Hi Gandhi, With updated customDictionary.xml all errors were gone.
I am not sure about the schema of the tables used. I have taken reference from JdbcRareWordDictionary.java - https://github.com/apache/ ctakes/blob/trunk/ctakes-dictionary-lookup-fast/src/ main/java/org/apache/ctakes/dictionary/lookup2/dictionary/ JdbcRareWordDictionary.java and JdbcConceptFactory.java - https://github.com/apache/ctakes/blob/trunk/ctakes- dictionary-lookup-fast/src/main/java/org/apache/ctakes/ dictionary/lookup2/concept/JdbcConceptFactory.java I am using the ctakes-rest-web server and getting all the annotation array as empty in the result json. Attached tomcat logs again. Regards Chahal Arora Software Engineer Raxa On Tue, Dec 19, 2017 at 6:44 PM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Not able to see any tomcat logs attached. > > Do you see any errors in tomcat console? > > Regards, > Gandhi > > From: Chahal Arora [mailto:chahal.ar...@raxa.com] > Sent: Tuesday, December 19, 2017 6:09 PM > To: dev@ctakes.apache.org > Subject: Re: Custom Dictionary connected to mysql > > Hi, > > I have updated the customDictionary.xml and all the erros have gone but > still not getting any result. I am attaching the latest > customDictionary.xml and tomcat logs file. > > > > Regards > Chahal Arora > Software Engineer > Raxa > > On Tue, Dec 19, 2017 at 5:45 PM, Chahal Arora <chahal.ar...@raxa.com > <mailto:chahal.ar...@raxa.com>> wrote: > Hi All, > > I was working on moving the terms from custom dictionary BSV file to MySQL > database in LabValueFinder. I am able to connect to the database but not > sure about the database schema. > > Is there an example available where the custom dictionary is connected to > mysql database instead of a bsv file or hsql database? > > Attached is the customDictionary.xml file that I am using. > > > Regards > Chahal Arora > Software Engineer > Raxa > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you are not the named addressee you should not disseminate, distribute > or copy this e-mail. Please notify the sender or system manager by email > immediately if you have received this e-mail by mistake and delete this > e-mail from your system. If you are not the intended recipient you are > notified that disclosing, copying, distributing or taking any action in > reliance on the contents of this information is strictly prohibited and > against the law. >
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 Dec 2017 17:55:59 INFO DispatcherServlet - FrameworkServlet 'ctakes-rest-service': initialization started 19 Dec 2017 17:55:59 INFO XmlWebApplicationContext - Refreshing WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Tue Dec 19 17:55:59 IST 2017]; root of context hierarchy 19 Dec 2017 17:55:59 INFO XmlBeanDefinitionReader - Loading XML bean definitions from ServletContext resource [/WEB-INF/ctakes-rest-service-servlet.xml] 19 Dec 2017 17:56:00 INFO RequestMappingHandlerMapping - Mapped "{[/analyze],methods=[POST]}" onto public java.util.Map<java.lang.String, java.util.List<java.lang.String>> org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(java.lang.String) throws javax.servlet.ServletException,java.io.IOException 19 Dec 2017 17:56:01 INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Tue Dec 19 17:55:59 IST 2017]; root of context hierarchy 19 Dec 2017 17:56:01 INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Tue Dec 19 17:55:59 IST 2017]; root of context hierarchy 19 Dec 2017 17:56:01 INFO CtakesRestController - Initializing analysis engine and jcas pool 19 Dec 2017 17:56:02 WARN PiperFileReader - Attempted to set Parameter by Command-line options. Command-line options are not specified. 19 Dec 2017 17:56:02 WARN PropertyAeFactory - No parameters specified. 19 Dec 2017 17:56:02 WARN PiperFileReader - Attempted to set Parameter by Command-line options. Command-line options are not specified. 19 Dec 2017 17:56:02 WARN PropertyAeFactory - No parameters specified. 19 Dec 2017 17:56:02 WARN PiperFileReader - Attempted to set Parameter by Command-line options. Command-line options are not specified. 19 Dec 2017 17:56:02 WARN PropertyAeFactory - No parameters specified. 