Tomcat errors about ctakes-rest-service

[MatthewVita]

Team is re-engaging with the project. Going to sort this out in other issues.

[MatthewVita]

@gandhirajan Looks like this has to do with LabValueFinder, right?

[MatthewVita]

Looks like I may be screwing something up with my local piper configs. Really not up to date on those :) Still in XML mode :)

[MatthewVita]

If I remove LabValueFinder from piper, I get a bit further, but this is the new error:

11 Feb 2018 19:23:16  WARN XmlWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: Error initializing "org.apache.ctakes.core.ae.BsvRegexSectionizer" from descriptor <unknown>.
11 Feb 2018 19:23:16 ERROR DispatcherServlet - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: Error initializing "org.apache.ctakes.core.ae.BsvRegexSectionizer" from descriptor <unknown>.
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
	at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
	at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
	at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
	at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
	at javax.servlet.GenericServlet.init(GenericServlet.java:158)
	at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1174)
	at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1090)
	at org.apache.catalina.core.StandardWrapper.allocate(StandardWrapper.java:770)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:133)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:651)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
	at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:417)
	at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
	at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:754)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1376)
	at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:748)
Caused by: javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: Error initializing "org.apache.ctakes.core.ae.BsvRegexSectionizer" from descriptor <unknown>.
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:98)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:85)
	at org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:60)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
	... 38 more
Caused by: org.apache.uima.resource.ResourceInitializationException: Error initializing "org.apache.ctakes.core.ae.BsvRegexSectionizer" from descriptor <unknown>.
	at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:139)
	at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:94)
	... 47 more
Caused by: org.apache.uima.resource.ResourceConfigurationException: No value has been assigned to the mandatory configuration parameter SectionsBsv.
	at org.apache.uima.resource.impl.ConfigurationManagerImplBase.validateConfigurationParameterSettings(ConfigurationManagerImplBase.java:540)
	at org.apache.uima.resource.impl.ConfigurationManagerImplBase.validateConfigurationParameterSettings(ConfigurationManagerImplBase.java:492)
	at org.apache.uima.resource.impl.ConfigurationManagerImplBase.createContext(ConfigurationManagerImplBase.java:146)
	at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:135)
	... 62 more

[gandhirajan]

@MatthewVita I am not sure with the issues above. But i could guess there could be some problem with the resources you are using. Is it all latest?

An other reason could be you may have to build the latest ctakes code base again from SVN.

[MatthewVita]

@gandhirajan I'm using this SVN: https://svn.apache.org/repos/asf/ctakes/branches/ctakes-4.0.0/

I may be a few days behind since my last build, but is the right branch?

[gandhirajan]

@MatthewVita Hi Matt, I m actually on trunk not on branch. My SVN codebase path is https://svn.apache.org/repos/asf/ctakes/trunk which has all latest changes

[MatthewVita]

@gandhirajan ohhhhh

[MatthewVita]

@gandhirajan:

We'll have to lock down a git commit hash (or whatever the equivalent concept is in SVN), but this got things to work a bit better. However, I'm seeing this issue:

Nothing is coming back :) but the catalina logs look ok.

This is using my custom dictionary GUI mysql tool in this repo. If you look at my umls schema, you get:

mysql> show tables;
+----------------+
| Tables_in_umls |
+----------------+
| cui_terms      |
| icd10pcs       |
| prefterm       |
| tui            |
+----------------+

In the startup of our web service I see:

14 Feb 2018 22:40:18  INFO JdbcConnectionFactory - Connecting to jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&characterEncoding=utf8&useSSL=false:
..
14 Feb 2018 22:40:19  INFO JdbcConnectionFactory -  Database connected
14 Feb 2018 22:40:19  INFO JdbcRareWordDictionary - Connected to cui and term table CUI_TERMS
14 Feb 2018 22:40:19  INFO JdbcConceptFactory - Connected to concept table TUI with class TUI
14 Feb 2018 22:40:19 ERROR JdbcConceptFactory - Table RXNORMTABLE and/or RXNORM not found in Database
14 Feb 2018 22:40:19  INFO JdbcConceptFactory - Connected to concept table PREFTERM with class PREFTERM
14 Feb 2018 22:40:19 ERROR JdbcConceptFactory - Table SNOMEDCT_USTABLE and/or SNOMEDCT_US not found in Database
14 Feb 2018 22:40:19 ERROR JdbcConceptFactory - Table MDRTABLE and/or MDR not found in Database
14 Feb 2018 22:40:19  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip

Thoughts?

