Update in cTAKES 3.2 (was Re: UMLS integration with cTAKES 3.1​)

[Natalia Connolly <na...@gmail.com>]

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 <
natalia.v.connolly@gmail.com> wrote:

> Yes, I did.  The same problem.
>
> Natalia
>
>
>
> On Fri, Jul 25, 2014 at 2:06 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu
> > 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" <
>> natalia.v.connolly@gmail.com> 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 <
>> Pei.Chen@childrens.harvard.edu> 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:natalia.v.connolly@gmail.com]
>>> *Sent:* Friday, July 25, 2014 1:54 PM
>>> *To:* user@ctakes.apache.org
>>>
>>> *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 <
>>> Pei.Chen@childrens.harvard.edu> 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:john.travis.green@gmail.com]
>>> > Sent: Friday, July 25, 2014 1:06 PM
>>> > To: user@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.studio@gmail.com>
>>> > wrote:
>>> >
>>> > > —
>>> > > ---------- Forwarded message ----------
>>> > > From: "Natalia Connolly" <na...@gmail.com>
>>> > > Date: Fri, Jul 25, 2014 at 12:35 PM
>>> > > Subject: UMLS integration with cTAKES 3.1
>>> > > To: "user@ctakes.apache.org" <us...@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
>>>
>>>
>>>
>>
>>
>