> I found the line which is causing the null pointer exception in the
> ctakes-LVG..
> its
> *String[] output = out.split("\\|");*
>
> *but issue seems *
>
> String out = lvgCmd.MutateToString(word);
>
> returns null
>
> This only happens when running the LVG via CAS pool.
>
> It seems it has been patched here ...
>
> https://github.com/meikeric/ytex/blob/master/workspace/
> ctakes-patches/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java
> .
>
> My Question is why this happens in CAS pool (where each CAS has its own
> resource.)
>
> and seems it happens on even ... normal words ... but when testing these
> words one by one on same code String out = lvgCmd.MutateToString(word); it
> returns back the canonical form
>
>
> Here is the log when
>
> String out = lvgCmd.MutateToString(word) *FAILS*
>
> WARN LvgAnnotator - mutateToString returned null for: anemia
>
> 12 Feb 2017 11:20:32 WARN LvgAnnotator - mutateToString returned null for:
> remained
>
> 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null for:
> course
>
> 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null for:
> profile.
>
> 12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null for:
> a
>
> 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null for:
> pre-specified
>
> 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null for:
> these
>
> 12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null for:
> inhibitors
>
> 12 Feb 2017 11:20:22 WARN LvgAnnotator - mutateToString returned null for:
> Many
>
> 12 Feb 2017 11:20:20 WARN LvgAnnotator - mutateToString returned null for:
> if
>
> 12 Feb 2017 11:20:15 WARN LvgAnnotator - mutateToString returned null for:
> third
>
> 12 Feb 2017 11:20:12 WARN LvgAnnotator - mutateToString returned null for:
> Prolonged
>
> When trying these on same code ... but single thread ... we are getting
> results from LVG...
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - process(JCas)
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - annotate over full doc text
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> anemia|anemia|1|1|l+b|1|
>
> anemia|anemia|2|1|l+b|1|
>
> anemia|anemia|128|1|l+b|1|
>
> anemia|anemia|1024|1|l+b|1|
>
> anemia|anemion|128|512|l+b|1|
>
> anemia|anemium|128|512|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> placebo|placebo|1|1|l+b|1|
>
> placebo|placebo|2|1|l+b|1|
>
> placebo|placebo|128|1|l+b|1|
>
> placebo|placebo|1024|1|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> Prolonged|prolong|1024|1024|l+b|1|
>
> Prolonged|prolonge|1024|1024|l+b|1|
>
> Prolonged|prolonged|1|1|l+b|1|
>
> Prolonged|prolonged|2|1|l+b|1|
>
> Prolonged|prolonged|128|1|l+b|1|
>
> Prolonged|prolonged|1024|1|l+b|1|
>
> Prolonged|prolongeed|1024|1024|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> third|third|1|1|l+b|1|
>
> third|third|2|1|l+b|1|
>
> third|third|128|1|l+b|1|
>
> third|third|1024|1|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> inhibitors|inhibitor|128|512|l+b|1|
>
> inhibitors|inhibitor|1024|1024|l+b|1|
>
> inhibitors|inhibitors|1|1|l+b|1|
>
> inhibitors|inhibitors|2|1|l+b|1|
>
> inhibitors|inhibitors|128|1|l+b|1|
>
> inhibitors|inhibitors|1024|1|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> these|these|1|1|l+b|1|
>
> these|these|2|1|l+b|1|
>
> these|these|128|1|l+b|1|
>
> these|these|1024|1|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> pre-specified|pre-specifi|1024|1024|l+b|1|
>
> pre-specified|pre-specifie|1024|1024|l+b|1|
>
> pre-specified|pre-specified|1|1|l+b|1|
>
> pre-specified|pre-specified|2|1|l+b|1|
>
> pre-specified|pre-specified|128|1|l+b|1|
>
> pre-specified|pre-specified|1024|1|l+b|1|
>
> pre-specified|pre-specifieed|1024|1024|l+b|1|
>
> pre-specified|pre-specify|1024|1024|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> profile.|profile.|1|1|l+b|1|
>
> profile.|profile.|2|1|l+b|1|
>
> profile.|profile.|128|1|l+b|1|
>
> profile.|profile.|1024|1|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> course|course|1|1|l+b|1|
>
> course|course|2|1|l+b|1|
>
> course|course|128|1|l+b|1|
>
> course|course|1024|1|l+b|1|
>
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
> canonical form
>
> 12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
> remained|remain|1024|1024|l+b|1|
>
> remained|remaine|1024|1024|l+b|1|
>
> remained|remained|1|1|l+b|1|
>
> remained|remained|2|1|l+b|1|
>
> remained|remained|128|1|l+b|1|
>
> remained|remained|1024|1|l+b|1|
>
> remained|remaineed|1024|1024|l+b|1|
>
>
>
>
> On Sat, Feb 11, 2017 at 2:51 AM, shahid ashraf <sh...@trialx.com> wrote:
>
> > To add more it only happens when using caspool
> >
> > On Sat, Feb 11, 2017 at 2:48 AM, Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> >> Yes, thanks. I will try to look into this a little later.
