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 <
[email protected]> wrote:
> Not able to see any tomcat logs attached.
>
> Do you see any errors in tomcat console?
>
> Regards,
> Gandhi
>
> From: Chahal Arora [mailto:[email protected]]
> Sent: Tuesday, December 19, 2017 6:09 PM
> To: [email protected]
> 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 <[email protected]
> <mailto:[email protected]>> 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
>
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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
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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
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19 Dec 2017 17:56:02 WARN PropertyAeFactory - No parameters specified.
19 Dec 2017 17:56:02 WARN PiperFileReader - Attempted to set Parameter by
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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
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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)
