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 <bouss...@bu.edu>
> 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 <bouss...@bu.edu>
> > 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
> > > <property key="jdbcUrl"
> > >
> >
> 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 <bouss...@bu.edu>
> > > 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 yyyy
> 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&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18&s=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU&e=
> > > 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&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18&s=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU&e=
> > > 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:
> > > <unknown>)
> > >
> > >
> > > 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 <bouss...@bu.edu<mailto:%
> > > >
> > >
> >
> 3d%3fiso-8859-1%3fq%3fs%3de9bastien%3f%3d%20boussard%20%3cbouss...@bu.edu
> > > > %3e>>
> > > > Reply-to: <dev@ctakes.apache.org>
> > > > 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
> > > >
> > > >
> > >
> >
>
