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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Date Fri, 27 Mar 2015 18:23:52 GMT
Yes, there is a null check near it but in a different method. I'm a
little confused though because his line numbers do align with the most
current version.

Anyways, Hoang, here are your options:
1) If you have the src distribution you can insert a null check yourself
based on the one in trunk and rebuild ctakes
2) If you have the bin distribution
 a) upgrade to a newer version
 b) Modify the descriptor to make the attribute classifiers not run

Anything I missed?

What's probably happening is that your dictionary is finding an
entity/event that the default dictionary doesn't, and there is a null
pointer in the dependency parse for that new entity.

Tim

On 03/27/2015 02:12 PM, Pei Chen wrote:
> Hoang,
> 3.0 was released a long time ago (02/2013).  (according to the tag/history,
> it did't have the null fix until 6/2013 3.1?)
> https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D3.0.0-2Dincubating_ctakes-2Ddependency-2Dparser_src_main_java_org_apache_ctakes_dependency_parser_util_DependencyUtility.java&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=lwkep42G2WNYF08UZTv_xXc3EX-jrqv-lnvHAIOTrFQ&s=W8vWGifRf7UeJlqO4n3TpeldqHKshhov_E9VwNlqqj4&e=

>
>
> On Fri, Mar 27, 2015 at 1:46 PM, Pham, Hoang <HPham@tuftsmedicalcenter.org>
> wrote:
>
>> To Timothy,
>>
>> Sorry, I misspell your name before.
>>
>> Thank You,
>>
>> Hoang Pham
>>
>>
>> -----Original Message-----
>> From: Pham, Hoang [mailto:HPham@tuftsmedicalcenter.org]
>> Sent: Fri 3/27/2015 1:38 PM
>> To: dev@ctakes.apache.org
>> Subject: RE: Ctakes Null Pointer Error for
>> org.apache.ctakes.dependency.parser.util.DependencyUtility
>>
>> To Tomothy,
>>
>> I have cTakes 3.0 install. I looked at the class and there is a null check
>> but for some reason, it is not catching. Also, when I use the indexes that
>> came with cTakes install, the program would parse without any errors.
>>
>> Thank You,
>>
>> Hoang Pham
>>
>>
>> -----Original Message-----
>> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
>> Sent: Fri 3/27/2015 9:38 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: Ctakes Null Pointer Error for
>> org.apache.ctakes.dependency.parser.util.DependencyUtility
>>
>> Hi Hoang,
>> Can you let me know what version of cTAKES you're using? I looked in
>> that location in trunk and found a null check, so it could be that it's
>> a bug that's been fixed already. In the meantime, if you just want to
>> see if your dictionary is working right, you could disable the
>> SubjectAttributeClassifier which seems to be the annotator where this
>> error is coming from. Some of the other attributes rely on dependency
>> features as well so you might disable them temporarily as well.
>> Tim
>>
>>
>> On 03/27/2015 08:32 AM, Pham, Hoang wrote:
>>> Hi All,
>>>
>>> I am trying to add my own dictionary to cTakes. I have added a lucene
>> index for the dictionary, but when the index is added, I would receive a
>> null pointer exception for the
>> org.apache.ctakes.dependency.parser.util.DependencyUtility class.
>>> The stack trace is:
>>>
>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
>> callAnalysisComponentProcess(407)
>>> SEVERE: Exception occurred
>>> org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>> Annotator processing failed.
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
>>>         at Parsing.main(Parsing.java:49)
>>> Caused by: java.lang.NullPointerException
>>>         at
>> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
>>>         at
>> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
>>>         at
>> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
>>>         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:375)
>>>         ... 13 more
>>>
>>> Mar 27, 2015 8:29:54 AM
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
>> processAndOutputNewCASes(275)
>>> SEVERE: Exception occurred
>>> org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>> Annotator processing failed.
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
>>>         at Parsing.main(Parsing.java:49)
>>> Caused by: java.lang.NullPointerException
>>>         at
>> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
>>>         at
>> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
>>>         at
>> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
>>>         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:375)
>>>         ... 13 more
>>>
>>> Mar 27, 2015 8:29:54 AM
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
>> processAndOutputNewCASes(275)
>>> SEVERE: Exception occurred
>>> org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>> Annotator processing failed.
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
>>>         at Parsing.main(Parsing.java:49)
>>> Caused by: java.lang.NullPointerException
>>>         at
>> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
>>>         at
>> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
>>>         at
>> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
>>>         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:375)
>>>         ... 13 more
>>>
>>> org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>> Annotator processing failed.
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
>>>         at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
>>>         at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
>>>         at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>>>         at
>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
>>>         at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
>>>         at Parsing.main(Parsing.java:49)
>>> Caused by: java.lang.NullPointerException
>>>         at
>> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
>>>         at
>> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
>>>         at
>> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
>>>         at
>> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
>>>         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:375)
>>>         ... 13 more
>>>
>>> Thank You,
>>>
>>> Hoang Pham
>>> The information in this e-mail is intended only for the person to whom
>> it is addressed. If you believe this e-mail was sent to you in error and
>> the e-mail contains patient information, please contact the Tufts Medical
>> Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in
>> error but does not contain patient information, please contact the sender
>> and properly dispose of the e-mail.
>>
>> The information in this e-mail is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Tufts Medical
>> Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in
>> error but does not contain patient information, please contact the sender
>> and properly dispose of the e-mail.
>>
>> The information in this e-mail is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Tufts Medical
>> Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in
>> error but does not contain patient information, please contact the sender
>> and properly dispose of the e-mail.
>>


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