Just a quick update: in cTAKES 3.2, using the same set up as what I described before, I see that it's connecting to my database:
"25 Jul 2014 15:14:41 INFO JdbcConnectionResourceImpl - Connection established to: jdbc:mysql://localhost:3306/umls" However, I still get an error, which appears to vary depending on what analysis engines in addition to DictionaryLookupAnnotatorDB are in my list. If I use AggregatePlaintextProcessor followed by DictionaryLookupAnnotatorDB, I get the following error: org.apache.uima.resource.ResourceInitializationException: Initialization of CAS Processor with name "DictionaryLookupAnnotator" failed. CausedBy: org.apache.uima.resource.ResourceConfigurationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator" failed. (Descriptor file:/usr/local/apache-ctakes-3.2.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorDB.xml) CausedBy:org.apache.uima.resource.ResourceInitializationException CausedBy: java.lang.Exception: Unable to find external resource with key:UmlsIndexReader. So a totally different error. Very confused. Natalia On Fri, Jul 25, 2014 at 2:09 PM, Natalia Connolly < [email protected]> wrote: > 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 >>> >>> >>> >> >> >
