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From James Masanz <masanz.ja...@gmail.com>
Subject Re: Custom Dictionary connected to mysql [EXTERNAL]
Date Sat, 23 Dec 2017 02:38:26 GMT
one advantage of having the database entries be lower-case is performance.

since a dictionary in a database is typically significantly larger than a
BSV file dictionary, it is advantageous to lower case the database
dictionary entries just once.


On Thu, Dec 21, 2017 at 4:17 PM, Chahal Arora <chahal.arora@raxa.com> wrote:

> Hi Sean,
>
> I wanted the lookup to be case insensitive. Also wanted to go away with the
> restriction of putting enteries in lowercase in database like the way it
> was working with BSV.
>
> But if lowercase enteries are expected in database then I guess modifying
> database will work for me.
>
> On Fri, 22 Dec 2017 at 12:46 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Do you want your lookup to be case sensitive?  If so then new code would
> > be required.  The lookup is case insensitive because it does expect the
> > dictionary/database to contain only lowercase entries.  If you are ok
> with
> > the case insensitivity then I propose that you modify your database.
> > Sean
> >
> >
> > -----Original Message-----
> > From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisglobal.com]
> > Sent: Thursday, December 21, 2017 11:06 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: Custom Dictionary connected to mysql [EXTERNAL]
> >
> > I feel Sean and Tim will be the right persons to answer this.
> >
> >
> >
> > Regards,
> >
> > Gandhi
> >
> >
> >
> > -----Original Message-----
> >
> > From: Chahal Arora [mailto:chahal.arora@raxa.com]
> >
> > Sent: Thursday, December 21, 2017 7:32 PM
> >
> > To: dev@ctakes.apache.org
> >
> > Subject: Re: Custom Dictionary connected to mysql
> >
> >
> >
> > Hi Gandhi, Thank you for your help. It's working now. In the
> > customDictionary.xml, I changed
> > org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
> to
> > org.apache.ctakes.dictionary.lookup2.dictionary.
> UmlsJdbcRareWordDictionary
> >
> > and org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory to
> > org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory. For
> > single word term, this worked without any change, but for a multi-word
> > term, this was returning empty results. When I debugged, I found that the
> > issue was coming at code below in DefaultJCasTermAnnotator class line
> 103-
> > if ( hitTokens[ hit ].equals(allTokens.get( i ).getText() ) || hitTokens[
> > hit ].equals( allTokens.get( i ).getVariant() ) ); This was happening due
> > to the difference in string case. The input string is converted to
> > lowercase, but the string from MySQL database is not converted. Right
> now I
> > have to put all terms in my database in lower case to make it work. Do
> you
> > know any configuration so that I don't have to deal with the case issue
> > without changing DefaultJCasTermAnnotator file? When using BSV file, I am
> > getting lower case sting for both input and term.
> >
> >
> >
> >
> >
> >
> >
> > Regards
> >
> > Chahal Arora
> >
> > Software Engineer
> >
> > Raxa
> >
> >
> >
> > On Tue, Dec 19, 2017 at 11:23 PM, Gandhi Rajan Natarajan <
> > Gandhi.Natarajan@arisglobal.com> wrote:
> >
> >
> >
> > > Hi Chahal,
> >
> > >
> >
> > > Looking at the error trace:
> >
> > > ‘javax.servlet.ServletException,java.io.IOException
> >
> > > 19 Dec 2017 17:56:01  INFO RequestMappingHandlerAdapter - Looking for
> >
> > > @ControllerAdvice: WebApplicationContext for namespace
> >
> > > 'ctakes-rest-service-servlet'’
> >
> > >
> >
> > > It looks like you are trying to mix match codes from both
> >
> > > ctakes-rest-service and ctakes-web-rest module I guess.
> >