> >>
> >>
> >>
> >> Sean
> >>
> >>
> >>
> >> *From:* shahid ashraf [mailto:shahid@trialx.com]
> >> *Sent:* Friday, February 10, 2017 3:45 PM
> >> *To:* Finan, Sean
> >> *Subject:* Re: CAS Pool
> >>
> >>
> >>
> >> Are you looking for these lines
> >>
> >>
> >>
> >> 11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
> >> org/apache/ctakes/postagger/models/mayo-pos.zip
> >>
> >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - Loading NLM Norm and
> >> Lvg with config file = /Users/shahid/projects/healthn
> >> lp/examples/ctakes-web-client/target/classes/org/apache/
> >> ctakes/lvg/data/config/lvg.properties
> >>
> >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - config file
> absolute
> >> path = /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
> >> target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cwd =
> >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
> >>
> >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
> >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
> >> target/classes/org/apache/ctakes/lvg/
> >>
> >> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
> >> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
> >>
> >> 11 Feb 2017 02:14:07 INFO DrugMentionAnnotator - Finite state machines
> >> loaded.
> >>
> >>
> >>
> >> On Sat, Feb 11, 2017 at 2:01 AM, Finan, Sean <
> >> Sean.Finan@childrens.harvard.edu> wrote:
> >>
> >> Hi Shahid,
> >>
> >>
> >>
> >> Are you getting any log information from the lvg classes during
> >> initialization?
> >>
> >>
> >>
> >> Sean
> >>
> >>
> >>
> >> *From:* shahid ashraf [mailto:shahid@trialx.com]
> >> *Sent:* Friday, February 10, 2017 2:50 PM
> >> *To:* dev@ctakes.apache.org; Finan, Sean
> >> *Subject:* CAS Pool
> >>
> >>
> >>
> >>
> >> Hi
> >>
> >>
> >>
> >> I was able to create the caspool using the descriptor approach, but
> >> instead of getting ctakes blocked which was happening without caspool
> when
> >> multiple threads are ran.
> >>
> >> Currently i am getting following error:
> >>
> >>
> >>
> >> Feb 10, 2017 8:44:06 PM org.apache.uima.analysis_engin
> >> e.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(430)
> >>
> >> SEVERE: Exception occurred
> >>
> >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> >>
> >> at org.apache.ctakes.lvg.ae
> >> <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> >> .LvgAnnotator.process(LvgAnnotator.java:310)
> >>
> >> at org.apache.uima.analysis_component.JCasAnnotator_
> ImplBase.
