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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu> on 2017/12/21 19:14:47 UTC
RE: Custom Dictionary connected to mysql [EXTERNAL]
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<ma...@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
> <ma...@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
>
> This email and any files transmitted with it are confidential and
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> This email and any files transmitted with it are confidential and
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This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: Custom Dictionary connected to mysql [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Chahal Arora,
That is strange. It looks like it had one good run, then a bad one, then a good one again ...
I have run in docker containers without problem. Would you mind sending me the contents of your dockerfile? I probably won't see anything that would point to a cause, but you never know.
Sean
________________________________
From: Chahal Arora <ch...@raxa.com>
Sent: Wednesday, December 27, 2017 3:59 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
Hi Sean,
I am not trying to run it with multiple threads and in fact, I haven't changed the code for the JdbcRareWordDictionary class. The changes are done in the customDictionary.xml file only.
The issue comes when I am running it in a docker container. I did not encounter this issue on my local machine.
Attaching logs file.
Regards
Chahal Arora
Software Engineer
Raxa
On Wed, Dec 27, 2017 at 8:30 PM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Hi Chahal Arora,
That is odd - I have never seen that message. Are you trying to run with multiple threads? Like most of ctakes, that class was designed to be run in a single thread. There are thread-safe wrappers that can be used if needed, but they should not be relied upon for speed increases.
Sean
-----Original Message-----
From: Chahal Arora [mailto:chahal.arora@raxa.com<ma...@raxa.com>]
Sent: Wednesday, December 27, 2017 7:53 AM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
Hi Gandhi, Sean, and James
Thank you all for your help.
It ran fine but after some time, I started getting the following error-
ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
The class giving the issue is -
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_apache_ctakes_blob_bed6cca07743e30aec40aae30af1738a0ba1a93d_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_dictionary_JdbcRareWordDictionary.java&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=VOGRYBwYyG1zdYg5tgQm1oZ7uLNttyQdSvc7jDT9SV0&s=4USoFHxgktikbJUwVl1joy0LisnxFzv6M8HGQnlaRVg&e=
It looks like the statement is getting closed by a thread and another thread is trying to use it.
mysqlUrl entred - jdbc:mysql://
127.0.0.1:3306/umlstest?useUnicode=true&characterEncoding=utf8&useSSL=false&<https://urldefense.proofpoint.com/v2/url?u=http-3A__127.0.0.1-3A3306_umlstest-3FuseUnicode-3Dtrue-26amp-3BcharacterEncoding-3Dutf8-26amp-3BuseSSL-3Dfalse-26amp&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=OtAYNwT2bbu1m08TwSrUBxNE0iWAIOvJO0Z5zctWDZc&s=jfxWPdvPNcvw7Nnn7egQDgBBez-2fUkwCP7qIBif1bw&e=>
Is there a MySQL setting I need to change or the code in JdbcRareWordDictionary.java like creating a connection pool?