BTW, if you'd like to try out my dictionary creator thing for yourself, I can walk you through the setup. It's not formally documented yet :).

[MatthewVita]

It does look like I'm getting the Results.xml from ByteArrayOutputStream in the relative directory though.

[MatthewVita]

Looks like the analysis text String is coming in as pipeline=Default&Enter+your+text+for+analysis so when it gets passed to the PipelineRunner.process method, it isn't a very well-formed search term.

[MatthewVita]

Hmm, even when I hardcode in a term ("pain" or "diabetes") the results are still not good**. Catalina output on the request looks ok though:

** meaning, I get this:

Text analyzed successfully !!! Response JSON - {"AnatomicalSiteMention":{},"MedicationMention":{},"DrugChangeStatusAnnotation":{},"StrengthAnnotation":{},"FractionStrengthAnnotation":{},"FrequencyUnitAnnotation":{},"DiseaseDisorderMention":{},"SignSymptomMention":{},"RouteAnnotation":{},"DateAnnotation":{},"MeasurementAnnotation":{},"ProcedureMention":{},"TimeMention":{},"StrengthUnitAnnotation":{}}

14 Feb 2018 23:20:48  INFO SentenceDetector - Starting processing.
14 Feb 2018 23:20:48  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 Feb 2018 23:20:48  INFO ContextDependentTokenizerAnnotator - process(JCas)
14 Feb 2018 23:20:48  INFO POSTagger - process(JCas)
14 Feb 2018 23:20:48  INFO Chunker -  process(JCas)
14 Feb 2018 23:20:48  INFO ChunkAdjuster -  process(JCas)
14 Feb 2018 23:20:48  INFO ChunkAdjuster -  process(JCas)
14 Feb 2018 23:20:48  INFO AbstractJCasTermAnnotator - Finding Named Entities ...
14 Feb 2018 23:20:48  INFO AbstractJCasTermAnnotator - Finished processing
14 Feb 2018 23:20:48  INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8080-exec-10
14 Feb 2018 23:20:48  INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8080-exec-10
14 Feb 2018 23:20:48  INFO CleartkAnalysisEngine - Assigning Attributes ...
14 Feb 2018 23:20:48  INFO CleartkAnalysisEngine - Finished Assigning Attributes

Will look more into it tomorrow.

I'm not super well informed on the pipeline classes and how they work. Surely more debugging will make this clear :)

[gandhirajan]

Hi Matt, can you give it a try with REST client. Also if you could send me db script file for MySQL and the custom dictionary XML file, I can give a try from my side

[MatthewVita]

Okay @gandhirajan, I'm off to bed now, but the basics are:

ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml:

<?xml version="1.0" encoding="UTF-8"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one
or more contributor license agreements.  See the NOTICE file
distributed with this work for additional information
regarding copyright ownership.  The ASF licenses this file
to you under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License.  You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, either express or implied.  See the License for the
specific language governing permissions and limitations
under the License.
-->

<!--    New format for the .xml lookup specification.  Uses table name and value type/class for Concept Factories.  -->
<lookupSpecification>
<dictionaries>
   <dictionary>
      <name>customDictionaryTerms</name>
      <implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary</implementationName>
      <properties>
<!-- urls for hsqldb memory connections must be file types in hsql 1.8.
These file urls must be either absolute path or relative to current working directory.
They cannot be based upon the classpath.
Though JdbcConnectionFactory will attempt to "find" a db based upon the parent dir of the url
for the sake of ide ease-of-use, the user should be aware of these hsql limitations.
-->
         <property key="jdbcDriver" value="com.mysql.jdbc.Driver"/>
         <property key="jdbcUrl" value="jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&amp;characterEncoding=utf8&amp;useSSL=false"/>
         <property key="jdbcUser" value="root"/>
         <property key="jdbcPass" value="root"/>
         <property key="rareWordTable" value="cui_terms"/>
         <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
         <property key="umlsVendor" value="NLM-6515182895"/>
         <property key="umlsUser" value="CHANGE_ME"/>
         <property key="umlsPass" value="CHANGE_ME"/>
      </properties>
   </dictionary>
</dictionaries>

