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
>
>