Regards
Chahal Arora
Regards
Chahal Arora
Software Engineer
Raxa
On Sat, Dec 23, 2017 at 8:08 AM, James Masanz <ma...@gmail.com>>
wrote:
> 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 <ch...@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<ma...@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<ma...@arisglobal.com>]
> > > Sent: Thursday, December 21, 2017 11:06 AM
> > > To: dev@ctakes.apache.org<ma...@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<ma...@raxa.com>]
> > >
> > > Sent: Thursday, December 21, 2017 7:32 PM
> > >
> > > To: dev@ctakes.apache.org<ma...@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.JdbcRareWordDictio
> > > nary
> > 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<ma...@arisglobal.com>> wrote:
> > >
> > >
> > >
> > > > Hi Chahal,
> > >
> > > >
> > >
> > > > Looking at the error trace:
> > >
> > > > ‘javax.servlet.ServletException,java.io<https://urldefense.proofpoint.com/v2/url?u=http-3A__java.io&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=OtAYNwT2bbu1m08TwSrUBxNE0iWAIOvJO0Z5zctWDZc&s=zuFuWd0OJ_AZFWdb8-R7FTxUGeX-O7Su8dW8n5DysV8&e=>.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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=
> > FqnIF6F3Z8G6N9y2xdT6hsGRUtI9Gkcio-84DqbbEJM&s=6B-VtVwKMYDaxqmRYJgeUq
> > -
> > 3W2oT9wb6XDlnckfJ9rU&e=
> > >
> > > > service/tree/master/ctakes-web-rest
> > >
> > > >
> > >
> > > > Regards,
> > >
> > > > Gandhi
> > >
> > > >
> > >
> > > > From: Chahal Arora [mailto:chahal.arora@raxa.com<ma...@raxa.com>]
> > >
> > > > Sent: Tuesday, December 19, 2017 8:20 PM
> > >
> > > > To: dev@ctakes.apache.org<ma...@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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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<ma...@arisglobal.com><mailto:Gandhi.Natarajan@<mailto:Gandhi.Natarajan@>
> arisglobal.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__arisglobal.com&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=OtAYNwT2bbu1m08TwSrUBxNE0iWAIOvJO0Z5zctWDZc&s=L4t5FZNT7UDWG9nuZF5bGk9ptyqgA9mrxyTb43rT9kQ&e=>
> > >
> > > > >>
> > >
> > > > 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<ma...@raxa.com><mailto:
> > >
> > > > chahal.arora@raxa.com<ma...@raxa.com>>]
> > >
> > > > Sent: Tuesday, December 19, 2017 6:09 PM
> > >
> > > > To: dev@ctakes.apache.org<ma...@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
> > > > <ch...@raxa.com>
> > >
> > > > <ma...@raxa.com><mail
> > > > to:c
> > >
> > > > hahal.arora@raxa.com<ma...@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
> > >
> > > >
> > >
> > > > This email and any files transmitted with it are confidential
> > > > and
> > >
> > > > intended solely for the use of the individual or entity to whom
> > > > they
> > are
> > > addressed.
> > >
> > > > If you are not the named addressee you should not disseminate,
> > >
> > > > distribute or copy this e-mail. Please notify the sender or
> > > > system
> > >
> > > > manager by email immediately if you have received this e-mail by
> > >
> > > > mistake and delete this e-mail from your system. If you are not
> > > > the
> > >
> > > > intended recipient you are notified that disclosing, copying,
> > >
> > > > distributing or taking any action in reliance on the contents of
> > > > this
> > >
> > > > information is strictly prohibited and against the law.
> > >
> > > >
> > >
> > > > This email and any files transmitted with it are confidential
> > > > and
> > >
> > > > intended solely for the use of the individual or entity to whom
> > > > they
> > are
> > > addressed.
> > >
> > > > If you are not the named addressee you should not disseminate,
> > >
> > > > distribute or copy this e-mail. Please notify the sender or
> > > > system
> > >
> > > > manager by email immediately if you have received this e-mail by
> > >
> > > > mistake and delete this e-mail from your system. If you are not
> > > > the
> > >
> > > > intended recipient you are notified that disclosing, copying,
> > >
> > > > distributing or taking any action in reliance on the contents of
> > > > this
> > >
> > > > information is strictly prohibited and against the law.
> > >
> > > >
> > >
> > > This email and any files transmitted with it are confidential and
> > intended
> > > solely for the use of the individual or entity to whom they are
> > addressed.
> > > If you are not the named addressee you should not disseminate,
> distribute
> > > or copy this e-mail. Please notify the sender or system manager by
> email
> > > immediately if you have received this e-mail by mistake and delete
> > > this e-mail from your system. If you are not the intended
> > > recipient you are notified that disclosing, copying, distributing
> > > or taking any action in reliance on the contents of this
> > > information is strictly prohibited and against the law.
> > >
> > > --
> > Regards
> > Chahal Arora
> > Software Engineer
> > Raxa
> >
>
Re: Custom Dictionary connected to mysql [EXTERNAL]
Posted by Chahal Arora <ch...@raxa.com>.