<conceptFactories>
   <conceptFactory>
      <name>customDictionaryConcepts</name>
      <implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
      <properties>
         <property key="jdbcDriver" value="com.mysql.jdbc.Driver"/>
         <property key="jdbcUrl" value="jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&amp;characterEncoding=utf8&amp;useSSL=false"/>
         <property key="jdbcUser" value="root"/>
         <property key="jdbcPass" value="root"/>
         <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
         <property key="umlsVendor" value="NLM-6515182895"/>
         <property key="umlsUser" value="CHANGE_ME"/>
         <property key="umlsPass" value="CHANGE_ME"/>
         <property key="tuiTable" value="tui"/>
         <property key="prefTermTable" value="prefTerm"/>
<!-- Optional tables for optional term info.
Uncommenting these lines alone may not persist term information;
persistence depends upon the TermConsumer.  -->
         <property key="rxnormTable" value="long"/>
         <property key="snomedct_usTable" value="long"/>
         <property key="mdrTable" value="long"/>
      </properties>
   </conceptFactory>
</conceptFactories>

<!--  Defines what terms and concepts will be used  -->
<dictionaryConceptPairs>
   <dictionaryConceptPair>
      <name>customDictionaryPair</name>
      <dictionaryName>customDictionaryTerms</dictionaryName>
      <conceptFactoryName>customDictionaryConcepts</conceptFactoryName>
   </dictionaryConceptPair>
</dictionaryConceptPairs>

<!-- DefaultTermConsumer will persist all spans.
PrecisionTermConsumer will only persist only the longest overlapping span of any semantic group.
SemanticCleanupTermConsumer works as Precision** but also removes signs/sympoms contained within disease/disorder,
and (just in case) removes any s/s and d/d that are also (exactly) anatomical sites. -->
<rareWordConsumer>
   <name>Term Consumer</name>
   <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
   <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>-->
   <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer</implementationName>-->
   <properties>
<!-- Depending upon the consumer, the value of codingScheme may or may not be used.  With the packaged consumers,
codingScheme is a default value used only for cuis that do not have secondary codes (snomed, rxnorm, etc.)  -->
         <property key="codingScheme" value="customDictionary"/>
   </properties>
</rareWordConsumer>

</lookupSpecification>

And I have built these tables by using my MySQL dictionary builder. Here's how to install this on Mac/Linux:

1. Pull latest code here
2. cd into the repo
3. mkdir ctakes-codebase-area
4. Run

svn ls 'https://svn.apache.org/repos/asf/ctakes/trunk/' | parallel svn export 'https://svn.apache.org/repos/asf/ctakes/trunk/'{}
#svn ls 'https://svn.apache.org/repos/asf/ctakes/branches/ctakes-4.0.0/' | parallel svn export 'https://svn.apache.org/repos/asf/ctakes/branches/ctakes-4.0.0/'{}

cp ../mysql-dictionary-gui/ctakes-distribution/src/main/assembly/bin.xml ctakes-distribution/src/main/assembly/bin.xml
cp ../mysql-dictionary-gui/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/*.java ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/
cp ../mysql-dictionary-gui/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/*.java ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/
cp ../mysql-dictionary-gui/ctakes-gui/pom.xml ctakes-gui/
mvn install -DskipTests

5. Make sure you have a fresh/empty MySQL schema named umls and the user/pass are root/root (just for dev/testing)

6. cd in ctakes-codebase-area/ctakes-distribution and unzip the apache-ctakes-4.0.1-SNAPSHOT-bin.zip

7. Go into the bin and run runDictionaryCreator.sh

8. Select UMLS install/select MySQL in the middle and build

9. Build our rest service and test :)

[MatthewVita]

Of course this is not amazingly well documented yet, but it should work if you're on Linux/Mac. Again, mysql-dictionary-gui of this repo is where the dictionary gets created and saved into MySQL

[MatthewVita]

@gandhirajan BTW, I am working on creating a org.apache.ctakes.gui.dictionary.DictionaryXmlWriter class that is MySQL-friendly. Thank you again for pointing out this issue.

