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 [[email protected]]
Sent: Wednesday, April 16, 2014 10:57 AM
To: [email protected]
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 [[email protected]]
Sent: Wednesday, April 16, 2014 10:30 AM
To: [email protected]
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:[email protected]]
Sent: Wednesday, April 16, 2014 1:25 PM
To: [email protected]
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:[email protected]]
> Sent: Wednesday, April 16, 2014 1:13 PM
> To: [email protected]
> 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
>
>
>