> >> process(JCasAnnotator_ImplBase.java:48)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentPro
> >> cess(PrimitiveAnalysisEngine_impl.java:396)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes
> >> (PrimitiveAnalysisEngine_impl.java:314)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOut
> >> putCas(ASB_impl.java:570)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
> >>
> >> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> process(
> >> ASB_impl.java:344)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes
> >> (AggregateAnalysisEngine_impl.java:265)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
> >>
> >> at org.apache.uima.analysis_engin
> >> e.impl.MultiprocessingAnalysisEngine_impl.process(Multiproce
> >> ssingAnalysisEngine_impl.java:199)
> >>
> >> at org.apache.ctakes.web.client.s
> >> ervlet.DemoServlet.doPost(DemoServlet.java:135)
> >>
> >> at javax.servlet.http.HttpServlet
> >> .service(HttpServlet.java:755)
> >>
> >> at javax.servlet.http.HttpServlet
> >> .service(HttpServlet.java:848)
> >>
> >> at org.eclipse.jetty.servlet.Serv
> >> letHolder.handle(ServletHolder.java:684)
> >>
> >> at org.eclipse.jetty.servlet.Serv
> >> letHandler.doHandle(ServletHandler.java:501)
> >>
> >> at org.eclipse.jetty.server.handl
> >> er.ScopedHandler.handle(ScopedHandler.java:137)
> >>
> >> at org.eclipse.jetty.security.Sec
> >> urityHandler.handle(SecurityHandler.java:557)
> >>
> >> at org.eclipse.jetty.server.session.SessionHandler.
> doHandle(
> >> SessionHandler.java:231)
> >>
> >> at org.eclipse.jetty.server.handler.ContextHandler.
> doHandle(
> >> ContextHandler.java:1086)
> >>
> >> at org.eclipse.jetty.servlet.Serv
> >> letHandler.doScope(ServletHandler.java:428)
> >>
> >> at org.eclipse.jetty.server.session.SessionHandler.doScope(
> >> SessionHandler.java:193)
> >>
> >> at org.eclipse.jetty.server.handler.ContextHandler.doScope(
> >> ContextHandler.java:1020)
> >>
> >> at org.eclipse.jetty.server.handl
> >> er.ScopedHandler.handle(ScopedHandler.java:135)
> >>
> >> at org.eclipse.jetty.server.handl
> >> er.HandlerWrapper.handle(HandlerWrapper.java:116)
> >>
> >> at org.eclipse.jetty.server.Server.handle(Server.java:370)
> >>
> >> at org.eclipse.jetty.server.Abstr
> >> actHttpConnection.handleRequest(AbstractHttpConnection.java:494)
> >>
> >> at org.eclipse.jetty.server.Abstr
> >> actHttpConnection.content(AbstractHttpConnection.java:982)
> >>
> >> at org.eclipse.jetty.server.Abstr
> >> actHttpConnection$RequestHandler.content(AbstractHttpConnect
> >> ion.java:1043)
> >>
> >> at org.eclipse.jetty.http.HttpPar
> >> ser.parseNext(HttpParser.java:865)
> >>
> >> at org.eclipse.jetty.http.HttpPar
> >> ser.parseAvailable(HttpParser.java:240)
> >>
> >> at org.eclipse.jetty.server.Async
> >> HttpConnection.handle(AsyncHttpConnection.java:82)
> >>
> >> at org.eclipse.jetty.io.nio.Selec
> >> tChannelEndPoint.handle(SelectChannelEndPoint.java:667)
> >>
> >> at org.eclipse.jetty.io.nio.Selec
> >> tChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
> >>
> >> at org.eclipse.jetty.util.thread.
> >> QueuedThreadPool.runJob(QueuedThreadPool.java:608)
> >>
> >> at org.eclipse.jetty.util.thread.
> >> QueuedThreadPool$3.run(QueuedThreadPool.java:543)
> >>
> >> at java.lang.Thread.run(Thread.java:745)
> >>
> >> Caused by: org.apache.uima.analysis_engine.