> > > Ctakes-rest-service module is obsolete now and request you to consider
> >
> > > only ctakes-web-rest module  in
> >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_GoTeamEpsilon_ctakes-2Drest-2D&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=6B-VtVwKMYDaxqmRYJgeUq-
> 3W2oT9wb6XDlnckfJ9rU&e=
> >
> > > service/tree/master/ctakes-web-rest
> >
> > >
> >
> > > Regards,
> >
> > > Gandhi
> >
> > >
> >
> > > From: Chahal Arora [mailto:chahal.arora@raxa.com]
> >
> > > Sent: Tuesday, December 19, 2017 8:20 PM
> >
> > > To: dev@ctakes.apache.org
> >
> > > Subject: Re: Custom Dictionary connected to mysql
> >
> > >
> >
> > > Hi Gandhi,
> >
> > >
> >
> > > With updated customDictionary.xml all errors were gone.
> >
> > >
> >
> > > I am not sure about the schema of the tables used. I have taken
> >
> > > reference from JdbcRareWordDictionary.java -
> >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_apache_&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=JLcnqVyhD1PRoXduqLRON_
> SkVHeLv0q7doqV6RSn-7A&e=
> >
> > > ctakes/blob/trunk/ctakes-dictionary-lookup-fast/src/
> >
> > > main/java/org/apache/ctakes/dictionary/lookup2/dictionary/
> >
> > > JdbcRareWordDictionary.java  and JdbcConceptFactory.java -
> >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_apache_ctakes_blob_trunk_ctakes-2D&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=cfygw3v7SDiH3Wjz_
> VepLVO006NEJBCH79qO3sHBlm4&e=
> >
> > > dictionary-lookup-fast/src/main/java/org/apache/ctakes/
> >
> > > dictionary/lookup2/concept/JdbcConceptFactory.java
> >
> > >
> >
> > > I am using the ctakes-rest-web server and getting all the annotation
> >
> > > array as empty in the result json.
> >
> > >
> >
> > > Attached tomcat logs again.
> >
> > >
> >
> > > Regards
> >
> > > Chahal Arora
> >
> > > Software Engineer
> >
> > > Raxa
> >
> > >
> >
> > > On Tue, Dec 19, 2017 at 6:44 PM, Gandhi Rajan Natarajan <
> >
> > > Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal.com
> >
> > > >>
> >
> > > wrote:
> >
> > > Not able to see any tomcat logs attached.
> >
> > >
> >
> > > Do you see any errors in tomcat console?
> >
> > >
> >
> > > Regards,
> >
> > > Gandhi
> >
> > >
> >
> > > From: Chahal Arora [mailto:chahal.arora@raxa.com<mailto:
> >
> > > chahal.arora@raxa.com>]
> >
> > > Sent: Tuesday, December 19, 2017 6:09 PM
> >
> > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
> >
> > > Subject: Re: Custom Dictionary connected to mysql
> >
> > >
> >
> > > Hi,
> >
> > >
> >
> > > I have updated the customDictionary.xml and all the erros have gone
> >
> > > but still not getting any result. I am attaching the latest
> >
> > > customDictionary.xml and tomcat logs file.
> >
> > >
> >
> > >
> >
> > >
> >
> > > Regards
> >
> > > Chahal Arora
> >
> > > Software Engineer
> >
> > > Raxa
> >
> > >
> >
> > > On Tue, Dec 19, 2017 at 5:45 PM, Chahal Arora <chahal.arora@raxa.com
> >
> > > <mailto:chahal.arora@raxa.com><mailto:chahal.arora@raxa.com<mailto:c
> >
> > > hahal.arora@raxa.com>>> wrote:
> >
> > > Hi All,
> >
> > >
> >
> > > I was working on moving the terms from custom dictionary BSV file to
> >
> > > MySQL database in LabValueFinder. I am able to connect to the database
> >
> > > but not sure about the database schema.
> >
> > >
> >
> > > Is there an example available where the custom dictionary is connected
> >
> > > to mysql database instead of a bsv file or hsql database?
> >
> > >
> >
> > > Attached is the customDictionary.xml file that I am using.
> >
> > >
> >
> > >
> >
> > > Regards
> >
> > > Chahal Arora
> >
> > > Software Engineer
> >
> > > Raxa
> >
> > >
> >
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> > --
> Regards
> Chahal Arora
> Software Engineer
> Raxa
>

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