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 <[email protected]> wrote:
> To add more it only happens when using caspool
>
> On Sat, Feb 11, 2017 at 2:48 AM, Finan, Sean <
> [email protected]> wrote:
>
>> Yes, thanks. I will try to look into this a little later.
>>
>>
>>
>> Sean
>>
>>
>>
>> *From:* shahid ashraf [mailto:[email protected]]
>> *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 <
>> [email protected]> wrote:
>>
>> Hi Shahid,
>>
>>
>>
>> Are you getting any log information from the lvg classes during
>> initialization?
>>
>>
>>
>> Sean
>>
>>
>>
>> *From:* shahid ashraf [mailto:[email protected]]
>> *Sent:* Friday, February 10, 2017 2:50 PM
>> *To:* [email protected]; 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