> AnalysisEngineProcessException
> >>
> >> at org.apache.ctakes.lvg.ae
> >> <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> >> .LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
> >>
> >> at org.apache.ctakes.lvg.ae
> >> <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> >> .LvgAnnotator.annotateRange(LvgAnnotator.java:342)
> >>
> >> at org.apache.ctakes.lvg.ae
> >> <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=
> mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> >> .LvgAnnotator.process(LvgAnnotator.java:307)
> >>
> >> ... 35 more
> >>
> >> Caused by: java.lang.NullPointerException
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> with Regards
> >>
> >> Shahid Ashraf
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> with Regards
> >>
> >> Shahid Ashraf
> >>
> >
> >
> >
> > --
> > with Regards
> > Shahid Ashraf
> >
>
>
>
> --
> with Regards
> Shahid Ashraf
>
Re: CAS Pool
Posted by shahid ashraf <sh...@trialx.com>.
Hi Sean
I found the line which is causing the null pointer exception in the
ctakes-LVG..
its
*String[] output = out.split("\\|");*
*but issue seems *
String out = lvgCmd.MutateToString(word);
returns null
This only happens when running the LVG via CAS pool.
It seems it has been patched here ...
https://github.com/meikeric/ytex/blob/master/workspace/ctakes-patches/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java
.
My Question is why this happens in CAS pool (where each CAS has its own
resource.)
and seems it happens on even ... normal words ... but when testing these
words one by one on same code String out = lvgCmd.MutateToString(word); it
returns back the canonical form
Here is the log when
String out = lvgCmd.MutateToString(word) *FAILS*
WARN LvgAnnotator - mutateToString returned null for: anemia
12 Feb 2017 11:20:32 WARN LvgAnnotator - mutateToString returned null for:
remained
12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null for:
course
12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null for:
profile.
12 Feb 2017 11:20:28 WARN LvgAnnotator - mutateToString returned null for:
a
12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null for:
pre-specified
12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null for:
these
12 Feb 2017 11:20:25 WARN LvgAnnotator - mutateToString returned null for:
inhibitors
12 Feb 2017 11:20:22 WARN LvgAnnotator - mutateToString returned null for:
Many
12 Feb 2017 11:20:20 WARN LvgAnnotator - mutateToString returned null for:
if
12 Feb 2017 11:20:15 WARN LvgAnnotator - mutateToString returned null for:
third
12 Feb 2017 11:20:12 WARN LvgAnnotator - mutateToString returned null for:
Prolonged
When trying these on same code ... but single thread ... we are getting
results from LVG...
12 Feb 2017 11:49:32 INFO LvgAnnotator - process(JCas)
12 Feb 2017 11:49:32 INFO LvgAnnotator - annotate over full doc text
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
anemia|anemia|1|1|l+b|1|
anemia|anemia|2|1|l+b|1|
anemia|anemia|128|1|l+b|1|
anemia|anemia|1024|1|l+b|1|
anemia|anemion|128|512|l+b|1|
anemia|anemium|128|512|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
placebo|placebo|1|1|l+b|1|
placebo|placebo|2|1|l+b|1|
placebo|placebo|128|1|l+b|1|
placebo|placebo|1024|1|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
Prolonged|prolong|1024|1024|l+b|1|
Prolonged|prolonge|1024|1024|l+b|1|
Prolonged|prolonged|1|1|l+b|1|
Prolonged|prolonged|2|1|l+b|1|
Prolonged|prolonged|128|1|l+b|1|
Prolonged|prolonged|1024|1|l+b|1|
Prolonged|prolongeed|1024|1024|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
third|third|1|1|l+b|1|
third|third|2|1|l+b|1|
third|third|128|1|l+b|1|
third|third|1024|1|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
inhibitors|inhibitor|128|512|l+b|1|
inhibitors|inhibitor|1024|1024|l+b|1|
inhibitors|inhibitors|1|1|l+b|1|
inhibitors|inhibitors|2|1|l+b|1|
inhibitors|inhibitors|128|1|l+b|1|