19 Dec 2017 17:56:04 INFO CleartkAnalysisEngine - Finished initializing 19 Dec 2017 17:56:04 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 19 Dec 2017 17:56:04 INFO CleartkAnalysisEngine - Starting initializing for Assigning Attributes 19 Dec 2017 17:56:05 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 19 Dec 2017 17:56:07 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence 19 Dec 2017 17:56:07 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 Dec 2017 17:56:07 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 19 Dec 2017 17:56:07 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/tinyDictSpec.xml 19 Dec 2017 17:56:07 INFO DictionaryDescriptorParser - Parsing dictionary specifications: Loading class `com.mysql.jdbc.Driver'. This is deprecated. The new driver class is `com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary. 19 Dec 2017 17:56:07 INFO JdbcConnectionFactory - Connecting to jdbc:mysql://127.0.0.1:3306/umlstest?useUnicode=true&characterEncoding=utf8&useSSL=false: 19 Dec 2017 17:56:08 INFO JdbcConnectionFactory - Database connected 19 Dec 2017 17:56:08 INFO JdbcRareWordDictionary - Connected to cui and term table RAREWORD 19 Dec 2017 17:56:19 ERROR JdbcConceptFactory - Table TUITABLE and/or TUI not found in Database 19 Dec 2017 17:56:19 ERROR JdbcConceptFactory - Table PREFTERMTABLE and/or PREFTERM not found in Database 19 Dec 2017 17:56:19 ERROR JdbcConceptFactory - Table RXNORMTABLE and/or RXNORM not found in Database 19 Dec 2017 17:56:19 INFO JdbcConceptFactory - Connected to concept table SNOMEDCT with class LONG 19 Dec 2017 17:56:20 INFO ClearNLPSemanticRoleLabelerAE - Finished initializing 19 Dec 2017 17:56:20 INFO ClearNLPSemanticRoleLabelerAE - Initializing ClearNLP semantic role labeler Loading configuration. 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Loading model: ............................. 19 Dec 2017 17:56:22 INFO ClearNLPSemanticRoleLabelerAE - Starting initializing 19 Dec 2017 17:56:22 INFO DrugMentionAnnotator - Finite state machines loaded. 19 Dec 2017 17:56:22 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence 19 Dec 2017 17:56:22 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 Dec 2017 17:56:22 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 19 Dec 2017 17:56:22 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/tinyDictSpec.xml 19 Dec 2017 17:56:22 INFO DictionaryDescriptorParser - Parsing dictionary specifications: 19 Dec 2017 17:56:22 INFO JdbcRareWordDictionary - Connected to cui and term table RAREWORD 19 Dec 2017 17:56:27 ERROR JdbcConceptFactory - Table TUITABLE and/or TUI not found in Database 19 Dec 2017 17:56:27 ERROR JdbcConceptFactory - Table PREFTERMTABLE and/or PREFTERM not found in Database 19 Dec 2017 17:56:27 ERROR JdbcConceptFactory - Table RXNORMTABLE and/or RXNORM not found in Database 19 Dec 2017 17:56:27 INFO JdbcConceptFactory - Connected to concept table SNOMEDCT with class LONG Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 19 Dec 2017 17:57:15 INFO ClearNLPDependencyParserAE - Initializing ClearNLP dependency parser, using lemmatizer: true 19 Dec 2017 17:57:15 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 19 Dec 2017 17:57:16 INFO LabValueFinder - 3 lab TUIs: [T060, T059, T201] 19 Dec 2017 17:57:16 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 19 Dec 2017 17:57:16 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 19 Dec 2017 17:57:23 INFO DispatcherServlet - FrameworkServlet 'ctakes-rest-service': initialization completed in 84552 ms 19 Dec 2017 17:57:26 INFO SentenceDetector - Starting processing. 19 Dec 2017 17:57:26 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 19 Dec 2017 17:57:26 INFO ContextDependentTokenizerAnnotator - process(JCas) 19 Dec 2017 17:57:26 INFO POSTagger - process(JCas) 19 Dec 2017 17:57:26 INFO Chunker - process(JCas) 19 Dec 2017 17:57:26 INFO ChunkAdjuster - process(JCas) 19 Dec 2017 17:57:26 INFO ChunkAdjuster - process(JCas) 19 Dec 2017 17:57:26 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 19 Dec 2017 17:57:26 INFO AbstractJCasTermAnnotator - Finished processing 19 Dec 2017 17:57:26 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8082-exec-95 19 Dec 2017 17:57:26 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:http-nio-8082-exec-95 19 Dec 2017 17:57:26 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 19 Dec 2017 17:57:26 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 19 Dec 2017 17:57:26 INFO CleartkAnalysisEngine - Assigning Attributes ... 19 Dec 2017 17:57:27 INFO CleartkAnalysisEngine - Finished Assigning Attributes 19 Dec 2017 17:57:27 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 19 Dec 2017 17:57:27 INFO AbstractJCasTermAnnotator - Finished processing 19 Dec 2017 17:57:27 INFO LabValueFinder - Associating Labs with values ... 19 Dec 2017 17:57:27 INFO LabValueFinder - Finished. 19 Dec 2017 17:57:27 INFO DrugMentionAnnotator - process(JCas)