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Posted to dev@ctakes.apache.org by "Liu, Ying" <Li...@advisory.com> on 2014/04/16 19:12:06 UTC
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.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath(AnalysisEngineFactory.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>(BagOfCUIsGenerator.java:16)
at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:49)
Caused by: org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:79)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(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.getNewHttpClient(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(Unknown Source)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:93)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:70)
... 19 more
Re: errors when run BagOfCUIsGenerator.java
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
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
RE: errors when run BagOfCUIsGenerator.java
Posted by "Liu, Ying" <Li...@advisory.com>.
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
>
>
>
RE: errors when run BagOfCUIsGenerator.java
Posted by "Liu, Ying" <Li...@advisory.com>.
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
>
>
>
RE: errors when run BagOfCUIsGenerator.java
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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
>
>
>
RE: errors when run BagOfCUIsGenerator.java
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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.initialize
> AnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
> (PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi
> 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.initAS
> B(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ
> eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ
> e(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi
> 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>(BagOf
> CUIsGenerator.java:16)
> at
> org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOf
> CUIsGenerator.java:49)
> Caused by: org.apache.uima.resource.ResourceInitializationException
> at
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initi
> alize(UmlsDictionaryLookupAnnotator.java:79)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
> 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.isV
> alidUMLSUser(UmlsDictionaryLookupAnnotator.java:93)
> at
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initi
> alize(UmlsDictionaryLookupAnnotator.java:70)
> ... 19 more
>
>
>