inhibitors|inhibitors|1024|1|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
these|these|1|1|l+b|1|
these|these|2|1|l+b|1|
these|these|128|1|l+b|1|
these|these|1024|1|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
pre-specified|pre-specifi|1024|1024|l+b|1|
pre-specified|pre-specifie|1024|1024|l+b|1|
pre-specified|pre-specified|1|1|l+b|1|
pre-specified|pre-specified|2|1|l+b|1|
pre-specified|pre-specified|128|1|l+b|1|
pre-specified|pre-specified|1024|1|l+b|1|
pre-specified|pre-specifieed|1024|1024|l+b|1|
pre-specified|pre-specify|1024|1024|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
profile.|profile.|1|1|l+b|1|
profile.|profile.|2|1|l+b|1|
profile.|profile.|128|1|l+b|1|
profile.|profile.|1024|1|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
course|course|1|1|l+b|1|
course|course|2|1|l+b|1|
course|course|128|1|l+b|1|
course|course|1024|1|l+b|1|
12 Feb 2017 11:49:32 INFO LvgAnnotator - apply LVG processing to get
canonical form
12 Feb 2017 11:49:32 INFO LvgAnnotator - canonicalForm == null:
remained|remain|1024|1024|l+b|1|
remained|remaine|1024|1024|l+b|1|
remained|remained|1|1|l+b|1|
remained|remained|2|1|l+b|1|
remained|remained|128|1|l+b|1|
remained|remained|1024|1|l+b|1|
remained|remaineed|1024|1024|l+b|1|
On Sat, Feb 11, 2017 at 2:51 AM, shahid ashraf <sh...@trialx.com> wrote:
> To add more it only happens when using caspool
>
> On Sat, Feb 11, 2017 at 2:48 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> Yes, thanks. I will try to look into this a little later.
>>
>>
>>
>> Sean
>>
>>
>>
>> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> *Sent:* Friday, February 10, 2017 3:45 PM
>> *To:* Finan, Sean
>> *Subject:* Re: CAS Pool
>>
>>
>>
>> Are you looking for these lines
>>
>>
>>
>> 11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
>> org/apache/ctakes/postagger/models/mayo-pos.zip
>>
>> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - Loading NLM Norm and
>> Lvg with config file = /Users/shahid/projects/healthn
>> lp/examples/ctakes-web-client/target/classes/org/apache/
>> ctakes/lvg/data/config/lvg.properties
>>
>> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - config file absolute
>> path = /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
>> target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
>>
>> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cwd =
>> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
>>
>> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
>> /Users/shahid/projects/healthnlp/examples/ctakes-web-client/
>> target/classes/org/apache/ctakes/lvg/
>>
>> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
>> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
>>
>> 11 Feb 2017 02:14:07 INFO DrugMentionAnnotator - Finite state machines
>> loaded.
>>
>>
>>
>> On Sat, Feb 11, 2017 at 2:01 AM, Finan, Sean <
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>> Hi Shahid,
>>
>>
>>
>> Are you getting any log information from the lvg classes during
>> initialization?
>>
>>
>>
>> Sean
>>
>>
>>
>> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> *Sent:* Friday, February 10, 2017 2:50 PM
>> *To:* dev@ctakes.apache.org; Finan, Sean
>> *Subject:* CAS Pool
>>
>>
>>
>>
>> Hi
>>
>>
>>
>> I was able to create the caspool using the descriptor approach, but
>> instead of getting ctakes blocked which was happening without caspool when
>> multiple threads are ran.
>>
>> Currently i am getting following error:
>>
>>
>>
>> Feb 10, 2017 8:44:06 PM org.apache.uima.analysis_engin
>> e.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(430)
>>
>> SEVERE: Exception occurred
>>
>> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>>
>> at org.apache.ctakes.lvg.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> .LvgAnnotator.process(LvgAnnotator.java:310)
>>
>> at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.
