Yes, I did. The same problem. Natalia
On Fri, Jul 25, 2014 at 2:06 PM, Chen, Pei <[email protected]> wrote: > Did you also try lower case in the table name? > > Sent from my iPhone > > On Jul 25, 2014, at 2:02 PM, "Natalia Connolly" < > [email protected]> wrote: > > Yes: > > > mysql> use umls; > Reading table information for completion of table and column names > You can turn off this feature to get a quicker startup with -A > > Database changed > mysql> show tables; > +-----------------+ > | Tables_in_umls | > +-----------------+ > | AMBIGLUI | > | AMBIGSUI | > | DELETEDCUI | > | DELETEDLUI | > ……. > > | umls_ms_2013 | > | umls_snomed_map | > +-----------------+ > 49 rows in set (0.00 sec) > > Natalia > > > > > On Fri, Jul 25, 2014 at 1:59 PM, Chen, Pei <[email protected] > > wrote: > >> That is odd. Nothing seems out of the ordinary… >> >> And the database name is umls? >> >> jdbc:mysql://localhost:3306/*umls* >> >> >> >> *From:* Natalia Connolly [mailto:[email protected]] >> *Sent:* Friday, July 25, 2014 1:54 PM >> *To:* [email protected] >> >> *Subject:* Re: Fwd: UMLS integration with cTAKES 3.1 >> >> >> >> Hi Pei, >> >> >> >> I can't see any issues with LookupDesc_Db, so I am attaching both it >> and DictionaryLookupAnnotatorDB.xml. I only modified the >> username/password in the second file to "myusername" and "mypassword" for >> security purposes. They were correct before, I checked it many times. >> >> >> >> Thank you so much for your help, >> >> >> >> Natalia >> >> >> >> >> >> On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei < >> [email protected]> wrote: >> >> 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:[email protected]] >> > Sent: Friday, July 25, 2014 1:06 PM >> > To: [email protected]; [email protected] >> > 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 < >> [email protected]> >> > wrote: >> > >> > > — >> > > ---------- Forwarded message ---------- >> > > From: "Natalia Connolly" <[email protected]> >> > > Date: Fri, Jul 25, 2014 at 12:35 PM >> > > Subject: UMLS integration with cTAKES 3.1 >> > > To: "[email protected]" <[email protected]> >> > >> 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 >> >> >> > >
