I'm new to Ctakes and am attempting to run the example in the Ctakes user
guide. I did the install as instructed. When I ran the runctakesCVD.bat,
the CAS Visusl Debugger window popped up but I got the following error:
...
19 Jan 2018 08:15:43 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user donflinn:
19 Jan 2018 08:15:44 ERROR UmlsUserApprover -
java.security.NoSuchAlgorithmException: Error constructing implementation
(algorithm: Default, provider: SunJSSE, class:
sun.security.ssl.SSLContextImpl$DefaultSSLContext)
I'm assuming this means that my login to UMLS failed. However, I have a UMLS
username and password and entered them into both the Java commands in the
batch files and also as environment variables. I can use these to log into
UMLS so I know that they are correct.
I'm running Windows 10 and ctakes 4.0.0.
If someone could let me know what I am doing wrong it would be greatly
appreciated.
The full debug output is below. Note I also tried to parse the text, which
as expected also failed. I also commented out the echo off in the script.
Don.
======================================== output
=============================
C:\apache-ctakes-4.0.0\bin>cd ..
C:\apache-ctakes-4.0.0>bin\runctakesCVD.bat
desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml
C:\apache-ctakes-4.0.0>set CURRENT_DIR=C:\apache-ctakes-4.0.0
C:\apache-ctakes-4.0.0>if not "C:\apache-ctakes-4.0.0" == "" goto gotHome
C:\apache-ctakes-4.0.0>if exist
"C:\apache-ctakes-4.0.0\bin\runctakesCVD.bat" goto okHome
C:\apache-ctakes-4.0.0>if exist "C:\Program
Files\Java\jdk1.8.0_144\bin\java.exe" set PATH=C:\Program
Files\Java\jdk1.8.0_144\bin;C:\ProgramData\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;c:\php;C:\Program
Files (x86)\Subversion\bin;C:\Program
Files\TortoiseSVN\bin;c:\unixcmds\usr\local\wbin;C:\Program
Files\nodejs\;C:\maven\bin;c:\program
files\java\jdk1.8.0_144\bin;c:\program
files\java\jdk1.8.0_144\lib;C:\Users\don\AppData\Roaming\npm;C:\Users\don\AppData\Local\Microsoft\WindowsApps;C:\Program
Files\Java\jdk1.8.0_144\bin;c:\openssl\bin;C:\apache-uima\bin;
C:\apache-ctakes-4.0.0>cd C:\apache-ctakes-4.0.0
C:\apache-ctakes-4.0.0>IF
"desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml"
== "" GOTO NoParam
C:\apache-ctakes-4.0.0>IF NOT "" == "" GOTO MoreThanOneParam
C:\apache-ctakes-4.0.0>if exist
"C:\apache-ctakes-4.0.0\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml"
(
echo CVD will load AE
"C:\apache-ctakes-4.0.0\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml"
java -Dctakes.umlsuser=donflinn -Dctakes.umlspw=threeOne4 -cp
"C:\apache-ctakes-4.0.0\desc\;C:\apache-ctakes-4.0.0\resources\;C:\apache-ctakes-4.0.0\lib\*"
-Dlog4j.configuration=file:\C:\apache-ctakes-4.0.0\config\log4j.xml
-Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD -desc
desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml
) else (
echo Unable to find descriptor
"desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml"
GOTO NoParam
)
CVD will load AE
"C:\apache-ctakes-4.0.0\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml"
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
19 Jan 2018 08:15:42 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
19 Jan 2018 08:15:43 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
19 Jan 2018 08:15:43 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
19 Jan 2018 08:15:43 INFO AbstractJCasTermAnnotator - Using dictionary
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
19 Jan 2018 08:15:43 INFO AbstractJCasTermAnnotator - Exclusion tagset
loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN
VBP VBZ WDT WP WPS WRB
19 Jan 2018 08:15:43 INFO AbstractJCasTermAnnotator - Using minimum term
text span: 3
19 Jan 2018 08:15:43 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
19 Jan 2018 08:15:43 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
19 Jan 2018 08:15:43 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user donflinn:
19 Jan 2018 08:15:44 ERROR UmlsUserApprover -
java.security.NoSuchAlgorithmException: Error constructing implementation
(algorithm: Default, provider: SunJSSE, class:
sun.security.ssl.SSLContextImpl$DefaultSSLContext)
19 Jan 2018 08:28:05 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
19 Jan 2018 08:28:06 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
19 Jan 2018 08:28:06 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
19 Jan 2018 08:28:06 INFO AbstractJCasTermAnnotator - Using dictionary
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
19 Jan 2018 08:28:06 INFO AbstractJCasTermAnnotator - Exclusion tagset
loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN
VBP VBZ WDT WP WPS WRB
19 Jan 2018 08:28:06 INFO AbstractJCasTermAnnotator - Using minimum term
text span: 3
19 Jan 2018 08:28:06 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
19 Jan 2018 08:28:06 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
19 Jan 2018 08:28:06 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user donflinn:
19 Jan 2018 08:28:06 ERROR UmlsUserApprover -
java.security.NoSuchAlgorithmException: Error constructing implementation
(algorithm: Default, provider: SunJSSE, class:
sun.security.ssl.SSLContextImpl$DefaultSSLContext)