>> process(JCasAnnotator_ImplBase.java:48)
>>
>> at org.apache.uima.analysis_engin
>> e.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentPro
>> cess(PrimitiveAnalysisEngine_impl.java:396)
>>
>> at org.apache.uima.analysis_engin
>> e.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes
>> (PrimitiveAnalysisEngine_impl.java:314)
>>
>> at org.apache.uima.analysis_engin
>> e.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOut
>> putCas(ASB_impl.java:570)
>>
>> at org.apache.uima.analysis_engin
>> e.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
>>
>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(
>> ASB_impl.java:344)
>>
>> at org.apache.uima.analysis_engin
>> e.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes
>> (AggregateAnalysisEngine_impl.java:265)
>>
>> at org.apache.uima.analysis_engin
>> e.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
>>
>> at org.apache.uima.analysis_engin
>> e.impl.MultiprocessingAnalysisEngine_impl.process(Multiproce
>> ssingAnalysisEngine_impl.java:199)
>>
>> at org.apache.ctakes.web.client.s
>> ervlet.DemoServlet.doPost(DemoServlet.java:135)
>>
>> at javax.servlet.http.HttpServlet
>> .service(HttpServlet.java:755)
>>
>> at javax.servlet.http.HttpServlet
>> .service(HttpServlet.java:848)
>>
>> at org.eclipse.jetty.servlet.Serv
>> letHolder.handle(ServletHolder.java:684)
>>
>> at org.eclipse.jetty.servlet.Serv
>> letHandler.doHandle(ServletHandler.java:501)
>>
>> at org.eclipse.jetty.server.handl
>> er.ScopedHandler.handle(ScopedHandler.java:137)
>>
>> at org.eclipse.jetty.security.Sec
>> urityHandler.handle(SecurityHandler.java:557)
>>
>> at org.eclipse.jetty.server.session.SessionHandler.doHandle(
>> SessionHandler.java:231)
>>
>> at org.eclipse.jetty.server.handler.ContextHandler.doHandle(
>> ContextHandler.java:1086)
>>
>> at org.eclipse.jetty.servlet.Serv
>> letHandler.doScope(ServletHandler.java:428)
>>
>> at org.eclipse.jetty.server.session.SessionHandler.doScope(
>> SessionHandler.java:193)
>>
>> at org.eclipse.jetty.server.handler.ContextHandler.doScope(
>> ContextHandler.java:1020)
>>
>> at org.eclipse.jetty.server.handl
>> er.ScopedHandler.handle(ScopedHandler.java:135)
>>
>> at org.eclipse.jetty.server.handl
>> er.HandlerWrapper.handle(HandlerWrapper.java:116)
>>
>> at org.eclipse.jetty.server.Server.handle(Server.java:370)
>>
>> at org.eclipse.jetty.server.Abstr
>> actHttpConnection.handleRequest(AbstractHttpConnection.java:494)
>>
>> at org.eclipse.jetty.server.Abstr
>> actHttpConnection.content(AbstractHttpConnection.java:982)
>>
>> at org.eclipse.jetty.server.Abstr
>> actHttpConnection$RequestHandler.content(AbstractHttpConnect
>> ion.java:1043)
>>
>> at org.eclipse.jetty.http.HttpPar
>> ser.parseNext(HttpParser.java:865)
>>
>> at org.eclipse.jetty.http.HttpPar
>> ser.parseAvailable(HttpParser.java:240)
>>
>> at org.eclipse.jetty.server.Async
>> HttpConnection.handle(AsyncHttpConnection.java:82)
>>
>> at org.eclipse.jetty.io.nio.Selec
>> tChannelEndPoint.handle(SelectChannelEndPoint.java:667)
>>
>> at org.eclipse.jetty.io.nio.Selec
>> tChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
>>
>> at org.eclipse.jetty.util.thread.
>> QueuedThreadPool.runJob(QueuedThreadPool.java:608)
>>
>> at org.eclipse.jetty.util.thread.
>> QueuedThreadPool$3.run(QueuedThreadPool.java:543)
>>
>> at java.lang.Thread.run(Thread.java:745)
>>
>> Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
>>
>> at org.apache.ctakes.lvg.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> .LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
>>
>> at org.apache.ctakes.lvg.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> .LvgAnnotator.annotateRange(LvgAnnotator.java:342)
>>
>> at org.apache.ctakes.lvg.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
>> .LvgAnnotator.process(LvgAnnotator.java:307)
>>
>> ... 35 more
>>
>> Caused by: java.lang.NullPointerException
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>
>
>
> --
> with Regards
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
Re: CAS Pool
Posted by shahid ashraf <sh...@trialx.com>.