[jbham]

Hey @MatthewVi -

After trying to figure out how to get up and running with ctakes rest service and not being able to get any where (due to my limited understanding/knowledge), I have a humble request: is it possible to update the Docker File setup with these findings/instruction or perhaps complete it with MYSQL dictionary? The reason I ask this is because if I run docker-compose up and try to perform GET on the URL, it gives me 404 saying that resource not found. Any help you could provide would be very helpful.

Thank you for your time!!

[MatthewVita]

Hi @legendactivated,

Sorry for the mess. We did note that it's alpha software on the README (our team has been on a hiatus from it - temporary, I'm sure). However, we have been working with people in the cTAKES community to spin it up and use it - sort of confusing :).

What you are asking about is the end goal. I would be able to coach you through how to finish the feature off if you're interested. Please let me know.

Thanks,
Matthew

[ultragen74]

Hi @MatthewVi is it resolved? Because I am facing the same issue of no results.

[ultragen74]

NO RESULTS :(

[jbham]

@ultragen74 - Try making a POST call using a tool like Postman, you should be able to see a valid response. I was getting the same thing for some of the text was I was pasting in the UI. But, Postman call worked and got a nicely formatted json response.

[ultragen74]

@legendactivated Thanks for your reply

But still I have the same problem.

[jbham]

Please make a call to:

http://<your_ip>:8080/ctakes-web-rest/service/analyze?pipeline=Full

In body, click raw >> type text >> click Send. You should see something.

You are passing pipeline in the body, instead, you would need to send it as query parameter ( as part of the url ).

[ultragen74]

@legendactivated
Can you please test: http://67.205.136.87:8080/ctakes-web-rest/service/analyze?pipeline=Full

[jbham]

I believe you would have to pass actual sentences to CTAKES. I don't believe it is suppose to work on single words like Cancer, I could be wrong. To verify whether something is medical related term, you can just use stand alone UMLS dictionary.

[ultragen74]

Still the Same

[jbham]

Hmm ... not sure then. This would be beyond me.

But, if I have to guess then it is not finding anything useful info in that paragraph except for measurement values.

[MatthewVita]

@ultragen74 Are you using the standard MySQL scripts found in this repo?

[ultragen74]

Hi @MatthewVi yes i using standard mysql script which is in the repo.

100% installed as per the readme file.

[ultragen74]

@legendactivated Following should the output as per ctakes

[ultragen74]

[ultragen74]

Hi All - Any help regarding this query?

[gandhirajan]

@ultragen74 I need to bring up my old Dev setup and check this. Will get back on this

[gandhirajan]

@ultragen74 I was able to get proper response for just the text - 'Cancer' The output is as follows:

Text analyzed successfully !!! Response JSON - {"AnatomicalSiteMention":{},"MedicationMention":{},"DrugChangeStatusAnnotation":{},"StrengthAnnotation":{},"FractionStrengthAnnotation":{},"FrequencyUnitAnnotation":{},"DiseaseDisorderMention":{"CANCER":["start: 17","end: 23","polarity: 1","[codingScheme: MDR, code: 10026655, cui: C0006826, tui: T191]","[codingScheme: SNOMEDCT_US, code: 363346000, cui: C0006826, tui: T191]","[codingScheme: MDR, code: 10007050, cui: C0006826, tui: T191]","[codingScheme: MDR, code: 10073835, cui: C0006826, tui: T191]","[codingScheme: MDR, code: 10028997, cui: C0006826, tui: T191]","[codingScheme: MDR, code: 10049516, cui: C0006826, tui: T191]"]},"SignSymptomMention":{},"RouteAnnotation":{},"DateAnnotation":{},"MeasurementAnnotation":{},"ProcedureMention":{},"TimeMention":{},"StrengthUnitAnnotation":{}}

Request you to check you DB connectivity and restart the application once and try

[ultragen74]

@gandhirajan Thanks for the reply!

Have you tested above output on my API? if yes, then let me know how you did it.
Otherwise, this is the API URL: http://67.205.136.87:8080/ctakes-web-rest/service/analyze?pipeline=Full

Can you please help me with achieving results for Ctakes.

[jawad-nafad]

Hi everyone,
I am trying this in windows version and I am capable to view the web page but I am getting internal server error. I am also a beginner, so probably missing out something silly, Could anyone please give me direction to sort it out? Thanks in advance. The errors are as follows: