Re: Clinical Processor [EXTERNAL]
The problem is I never created it, it is something that ctakes was looking
for that I didn't have on my computer.
On Sat, Aug 24, 2019 at 11:10 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Did you create a dictionary named "sno_rx_16abTerms" ? If so it looks
> like ctakes can't find it. Make sure that the jdbc specification is in the
> configuration .xml file is correct.
>
> Sean
>
>
>
> From: Sébastien Boussard
> Sent: Saturday, August 24, 2019 1:09 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Processor [EXTERNAL]
>
> Oops, I didnt paste the error message!, The message I got was:
>
> ERROR JdbcRareWordDictionary - Could not Connect to Dictionary
> sno_rx_16abTerms
>
> On Sat, Aug 24, 2019 at 8:55 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Sebastien,
> >
> > What message? What have you done differently "now"?
> >
> > Sean
> > ____
> > From: Sébastien Boussard
> > Sent: Friday, August 23, 2019 10:42 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Clinical Processor [EXTERNAL]
> >
> > I am now getting this message as well
> >
> > On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
> > sean.fi...@childrens.harvard.edu> wrote:
> >
> > > Hi Sebastien,
> > >
> > > Can you look at the referenced file
> > > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
> > >
> > > It should be in resources/
> > >
> > > If it is the default version then it contains the line
> > > > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
> > >
> > > Can you look at the referenced directory
> > > resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> > > It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
> > >
> > > All of the above is for the default configuration.
> > >
> > > You mentioned
> > > >I have the dictionary and I tried to make a custom dictionary.
> > >
> > > If you made a custom dictionary then you'll need to make the
> connections
> > > appropriately.
> > >
> > > Sean
> > >
> > > From: Sébastien Boussard
> > > Sent: Friday, August 23, 2019 1:45 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: Clinical Processor [EXTERNAL]
> > >
> > > 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
> HH:mm:ss}
> > > %5p %c{1} - %m%n].
> > >
> > > log4j: Adding appender named [consoleAppender] to category [root].
> > >
> > > 23 Aug 2019 10:44:05 IN
Re: Clinical Processor [EXTERNAL]
Did you create a dictionary named "sno_rx_16abTerms" ? If so it looks like
ctakes can't find it. Make sure that the jdbc specification is in the
configuration .xml file is correct.
Sean
From: Sébastien Boussard
Sent: Saturday, August 24, 2019 1:09 PM
To: dev@ctakes.apache.org
Subject: Re: Clinical Processor [EXTERNAL]
Oops, I didnt paste the error message!, The message I got was:
ERROR JdbcRareWordDictionary - Could not Connect to Dictionary
sno_rx_16abTerms
On Sat, Aug 24, 2019 at 8:55 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sebastien,
>
> What message? What have you done differently "now"?
>
> Sean
>
> From: Sébastien Boussard
> Sent: Friday, August 23, 2019 10:42 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Processor [EXTERNAL]
>
> I am now getting this message as well
>
> On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Sebastien,
> >
> > Can you look at the referenced file
> > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
> >
> > It should be in resources/
> >
> > If it is the default version then it contains the line
> > >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
> >
> > Can you look at the referenced directory
> > resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> > It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
> >
> > All of the above is for the default configuration.
> >
> > You mentioned
> > >I have the dictionary and I tried to make a custom dictionary.
> >
> > If you made a custom dictionary then you'll need to make the connections
> > appropriately.
> >
> > Sean
> >
> > From: Sébastien Boussard
> > Sent: Friday, August 23, 2019 1:45 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Clinical Processor [EXTERNAL]
> >
> > 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 HH:mm:ss}
> > %5p %c{1} - %m%n].
> >
> > log4j: Adding appender named [consoleAppender] to category [root].
> >
> > 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model
> file:
> > org/apache/ctakes/core/sentdetect/sd-med-model.zip
> >
> > 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> >
> > 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> >
> > 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> > org/apache/ctakes/postagger/models/mayo-pos.zip
> >
> > 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> > org/apache/ctakes/chunker/models/chunker-model.zip
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> > lookup window type: org.apac
Re: Clinical Processor [EXTERNAL]
Oops, I didnt paste the error message!, The message I got was:
ERROR JdbcRareWordDictionary - Could not Connect to Dictionary
sno_rx_16abTerms
On Sat, Aug 24, 2019 at 8:55 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sebastien,
>
> What message? What have you done differently "now"?
>
> Sean
>
> From: Sébastien Boussard
> Sent: Friday, August 23, 2019 10:42 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Processor [EXTERNAL]
>
> I am now getting this message as well
>
> On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Sebastien,
> >
> > Can you look at the referenced file
> > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
> >
> > It should be in resources/
> >
> > If it is the default version then it contains the line
> > >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
> >
> > Can you look at the referenced directory
> > resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> > It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
> >
> > All of the above is for the default configuration.
> >
> > You mentioned
> > >I have the dictionary and I tried to make a custom dictionary.
> >
> > If you made a custom dictionary then you'll need to make the connections
> > appropriately.
> >
> > Sean
> >
> > From: Sébastien Boussard
> > Sent: Friday, August 23, 2019 1:45 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Clinical Processor [EXTERNAL]
> >
> > 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 HH:mm:ss}
> > %5p %c{1} - %m%n].
> >
> > log4j: Adding appender named [consoleAppender] to category [root].
> >
> > 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model
> file:
> > org/apache/ctakes/core/sentdetect/sd-med-model.zip
> >
> > 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> >
> > 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> >
> > 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> > org/apache/ctakes/postagger/models/mayo-pos.zip
> >
> > 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> > org/apache/ctakes/chunker/models/chunker-model.zip
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> > lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
> >
> > 23 Aug 2019 10:44:06 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
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
> > text span: 3
> >
> > 23 Aug 20
Re: Clinical Processor [EXTERNAL]
Hi Sebastien,
What message? What have you done differently "now"?
Sean
From: Sébastien Boussard
Sent: Friday, August 23, 2019 10:42 PM
To: dev@ctakes.apache.org
Subject: Re: Clinical Processor [EXTERNAL]
I am now getting this message as well
On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sebastien,
>
> Can you look at the referenced file
> org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
>
> It should be in resources/
>
> If it is the default version then it contains the line
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
>
> Can you look at the referenced directory
> resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
>
> All of the above is for the default configuration.
>
> You mentioned
> >I have the dictionary and I tried to make a custom dictionary.
>
> If you made a custom dictionary then you'll need to make the connections
> appropriately.
>
> Sean
>
> From: Sébastien Boussard
> Sent: Friday, August 23, 2019 1:45 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Processor [EXTERNAL]
>
> 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 HH:mm:ss}
> %5p %c{1} - %m%n].
>
> log4j: Adding appender named [consoleAppender] to category [root].
>
> 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
>
> 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>
> 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
>
> 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
>
> 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 23 Aug 2019 10:44:06 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
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
>
> 23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
>
> 23 Aug 2019 10:44:06 INFO UmlsUserApprover - Checking UMLS Account at
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU=
> for user boussard:
>
> ..23 Aug 2019 10:44:07 INFO UmlsUserApprover - UMLS Account at
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
Re: Clinical Processor [EXTERNAL]
Hi Sebastien,
You can refer to this file -
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
for custom dictionary configuration.
On Saturday, August 24, 2019, Sébastien Boussard wrote:
> I am now getting this message as well
>
> On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Sebastien,
> >
> > Can you look at the referenced file
> > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
> >
> > It should be in resources/
> >
> > If it is the default version then it contains the line
> > > value="jdbc:hsqldb:file:resources/org/apache/ctakes/
> dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
> >
> > Can you look at the referenced directory
> > resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> > It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
> >
> > All of the above is for the default configuration.
> >
> > You mentioned
> > >I have the dictionary and I tried to make a custom dictionary.
> >
> > If you made a custom dictionary then you'll need to make the connections
> > appropriately.
> >
> > Sean
> >
> > From: Sébastien Boussard
> > Sent: Friday, August 23, 2019 1:45 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Clinical Processor [EXTERNAL]
> >
> > 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 HH:mm:ss}
> > %5p %c{1} - %m%n].
> >
> > log4j: Adding appender named [consoleAppender] to category [root].