To add more it only happens when using caspool
On Sat, Feb 11, 2017 at 2:48 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Yes, thanks. I will try to look into this a little later.
>
>
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Friday, February 10, 2017 3:45 PM
> *To:* Finan, Sean
> *Subject:* Re: CAS Pool
>
>
>
> Are you looking for these lines
>
>
>
> 11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
>
> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - Loading NLM Norm and
> Lvg with config file = /Users/shahid/projects/
> healthnlp/examples/ctakes-web-client/target/classes/org/
> apache/ctakes/lvg/data/config/lvg.properties
>
> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - config file absolute
> path = /Users/shahid/projects/healthnlp/examples/ctakes-web-
> client/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
>
> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cwd =
> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
>
> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
> /Users/shahid/projects/healthnlp/examples/ctakes-web-
> client/target/classes/org/apache/ctakes/lvg/
>
> 11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd
> /Users/shahid/projects/healthnlp/examples/ctakes-web-client
>
> 11 Feb 2017 02:14:07 INFO DrugMentionAnnotator - Finite state machines
> loaded.
>
>
>
> On Sat, Feb 11, 2017 at 2:01 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Hi Shahid,
>
>
>
> Are you getting any log information from the lvg classes during
> initialization?
>
>
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Friday, February 10, 2017 2:50 PM
> *To:* dev@ctakes.apache.org; Finan, Sean
> *Subject:* CAS Pool
>
>
>
>
> Hi
>
>
>
> I was able to create the caspool using the descriptor approach, but
> instead of getting ctakes blocked which was happening without caspool when
> multiple threads are ran.
>
> Currently i am getting following error:
>
>
>
> Feb 10, 2017 8:44:06 PM org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
> callAnalysisComponentProcess(430)
>
> SEVERE: Exception occurred
>
> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>
> at org.apache.ctakes.lvg.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> .LvgAnnotator.process(LvgAnnotator.java:310)
>
> 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:396)
>
> at org.apache.uima.analysis_engine.impl.
> PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(
> PrimitiveAnalysisEngine_impl.java:314)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
> AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
> AggregateCasIterator.<init>(ASB_impl.java:412)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> process(ASB_impl.java:344)
>
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.processAndOutputNewCASes(
> AggregateAnalysisEngine_impl.java:265)
>
> at org.apache.uima.analysis_engine.impl.
> AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
>
> at org.apache.uima.analysis_engine.impl.
> MultiprocessingAnalysisEngine_impl.process(MultiprocessingAnalysisEngine_
> impl.java:199)
>
> at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(
> DemoServlet.java:135)
>
> at javax.servlet.http.HttpServlet.service(
> HttpServlet.java:755)
>
> at javax.servlet.http.HttpServlet.service(
> HttpServlet.java:848)
>
> at org.eclipse.jetty.servlet.ServletHolder.handle(
> ServletHolder.java:684)
>
> at org.eclipse.jetty.servlet.ServletHandler.doHandle(
> ServletHandler.java:501)
>
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(
> ScopedHandler.java:137)
>
> at org.eclipse.jetty.security.SecurityHandler.handle(
> SecurityHandler.java:557)
>
> at org.eclipse.jetty.server.session.SessionHandler.
> doHandle(SessionHandler.java:231)
>
> at org.eclipse.jetty.server.handler.ContextHandler.
> doHandle(ContextHandler.java:1086)
>
> at org.eclipse.jetty.servlet.ServletHandler.doScope(
> ServletHandler.java:428)
>
> at org.eclipse.jetty.server.session.SessionHandler.
> doScope(SessionHandler.java:193)
>
> at org.eclipse.jetty.server.handler.ContextHandler.
