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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: errors when run BagOfCUIsGenerator.java
Date Thu, 24 Apr 2014 21:25:12 GMT
Have you figured this one out? It looks like it's having trouble finding
a class that maven should download? Maybe check your .m2/repository
directory and see if it has the path org/springframework/spring-beans?
Tim


On 04/22/2014 05:54 PM, Liu, Ying wrote:
> I installed cTAKES on another computer and ran the same code. I think this time is not
because UMLS username/password. I couldn't figure out why. Thank you for your help!
> Ying
>
>
> Exception in thread "main" java.lang.NoClassDefFoundError: org/springframework/beans/TypeMismatchException
> 	at org.uimafit.factory.ResourceCreationSpecifierFactory.createResourceCreationSpecifier(ResourceCreationSpecifierFactory.java:72)
> 	at org.uimafit.factory.ResourceCreationSpecifierFactory.createResourceCreationSpecifier(ResourceCreationSpecifierFactory.java:96)
> 	at org.uimafit.factory.CollectionReaderFactory.createCollectionReaderFromPath(CollectionReaderFactory.java:75)
> 	at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:40)
> 	at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:36)
> 	at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:16)
> 	at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:49)
> Caused by: java.lang.ClassNotFoundException: org.springframework.beans.TypeMismatchException
> 	at java.net.URLClassLoader$1.run(Unknown Source)
> 	at java.net.URLClassLoader$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at java.net.URLClassLoader.findClass(Unknown Source)
> 	at java.lang.ClassLoader.loadClass(Unknown Source)
> 	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> 	at java.lang.ClassLoader.loadClass(Unknown Source)
> 	... 7 more
> Caused by: java.util.zip.ZipException: invalid LOC header (bad signature)
> 	at java.util.zip.ZipFile.read(Native Method)
> 	at java.util.zip.ZipFile.access$1400(Unknown Source)
> 	at java.util.zip.ZipFile$ZipFileInputStream.read(Unknown Source)
> 	at java.util.zip.ZipFile$ZipFileInflaterInputStream.fill(Unknown Source)
> 	at java.util.zip.InflaterInputStream.read(Unknown Source)
> 	at java.util.jar.Manifest$FastInputStream.fill(Unknown Source)
> 	at java.util.jar.Manifest$FastInputStream.readLine(Unknown Source)
> 	at java.util.jar.Manifest$FastInputStream.readLine(Unknown Source)
> 	at java.util.jar.Attributes.read(Unknown Source)
> 	at java.util.jar.Manifest.read(Unknown Source)
> 	at java.util.jar.Manifest.<init>(Unknown Source)
> 	at java.util.jar.JarFile.getManifestFromReference(Unknown Source)
> 	at java.util.jar.JarFile.getManifest(Unknown Source)
> 	at sun.misc.URLClassPath$JarLoader$2.getManifest(Unknown Source)
> 	at java.net.URLClassLoader.defineClass(Unknown Source)
> 	at java.net.URLClassLoader.access$100(Unknown Source)
> 	... 14 more
>
>
>
>
>
> ________________________________________
> From: Liu, Ying [LiuY@advisory.com]
> Sent: Wednesday, April 16, 2014 10:57 AM
> To: dev@ctakes.apache.org
> Subject: RE: errors when run BagOfCUIsGenerator.java
>
> Sorry bother the email list. The problem is caused by my VPN connection. I connected
to VPN and it didn't allow me to access any other website. So, my UMLS username and password
didn't get through.
>
> Thanks,
> Ying
>
>
> ________________________________________
> From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
> Sent: Wednesday, April 16, 2014 10:30 AM
> To: dev@ctakes.apache.org
> Subject: RE: errors when run BagOfCUIsGenerator.java
>
> Try to open  https://uts-ws.nlm.nih.gov
> If that works then try https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser and
see if you get a message like
> "This XML file does not appear to have any style information associated with it. The
document tree is shown below."
>
>
> If that works and you are comfortable with the code, try with
> umlsaddr : https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser
> vendor : NLM-6515182895
>
>
>    /**
>     * @param umlsaddr -
>     * @param vendor   -
>     * @param username -
>     * @param password -
>     * @return true if the server at umlsaddr approves of the vendor, user, password combination
>     */
>    public static boolean isValidUMLSUser( final String umlsaddr, final String vendor,
>                                           final String username, final String password
) {
>       String data;
>       try {
>          data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "=" + URLEncoder.encode(
vendor, "UTF-8" );
>          data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "=" + URLEncoder.encode(
username, "UTF-8" );
>          data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "=" + URLEncoder.encode(
password, "UTF-8" );
>       } catch ( UnsupportedEncodingException unseE ) {
>          LOGGER.error( "Could not encode URL for " + username + " with vendor license
" + vendor );
>          return false;
>       }
>       try {
>          final URL url = new URL( umlsaddr );
>          final URLConnection connection = url.openConnection();
>          connection.setDoOutput( true );
>          final OutputStreamWriter writer = new OutputStreamWriter( connection.getOutputStream()
);
>          writer.write( data );
>          writer.flush();
>          boolean result = false;
>          final BufferedReader reader = new BufferedReader( new InputStreamReader( connection.getInputStream()
) );
>          String line;
