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 > > >
