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
> > >
> > >
> >
>
