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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 14:35:21 GMT
Joshua,
By any chance, are you behind a firewall or proxy server?

This annotator essentially tries to connect to the UMLS web service[1] to validate your credentials/license...


[1] https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser


--Pei

From: joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Tuesday, December 24, 2013 9:30 AM
To: user@ctakes.apache.org
Subject: Re: Adding UMLS username and password ....

Here is what the log file says... hopefully this drives to the answer..

12/24/13 9:26:58 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
failed.  (Descriptor: file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed.  (Descriptor:
file:/C:/apache-ctakes-3.1.0/desc/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.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
          at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
          at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.AbstractButton.doClick(Unknown Source)
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
          at java.awt.EventQueue.access$200(Unknown Source)
          at java.awt.EventQueue$3.run(Unknown Source)
          at java.awt.EventQueue$3.run(Unknown Source)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
          at java.awt.EventQueue$4.run(Unknown Source)
          at java.awt.EventQueue$4.run(Unknown Source)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.run(Unknown Source)
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)
          ... 54 more
Caused by: java.net.ConnectException: connect: Address is invalid on local machine, or port
is not valid on remote machine
          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)
          ... 55 more


On Tue, Dec 24, 2013 at 12:22 AM, Karthik Sarma <ksarma@ksarma.com<mailto:ksarma@ksarma.com>>
wrote:
Hmm looks like there actually might be a typo in the descriptor -- it had to be modified to
set for UMLS. Check the aggregate processor xml file for the typo





--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical Association
ksarma@ksarma.com<mailto:ksarma@ksarma.com>
gchat: ksarma@gmail.com<mailto:ksarma@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>

On Mon, Dec 23, 2013 at 10:28 PM, Pei Chen <chenpei@apache.org<mailto:chenpei@apache.org>>
wrote:
not sure if it's a email copy and paste error or is it just a typo:
DcitionaryLookupAnnotatorUMLS.xml
instead ??? DictionaryLookupAnnotatorUMLS.xml  ???
Would you be able to go to View > Log > there's usually a bit more info in the ~/uima.log
file.

On Mon, Dec 23, 2013 at 11:21 PM, Joshua Weiner <joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>>
wrote:
I changed my password so it no loner has a %... and I also set the password in the dictionarylookupannotatorUMLS.xml
file as you described...

I still get the same error...
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor:
file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml)
...

What is going on???

On Mon, Dec 23, 2013 at 10:49 PM, Pei Chen <chenpei@apache.org<mailto:chenpei@apache.org>>
wrote:
Hi Joshua,
I just noticed that you figured out the escaping issue.  But based on the error, it probably
still failed due to invalid umls pw (if you check the uima.log files you will probably see
the out put.)
If you want to bypass the entire escaping the environment var issue, you can also set the
umls credentials within the xml file itself:
Which should be inside your:
C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml

On Mon, Dec 23, 2013 at 10:26 PM, Joshua Weiner <joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>>
wrote:
Gah .. I am not sure why this is so challenging... Now I try to run; AggregatePlaintextUMLSProcessor.xml

and I get the error:
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor:
file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml)
...

hopefully this is my last problem!! Thank you for your help.!!!!!!!!!!!

Josh

On Mon, Dec 23, 2013 at 10:21 PM, Joshua Weiner <joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>>
wrote:

Smart man karthik. I do have a percent sign in my password. Thank you for your help here,
both of you.

Works now! Great tip.
On Dec 23, 2013 7:11 PM, "Karthik Sarma" <ksarma@ksarma.com<mailto:ksarma@ksarma.com>>
wrote:
Ah, I think I might know the problem. You probably have a percent sign in your password. If
so, you should replace it with a double percent (%%) in the batch file, as the % sign is a
reserved character in batch files.





--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical Association
ksarma@ksarma.com<mailto:ksarma@ksarma.com>
gchat: ksarma@gmail.com<mailto:ksarma@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>

On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner <joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>>
wrote:
when I run the script I get the following error: ((see below the


I run: bin\runctakesCVD.bat
I get:

C:\apache-ctakes-3.1.00>java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=mypasswordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-ctakes-3.1.0/config/log4j.xml
-Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD
Error: Could not find or load main class org.apache.uima.tools.cvd.CVD


On Mon, Dec 23, 2013 at 10:02 PM, Karthik Sarma <ksarma@ksarma.com<mailto:ksarma@ksarma.com>>
wrote:
OK, and what is the output when you run the script?





--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical Association
ksarma@ksarma.com<mailto:ksarma@ksarma.com>
gchat: ksarma@gmail.com<mailto:ksarma@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>

On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner <joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>>
wrote:
based on the code below I see the home directory as being set to the current_dir which is
C:\apache-ctakes-3.0.1..............

I also tried using James code to re-set the directory .. did not work.