Hi Sean,
I am not trying to run it with multiple threads and in fact, I haven't
changed the code for the JdbcRareWordDictionary class. The changes are done
in the customDictionary.xml file only.
The issue comes when I am running it in a docker container. I did not
encounter this issue on my local machine.
Attaching logs file.
Regards
Chahal Arora
Software Engineer
Raxa
On Wed, Dec 27, 2017 at 8:30 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Chahal Arora,
>
> That is odd - I have never seen that message. Are you trying to run with
> multiple threads? Like most of ctakes, that class was designed to be run
> in a single thread. There are thread-safe wrappers that can be used if
> needed, but they should not be relied upon for speed increases.
>
> Sean
>
> -----Original Message-----
> From: Chahal Arora [mailto:chahal.arora@raxa.com]
> Sent: Wednesday, December 27, 2017 7:53 AM
> To: dev@ctakes.apache.org
> Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
>
> Hi Gandhi, Sean, and James
>
> Thank you all for your help.
>
> It ran fine but after some time, I started getting the following error-
>
> ERROR JdbcRareWordDictionary - No operations allowed after statement
> closed.
>
> The class giving the issue is -
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_apache_ctakes_blob_bed6cca07743e30aec40aae30af1738a0ba1a93d_ctakes-
> 2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_
> ctakes_dictionary_lookup2_dictionary_JdbcRareWordDictionary.java&d=
> DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> VOGRYBwYyG1zdYg5tgQm1oZ7uLNttyQdSvc7jDT9SV0&s=
> 4USoFHxgktikbJUwVl1joy0LisnxFzv6M8HGQnlaRVg&e=
>
> It looks like the statement is getting closed by a thread and another
> thread is trying to use it.
>
> mysqlUrl entred - jdbc:mysql://
> 127.0.0.1:3306/umlstest?useUnicode=true&characterEncoding=utf8&
> useSSL=false&
>
> Is there a MySQL setting I need to change or the code in
> JdbcRareWordDictionary.java like creating a connection pool?
>
> Regards
> Chahal Arora
>
> Regards
> Chahal Arora
> Software Engineer
> Raxa
>
> On Sat, Dec 23, 2017 at 8:08 AM, James Masanz <ma...@gmail.com>
> wrote:
>
> > 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 <ch...@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.JdbcRareWordDictio
> > > > nary
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > pKGd4f7d4gTao&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<ma...@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
> > > >
> > > > > <ma...@raxa.com><mailto:chahal.arora@raxa.com<mail
> > > > > to: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
> > > >
> > > > >
> > > >
> > > > > This email and any files transmitted with it are confidential
> > > > > and
> > > >
> > > > > intended solely for the use of the individual or entity to whom
> > > > > they
> > > are
> > > > addressed.
> > > >
> > > > > If you are not the named addressee you should not disseminate,
> > > >
> > > > > distribute or copy this e-mail. Please notify the sender or
> > > > > system
> > > >
> > > > > manager by email immediately if you have received this e-mail by
> > > >
> > > > > mistake and delete this e-mail from your system. If you are not
> > > > > the
> > > >
> > > > > intended recipient you are notified that disclosing, copying,
> > > >
> > > > > distributing or taking any action in reliance on the contents of
> > > > > this
> > > >
> > > > > information is strictly prohibited and against the law.
> > > >
> > > > >
> > > >
> > > > > This email and any files transmitted with it are confidential
> > > > > and
> > > >
> > > > > intended solely for the use of the individual or entity to whom
> > > > > they
> > > are
> > > > addressed.
> > > >
> > > > > If you are not the named addressee you should not disseminate,
> > > >
> > > > > distribute or copy this e-mail. Please notify the sender or
> > > > > system
> > > >
> > > > > manager by email immediately if you have received this e-mail by
> > > >
> > > > > mistake and delete this e-mail from your system. If you are not
> > > > > the
> > > >
> > > > > intended recipient you are notified that disclosing, copying,
> > > >
> > > > > distributing or taking any action in reliance on the contents of
> > > > > this
> > > >
> > > > > information is strictly prohibited and against the law.
