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Posted to user@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2018/01/19 19:57:13 UTC
Re: Error running CAS Visual Debugger [EXTERNAL]
I'm having trouble loading the url in my browser too. Could be that the
UMLS web service is down. Is there a person at the NLM to contact about
this?
Tim
On Fri, 2018-01-19 at 14:45 -0500, Don Flinn wrote:
> 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:\WI
> NDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System3
> 2\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$DefaultSSLContext)
>
>
Re: Error running CAS Visual Debugger [EXTERNAL]
Posted by Don Flinn <fl...@alum.mit.edu>.
Thanks Gundolf, I tried your suggestion, but it didn't correct my problem.
I have something else wrong.
Don
On Fri, Jan 19, 2018 at 3:01 PM, Schenk, Gundolf <Gu...@ucsf.edu>
wrote:
> Hi,
>
> The authentication works for me.
>
> Don, did you try
>
> C:\apache-ctakes-4.0.0>bin\runctakesCVD.bat -Dctakes.umlsuser=donflinn
> -Dctakes.umlspw="yourpassw@rd"
>
> Cheers,
> Gundolf.
>
> On 1/19/18, 11:57 AM, "Miller, Timothy" <Timothy.Miller@childrens.
> harvard.edu> wrote:
>
> I'm having trouble loading the url in my browser too. Could be that the
> UMLS web service is down. Is there a person at the NLM to contact about
> this?
>
> Tim
>
> On Fri, 2018-01-19 at 14:45 -0500, Don Flinn wrote:
> > I'm new to Ctakes and am attempting to run the example in the Ctakes
> > user guide. I did the install as instructed. When I ran
> > the runctakesCVD.bat, the CAS Visusl Debugger window popped up but I
> > got the following error:
> > ...
> > 19 Jan 2018 08:15:43 INFO UmlsUserApprover - Checking UMLS Account
> > at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user
> > donflinn:
> >
> > 19 Jan 2018 08:15:44 ERROR UmlsUserApprover -
> > java.security.NoSuchAlgorithmException: Error constructing
> > implementation (algorithm: Default, provider: SunJSSE, class:
> > sun.security.ssl.SSLContextImpl$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\AggregatePlaintextFastUMLSProc
> essor.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:\WI
> > NDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\
> WINDOWS\System3
> > 2\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\AggregatePlaintextFastUMLSProc
> essor.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\AggregatePlaintextFastUMLSProc
> essor.xml
> > " (
> > echo CVD will load AE "C:\apache-ctakes-4.0.0\desc\ctakes-clinical-
> > pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProc
> essor.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\AggregatePlaintextFastUMLSProc
> essor.xml
> > ) else (
> > echo Unable to find descriptor "desc\ctakes-clinical-
> > pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProc
> essor.xml
> > "
> > GOTO NoParam
> > )
> > CVD will load AE "C:\apache-ctakes-4.0.0\desc\ctakes-clinical-
> > pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProc
> essor.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$DefaultSSLContext)
> >
> >
>
>
Re: Error running CAS Visual Debugger [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
The UMLS authentication is working for me right now, running from a 4.0
binary install.
Don, is it still not working for you? are you by any chance running from
the binary install or are you running within an IDE, and using the "trunk"
version of the code?
Otherwise I wonder if something in your PATH is not playing nice.
-- James
On Fri, Jan 19, 2018 at 3:01 PM, Schenk, Gundolf <Gu...@ucsf.edu>
wrote:
> Hi,
>
> The authentication works for me.
>
> Don, did you try
>
> C:\apache-ctakes-4.0.0>bin\runctakesCVD.bat -Dctakes.umlsuser=donflinn
> -Dctakes.umlspw="yourpassw@rd"
>
> Cheers,
> Gundolf.
>
> On 1/19/18, 11:57 AM, "Miller, Timothy" <Timothy.Miller@childrens.
> harvard.edu> wrote:
>
> I'm having trouble loading the url in my browser too. Could be that the
> UMLS web service is down. Is there a person at the NLM to contact about
> this?
>
> Tim
>
> On Fri, 2018-01-19 at 14:45 -0500, Don Flinn wrote:
> > I'm new to Ctakes and am attempting to run the example in the Ctakes
> > user guide. I did the install as instructed. When I ran
> > the runctakesCVD.bat, the CAS Visusl Debugger window popped up but I
> > got the following error:
> > ...
> > 19 Jan 2018 08:15:43 INFO UmlsUserApprover - Checking UMLS Account
> > at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user
> > donflinn:
> >
> > 19 Jan 2018 08:15:44 ERROR UmlsUserApprover -
> > java.security.NoSuchAlgorithmException: Error constructing
> > implementation (algorithm: Default, provider: SunJSSE, class:
> > sun.security.ssl.SSLContextImpl$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\AggregatePlaintextFastUMLSProc
> essor.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:\WI
> > NDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\
> WINDOWS\System3
> > 2\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\AggregatePlaintextFastUMLSProc
> essor.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\AggregatePlaintextFastUMLSProc
> essor.xml
> > " (
> > echo CVD will load AE "C:\apache-ctakes-4.0.0\desc\ctakes-clinical-
> > pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProc
> essor.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\AggregatePlaintextFastUMLSProc
> essor.xml
> > ) else (
> > echo Unable to find descriptor "desc\ctakes-clinical-
> > pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProc
> essor.xml
> > "
> > GOTO NoParam
> > )
> > CVD will load AE "C:\apache-ctakes-4.0.0\desc\ctakes-clinical-
> > pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProc
> essor.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$DefaultSSLContext)
> >
> >
>
>
Re: Error running CAS Visual Debugger [EXTERNAL]
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Hi,
The authentication works for me.
Don, did you try
C:\apache-ctakes-4.0.0>bin\runctakesCVD.bat -Dctakes.umlsuser=donflinn -Dctakes.umlspw="yourpassw@rd"
Cheers,
Gundolf.
On 1/19/18, 11:57 AM, "Miller, Timothy" <Ti...@childrens.harvard.edu> wrote:
I'm having trouble loading the url in my browser too. Could be that the
UMLS web service is down. Is there a person at the NLM to contact about
this?
Tim
On Fri, 2018-01-19 at 14:45 -0500, Don Flinn wrote:
> I'm new to Ctakes and am attempting to run the example in the Ctakes
> user guide. I did the install as instructed. When I ran
> the runctakesCVD.bat, the CAS Visusl Debugger window popped up but I
> got the following error:
> ...
> 19 Jan 2018 08:15:43 INFO UmlsUserApprover - Checking UMLS Account
> at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user
> donflinn:
>
> 19 Jan 2018 08:15:44 ERROR UmlsUserApprover -
> java.security.NoSuchAlgorithmException: Error constructing
> implementation (algorithm: Default, provider: SunJSSE, class:
> sun.security.ssl.SSLContextImpl$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:\WI
> NDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System3
> 2\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)
>
>