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
cd %CTAKES_HOME%
java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=56Kmartin% -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD

:end

On Mon, Dec 23, 2013 at 9:55 PM, Karthik Sarma <ksarma@ksarma.com<mailto:ksarma@ksarma.com>>
wrote:
What is your CTAKES_HOME set to?





--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical Association
ksarma@ksarma.com<mailto:ksarma@ksarma.com>
gchat: ksarma@gmail.com<mailto:ksarma@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>

On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner <joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>>
wrote:
Where do you see this James?

Here is my code... I see the -cp parameter and its arguements right after "mypassword" ...
right?

:okHome
cd %CTAKES_HOME%
java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=mypassword -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD

:end

On Mon, Dec 23, 2013 at 9:44 PM, Masanz, James J. <Masanz.James@mayo.edu<mailto:Masanz.James@mayo.edu>>
wrote:
I see now that the java command in your previous post didn't include the -cp parameter and
its arguments.
Please add that back in.


From: joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com> [mailto:joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com>]
On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 8:12 PM

To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: Adding UMLS username and password ....

James,

I appreciate your persistence, it means quite a lot. Unfortunately, even with your latest
attempt I still get the same error:
Error: Could not find or load main class org.apache.uima.tools.cvd.CVD

I am on windows 8, 8gb of ram.

Thank you for your persistence.

Josh

On Mon, Dec 23, 2013 at 9:07 PM, Masanz, James J. <Masanz.James@mayo.edu<mailto:Masanz.James@mayo.edu>>
wrote:
Try this
CD  C:\apache-ctakes-3.1.0
set CTAKES_HOME=C:\apache-ctakes-3.1.0
then enter the java command from the command line that you were entering

Note: in my previous post, it was my mistake of including the percent signs in the SET command.

I meant to suggest
set CTAKES_HOME=""


From: joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com> [mailto:joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com>]
On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:55 PM

To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: Adding UMLS username and password ....

James,

Thank you for your continual prompt responses. Unfortunately, even after I did set%CTAKES_HOME%=""
I still get the following errror:

C:\apache-ctakes-3.1.0>java -Dctakes.umlsuser=joshuawiener2 =DCtakes.umlspw=mypasswwordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-ctakes-3.1.0/config/log4j.xml
-Xmd512M -Xmx2048M org.apache.uima.tools.cvd.CVD
Error: Could not find or load main class org.apache.uima.tools.cvd.CVD

once again my code in the runctakesCVD.bat file is:


:okHome
cd %CTAKES_HOME%
java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=passwordd -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD

:end

On Mon, Dec 23, 2013 at 8:45 PM, Masanz, James J. <Masanz.James@mayo.edu<mailto:Masanz.James@mayo.edu>>
wrote:

You might try from the command line

echo  %CTAKES_HOME%

or even better for debug purposes put it just before the  CD %CTAKES_HOME%  line.

It should respond with the parent of the bin, desc, and resources directory.

If it responds with something else, try clearing %CTAKES_HOME% by entering the following on
the command line and then trying the bat file again.
set %CTAKES_HOME%=""

Oh, and you'll probably want to change -Xmx1024M  to be  -Xmx2048M or even larger or you will
run into a heap space error for many parts of cTAKES.

-- James


From: joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com> [mailto:joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com>]
On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:36 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: Adding UMLS username and password ....

James,

Thanks so much for your response. When I remove the brackets I still get an error, I get:

"Error: could not find or load main class org.apache.uima.tools.cvd.CVD


Thank you so much for your help. I appreciate your dilligence.

Sincerely,
Josh

On Mon, Dec 23, 2013 at 8:32 PM, Masanz, James J. <Masanz.James@mayo.edu<mailto:Masanz.James@mayo.edu>>
wrote:
Sorry for the confusion, don't include the brackets, so it should look like this:

-Dctakes.umlsuser=joshuawiener2  -Dctakes.umlspw=mypassword

From: joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com> [mailto:joshuaweiner89@gmail.com<mailto:joshuaweiner89@gmail.com>]
On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Adding UMLS username and password ....


Hey guys,

I know this is probably a dumb question but I can't for the life of me figure it out. I finally
got a UMLS username and password, but I don't think I am updating the BAT files correctly...
here is what I did: note my username is joshuaweiner2 and my password (for this example) is
mypasswordd (see below).... I now can't get the CVD to run.

Thank you for your help...

:okHome
cd %CTAKES_HOME%
java -Dctakes.umlsuser=<joshuawiener2> -Dctakes.umlspw=<mypasswordd> -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD

:end


--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>



--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>



--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>



--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>



--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>




--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>




--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>




--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>




--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047<tel:201.638.0047>





--
Joshua S. Weiner
joshuaweiner2@gmail.com<mailto:joshuaweiner2@gmail.com>
201.638.0047

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