>          while ( (line = reader.readLine()) != null ) {
>             final String trimline = line.trim();
>             if ( trimline.isEmpty() ) {
>                break;
>             }
>             result = trimline.equalsIgnoreCase( "<Result>true</Result>" );
>          }
>          writer.close();
>          reader.close();
>          return result;
>       } catch ( IOException ioE ) {
>          LOGGER.error( ioE.getMessage() );
>          return false;
>       }
>    }
>
>
>
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Wednesday, April 16, 2014 1:25 PM
> To: dev@ctakes.apache.org
> Subject: RE: errors when run BagOfCUIsGenerator.java
>
> Ying,
> Are you behind a proxy or firewall?
> If you're trying to use the umls resources, it attempts to make a call to their umls
service to validate your credentials.
> --Pei
>
>> -----Original Message-----
>> From: Liu, Ying [mailto:LiuY@advisory.com]
>> Sent: Wednesday, April 16, 2014 1:13 PM
>> To: dev@ctakes.apache.org
>> Subject: errors when run BagOfCUIsGenerator.java
>>
>> It failed when run BagOfCUIsGenerator.java. The followings are the
>> error information. Thanks for your help.
>> Ying
>>
>>
>>
>> Exception in thread "main"
>> org.apache.uima.resource.ResourceInitializationException:
>> Initialization of annotator class
>> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
>> failed.  (Descriptor:
>> file:/C:/Users/Ying/workspacectakes/ctakes/ctakes-
>> dictionary-
>> lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
>>     at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
>> ialize
>> AnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>     at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
>> ialize
>> (PrimitiveAnalysisEngine_impl.java:156)
>>     at
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
>> i
>> sEngineFactory_impl.java:94)
>>     at
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
>> ompositeResourceFactory_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:
>> 25
>> 4)
>>     at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
>> AS
>> B(AggregateAnalysisEngine_impl.java:431)
>>     at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
>> ializ
>> eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>     at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
>> ializ
>> e(AggregateAnalysisEngine_impl.java:185)
>>     at
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
>> i
>> sEngineFactory_impl.java:94)
>>     at
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
>> ompositeResourceFactory_impl.java:62)
>>     at
>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
>> 269)
>>     at
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
>> .java:354)
>>     at
>> org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath
>> (An
>> alysisEngineFactory.java:147)
>>     at
>> org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<
>> init
>>> (BagOfAnnotationsGenerator.java:42)
>>     at
>> org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<
>> init
>>> (BagOfAnnotationsGenerator.java:36)
>>     at
>> org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.<init>(B
>> agOf
>> CUIsGenerator.java:16)
>>     at
>> org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(Bag
>> Of
>> CUIsGenerator.java:49)
>> Caused by: org.apache.uima.resource.ResourceInitializationException
>>     at
>> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.i
>> niti
>> alize(UmlsDictionaryLookupAnnotator.java:79)
>>     at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
>> ialize
>> AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>     ... 18 more
>> Caused by: java.net.ConnectException: Connection timed out: connect
>>     at java.net.DualStackPlainSocketImpl.connect0(Native Method)
>>     at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
>>     at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
>>     at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
>>     at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
>>     at java.net.PlainSocketImpl.connect(Unknown Source)
>>     at java.net.SocksSocketImpl.connect(Unknown Source)
>>     at java.net.Socket.connect(Unknown Source)
>>     at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
>>     at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
>>     at sun.net.NetworkClient.doConnect(Unknown Source)
>>     at sun.net.www.http.HttpClient.openServer(Unknown Source)
>>     at sun.net.www.http.HttpClient.openServer(Unknown Source)
>>     at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
>>     at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
>>     at
>> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNew
>> HttpClient(Unknown Source)
>>     at
>> sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown
>> Source)
>>     at
>> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(
>> Unknown Source)
>>     at
>> sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknow
>> n Source)
>>     at
>> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Un
>> known Source)
>>     at
>> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.i
>> sV
>> alidUMLSUser(UmlsDictionaryLookupAnnotator.java:93)
>>     at
>> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.i
>> niti
>> alize(UmlsDictionaryLookupAnnotator.java:70)
>>     ... 19 more
>>
>>
>>
>
>
>

-- 
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu
617-919-1223


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