> doScope(ContextHandler.java:1020)
>
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(
> ScopedHandler.java:135)
>
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(
> HandlerWrapper.java:116)
>
> at org.eclipse.jetty.server.Server.handle(Server.java:370)
>
> at org.eclipse.jetty.server.AbstractHttpConnection.
> handleRequest(AbstractHttpConnection.java:494)
>
> at org.eclipse.jetty.server.AbstractHttpConnection.content(
> AbstractHttpConnection.java:982)
>
> at org.eclipse.jetty.server.AbstractHttpConnection$
> RequestHandler.content(AbstractHttpConnection.java:1043)
>
> at org.eclipse.jetty.http.HttpParser.parseNext(
> HttpParser.java:865)
>
> at org.eclipse.jetty.http.HttpParser.parseAvailable(
> HttpParser.java:240)
>
> at org.eclipse.jetty.server.AsyncHttpConnection.handle(
> AsyncHttpConnection.java:82)
>
> at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(
> SelectChannelEndPoint.java:667)
>
> at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(
> SelectChannelEndPoint.java:52)
>
> at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(
> QueuedThreadPool.java:608)
>
> at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(
> QueuedThreadPool.java:543)
>
> at java.lang.Thread.run(Thread.java:745)
>
> Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
>
> at org.apache.ctakes.lvg.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> .LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
>
> at org.apache.ctakes.lvg.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> .LvgAnnotator.annotateRange(LvgAnnotator.java:342)
>
> at org.apache.ctakes.lvg.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>
> .LvgAnnotator.process(LvgAnnotator.java:307)
>
> ... 35 more
>
> Caused by: java.lang.NullPointerException
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
RE: CAS Pool
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Yes, thanks. I will try to look into this a little later.
Sean
From: shahid ashraf [mailto:shahid@trialx.com]
Sent: Friday, February 10, 2017 3:45 PM
To: Finan, Sean
Subject: Re: CAS Pool
Are you looking for these lines
11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = /Users/shahid/projects/healthnlp/examples/ctakes-web-client/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - config file absolute path = /Users/shahid/projects/healthnlp/examples/ctakes-web-client/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cwd = /Users/shahid/projects/healthnlp/examples/ctakes-web-client
11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd /Users/shahid/projects/healthnlp/examples/ctakes-web-client/target/classes/org/apache/ctakes/lvg/
11 Feb 2017 02:14:06 INFO LvgCmdApiResourceImpl - cd /Users/shahid/projects/healthnlp/examples/ctakes-web-client
11 Feb 2017 02:14:07 INFO DrugMentionAnnotator - Finite state machines loaded.
On Sat, Feb 11, 2017 at 2:01 AM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Hi Shahid,
Are you getting any log information from the lvg classes during initialization?
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Friday, February 10, 2017 2:50 PM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>; Finan, Sean
Subject: CAS Pool
Hi
I was able to create the caspool using the descriptor approach, but instead of getting ctakes blocked which was happening without caspool when multiple threads are ran.
Currently i am getting following error:
Feb 10, 2017 8:44:06 PM org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(430)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>.LvgAnnotator.process(LvgAnnotator.java:310)
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:396)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at org.apache.uima.analysis_engine.impl.MultiprocessingAnalysisEngine_impl.process(MultiprocessingAnalysisEngine_impl.java:199)
at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(DemoServlet.java:135)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:501)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:667)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException
at org.apache.ctakes.lvg.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>.LvgAnnotator.setCanonicalForm(LvgAnnotator.java:372)
at org.apache.ctakes.lvg.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>.LvgAnnotator.annotateRange(LvgAnnotator.java:342)
at org.apache.ctakes.lvg.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.lvg.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZDqfnqc8s6SO7UnXkW_LfiKDd3-1jgYMVLoLMdCrVC8&s=mz9hN1V1RYm97GOnmPU3P52EoPoye6lBvN6AhIFsTL8&e=>.LvgAnnotator.process(LvgAnnotator.java:307)
... 35 more
Caused by: java.lang.NullPointerException
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf