CTAKES_HOME\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED. *template*.xml will have this line: <jdbcImpl tableName="@[email protected]_snomed_fword_lookup"/>
During the setup, ytex looks at the ytex.properties file and substitutes @db.schema@ with the name of your schema. E.g. if I have this in ytex.properties: db.schema=ytex CTAKES_HOME\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.xml will have this line: <jdbcImpl tableName="ytex.v_snomed_fword_lookup"/> Either the ytex ant setup failed for some reason (did you send the output to a file?), or hasn't been run. If it hasn't run, then there might be other issues. -vj On Wed, Jun 11, 2014 at 12:46 PM, Abhishek Raj <[email protected]> wrote: > I think the error is in the ytex.profile file. I am not really sure > though. I am attaching the file. Please let me know if there is anything to > be changed in the file that might fix the issue. Thanks. > > > On Wed, Jun 11, 2014 at 10:04 PM, Lee, Richard A. [USA] < > [email protected]> wrote: > >> This is the same error I reported a few weeks ago, but it probably got >> missed because I was also reporting that using the ytex-specific AE failed >> to produce any MedicalAnnotations… >> >> >> >> *From:* Abhishek Raj [mailto:[email protected]] >> *Sent:* Wed, 11 Jun, 2014 12:11 >> *To:* [email protected] >> *Subject:* [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml >> >> >> >> Thanks for the reply. I am using apace-cTakes-3.1.2 and yes, this is >> using YTEX. I followed these >> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> >> instructions >> for installing ytex and #1 in the installation procedure was " installing >> ctakes+ytex >> distro 'as usual' " by following these >> <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide> >> instructions. >> Not sure what is the reason for the error though. I have UMLS installed in >> my SQL database already. >> >> >> >> On Wed, Jun 11, 2014 at 9:24 PM, Chen, Pei < >> [email protected]> wrote: >> >> Abhishek, >> >> There is an SQL exception because of the “@db.schema@.” in the sql: >> >> SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE >> fword = ? >> >> >> >> Which version of cTAKES are you using and also is this using YTEX? As I >> am not sure where the special parameter markers are coming from. Normally, >> it would look something like: >> >> >> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml >> >> >> >> >> >> >> >> >> >> *From:* Abhishek Raj [mailto:[email protected]] >> *Sent:* Wednesday, June 11, 2014 11:39 AM >> *To:* [email protected] >> *Subject:* Re: Cannot load AggregatePlainTextUmlsProcessor.xml >> >> >> >> Hey! Thanks a lot for the reply. That totally worked. However, I have run >> into another problem now. After loading the >> "AggregatePlainTextUmlsProcessor.xml", when I try to run the it on some >> text sample I get an error saying >> >> org.apache.uima.analysis_engine.AnalysisEngineProcessException . More >> detailed information is in the log file >> >> >> I have attached the log in the attachments. Please do have a look. Any >> help will be appreciated. >> >> >> >> On Wed, Jun 11, 2014 at 7:06 PM, Chen, Pei < >> [email protected]> wrote: >> >> Abhishek, >> >> Have you tried some of the suggestions from this thread: >> >> >> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201304.mbox/%3CCD84AD35.169BD%25mcoarr%40mitre.org%3E >> >> >> >> >> >> *From:* Abhishek Raj [mailto:[email protected]] >> *Sent:* Wednesday, June 11, 2014 4:17 AM >> *To:* [email protected] >> *Subject:* Cannot load AggregatePlainTextUmlsProcessor.xml >> >> >> >> Hello I installed ctakes following >> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation and >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide >> . After installation I ran the CVD for annotation purpose. When I try to >> load the AggregatePlainTextUmlsProcessor.xml I get error saying >> >> org.apache.uima.resource.ResourceInitializationException: >> >> Initialization of annotator class >> >> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" >> failed. (Descriptor: >> file:/home/gamerboy/apache-ctakes-3.1.2-SNAPSHOT/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) >> >> >> >> I am behind a proxy network. Not sure this could be the reason though. >> >> >> >> >> > >
