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) > >
