Natalia, That is strange. It sounds like it isn't configured to use the right resource. Could you double check the mappings, in particular: in your LookupDesc_Db.xml: externalResourceKey="DbConnection" to ensure it's using the right resource that was added in your DictionaryLookupAnnotatorDB.xml? If it still doesn't work, would you mind attaching the xml config files?
--Pei > -----Original Message----- > From: John Green [mailto:john.travis.gr...@gmail.com] > Sent: Friday, July 25, 2014 1:06 PM > To: u...@ctakes.apache.org; dev@ctakes.apache.org > Subject: Re: Fwd: UMLS integration with cTAKES 3.1 > > This sounds just like jira ctakes-306. > > > JG > — > > On Fri, Jul 25, 2014 at 1:04 PM, John Green <hephaestus.stu...@gmail.com> > wrote: > > > — > > ---------- Forwarded message ---------- > > From: "Natalia Connolly" <natalia.v.conno...@gmail.com> > > Date: Fri, Jul 25, 2014 at 12:35 PM > > Subject: UMLS integration with cTAKES 3.1 > > To: "u...@ctakes.apache.org" <u...@ctakes.apache.org> > >> Hello, > >> I am trying to supplement the basic cTAKES dictionary with the > >> latest UMLS release. Following the instructions here ( > >> https://cabig- > kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25 > >> 8), I built a mysql database and imported UMLS data into it as two tables, > >> umls_ms_2013 and umls_snomed_map. I then modified > >> DictionaryLookupAnnotatorDB.xml as follows: > >> <name>URL</name> > >> <value> > >> <string>jdbc:mysql://localhost:3306/umls</string> > >> </value> > >> and I also changed LookupDesc_Db.xml to reflect my two table names. > >> After I added DictionaryLookupAnnotatorDB.xml to my analysis > >> engines in runctakesCPE.sh, I got the following error: > >> org.apache.uima.analysis_engine.AnalysisEngineProcessException > CausedBY: > >> org.apache.ctakes.dictionary.lookup.DictionaryException: > >> java.sql.SQLException: Table not found in statement [SELECT tui, > >> text, cui from UMLS_MS_2013 where fword =?] > >> This is strange because the table does exist and it's not empty: > >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2; > >> +------+--------+----------+ > >> | tui | text | cui | > >> +------+--------+----------+ > >> | T121 | MSH | C0000005 | > >> | T121 | MSHFRE | C0000005 | > >> +------+--------+----------+ > >> 2 rows in set (0.00 sec) > >> Can someone please help? > >> Thank you, > >> Natalia Connolly