> >
> > 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model
> file:
> > org/apache/ctakes/core/sentdetect/sd-med-model.zip
> >
> > 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> >
> > 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> >
> > 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> > org/apache/ctakes/postagger/models/mayo-pos.zip
> >
> > 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> > org/apache/ctakes/chunker/models/chunker-model.zip
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> > lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
> >
> > 23 Aug 2019 10:44:06 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
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
> > text span: 3
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
> > Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
> >
> > 23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing
> dictionary
> > specifications:
> &
Re: Clinical Processor [EXTERNAL]
I am now getting this message as well
On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sebastien,
>
> Can you look at the referenced file
> org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
>
> It should be in resources/
>
> If it is the default version then it contains the line
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
>
> Can you look at the referenced directory
> resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
>
> All of the above is for the default configuration.
>
> You mentioned
> >I have the dictionary and I tried to make a custom dictionary.
>
> If you made a custom dictionary then you'll need to make the connections
> appropriately.
>
> Sean
>
> From: Sébastien Boussard
> Sent: Friday, August 23, 2019 1:45 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Processor [EXTERNAL]
>
> 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 HH:mm:ss}
> %5p %c{1} - %m%n].
>
> log4j: Adding appender named [consoleAppender] to category [root].
>
> 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
>
> 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>
> 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
>
> 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
>
> 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 23 Aug 2019 10:44:06 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
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
>
> 23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
>
> 23 Aug 2019 10:44:06 INFO UmlsUserApprover - Checking UMLS Account at
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU=
> for user boussard:
>
> ..23 Aug 2019 10:44:07 INFO UmlsUserApprover - UMLS Account at
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU=
> for user boussard has
> been validated
>
>
> 23 Aug 2019 10:44:07 ERROR ProcessLinesClinicalRunne
Re: Clinical Processor [EXTERNAL]
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 HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
23 Aug 2019 10:44:06 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
23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
text span: 3
23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
23 Aug 2019 10:44:06 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard:
..23 Aug 2019 10:44:07 INFO UmlsUserApprover - UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard has
been validated
23 Aug 2019 10:44:07 ERROR ProcessLinesClinicalRunner - Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
failed. (Descriptor:
)
This is the error message, The last step it completed was looking up the
umls through the sno_rx16
On Tue, Aug 20, 2019 at 1:26 PM Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Can you send an error message that is as complete as possible? It is hard
> to tell from the information you've given.
> Thanks
> Tim
>
>
> -Original Message-
> From: Sébastien Boussard 3d%3fiso-8859-1%3fq%3fs%3de9bastien%3f%3d%20boussard%20%3cbouss...@bu.edu
> %3e>>
> Reply-to:
> To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
> Subject: Clinical Processor [EXTERNAL]
> Date: Thu, 15 Aug 2019 10:28:51 -0700
>
>
> I'm working on making a clinical processor, and I've been having a lot of
> trouble with the JCasTermAnnotator. It's telling me that it's failing to
> initialize. It is connecting to umls and validating. I've had this problem
> for a while, is there any other java class I could use. I have the
> dictionary and I tried to make a custom dictionary.
>
> Thanks,
> Sebastien Boussard
>
>
Re: Clinical Processor [EXTERNAL]
Can you send an error message that is as complete as possible? It is hard to tell from the information you've given. Thanks Tim -Original Message- From: Sébastien Boussard mailto:%3d%3fiso-8859-1%3fq%3fs%3de9bastien%3f%3d%20boussard%20%3cbouss...@bu.edu%3e>> Reply-to: To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Clinical Processor [EXTERNAL] Date: Thu, 15 Aug 2019 10:28:51 -0700 I'm working on making a clinical processor, and I've been having a lot of trouble with the JCasTermAnnotator. It's telling me that it's failing to initialize. It is connecting to umls and validating. I've had this problem for a while, is there any other java class I could use. I have the dictionary and I tried to make a custom dictionary. Thanks, Sebastien Boussard
Clinical Processor
I'm working on making a clinical processor, and I've been having a lot of trouble with the JCasTermAnnotator. It's telling me that it's failing to initialize. It is connecting to umls and validating. I've had this problem for a while, is there any other java class I could use. I have the dictionary and I tried to make a custom dictionary. Thanks, Sebastien Boussard