> > > >
> > > > >
> > > >
> > > > This email and any files transmitted with it are confidential and
> > > intended
> > > > solely for the use of the individual or entity to whom they are
> > > addressed.
> > > > If you are not the named addressee you should not disseminate,
> > distribute
> > > > or copy this e-mail. Please notify the sender or system manager by
> > email
> > > > immediately if you have received this e-mail by mistake and delete
> > > > this e-mail from your system. If you are not the intended
> > > > recipient you are notified that disclosing, copying, distributing
> > > > or taking any action in reliance on the contents of this
> > > > information is strictly prohibited and against the law.
> > > >
> > > > --
> > > Regards
> > > Chahal Arora
> > > Software Engineer
> > > Raxa
> > >
> >
>
RE: Custom Dictionary connected to mysql [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Chahal Arora,
That is odd - I have never seen that message. Are you trying to run with multiple threads? Like most of ctakes, that class was designed to be run in a single thread. There are thread-safe wrappers that can be used if needed, but they should not be relied upon for speed increases.
Sean
-----Original Message-----
From: Chahal Arora [mailto:chahal.arora@raxa.com]
Sent: Wednesday, December 27, 2017 7:53 AM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
Hi Gandhi, Sean, and James
Thank you all for your help.
It ran fine but after some time, I started getting the following error-
ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
The class giving the issue is -
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_apache_ctakes_blob_bed6cca07743e30aec40aae30af1738a0ba1a93d_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_dictionary_JdbcRareWordDictionary.java&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=VOGRYBwYyG1zdYg5tgQm1oZ7uLNttyQdSvc7jDT9SV0&s=4USoFHxgktikbJUwVl1joy0LisnxFzv6M8HGQnlaRVg&e=
It looks like the statement is getting closed by a thread and another thread is trying to use it.
mysqlUrl entred - jdbc:mysql://
127.0.0.1:3306/umlstest?useUnicode=true&characterEncoding=utf8&useSSL=false&
Is there a MySQL setting I need to change or the code in JdbcRareWordDictionary.java like creating a connection pool?
Regards
Chahal Arora
Regards
Chahal Arora
Software Engineer
Raxa
On Sat, Dec 23, 2017 at 8:08 AM, James Masanz <ma...@gmail.com>
wrote:
> 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 <ch...@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.JdbcRareWordDictio
> > > nary
> > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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<ma...@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
> > >
> > > > <ma...@raxa.com><mailto:chahal.arora@raxa.com<mail
> > > > to: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
> > >
> > > >
> > >
> > > > This email and any files transmitted with it are confidential
> > > > and
> > >
> > > > intended solely for the use of the individual or entity to whom
> > > > they
> > are
> > > addressed.
> > >
> > > > If you are not the named addressee you should not disseminate,
> > >
> > > > distribute or copy this e-mail. Please notify the sender or
> > > > system
> > >
> > > > manager by email immediately if you have received this e-mail by
> > >
> > > > mistake and delete this e-mail from your system. If you are not
> > > > the
> > >
> > > > intended recipient you are notified that disclosing, copying,
> > >
> > > > distributing or taking any action in reliance on the contents of
> > > > this
> > >
> > > > information is strictly prohibited and against the law.
> > >
> > > >
> > >
> > > > This email and any files transmitted with it are confidential
> > > > and
> > >
> > > > intended solely for the use of the individual or entity to whom
> > > > they
> > are
> > > addressed.
> > >
> > > > If you are not the named addressee you should not disseminate,
> > >
> > > > distribute or copy this e-mail. Please notify the sender or
> > > > system
> > >
> > > > manager by email immediately if you have received this e-mail by
> > >
> > > > mistake and delete this e-mail from your system. If you are not
> > > > the
> > >
> > > > intended recipient you are notified that disclosing, copying,
> > >
> > > > distributing or taking any action in reliance on the contents of
> > > > this
> > >
> > > > information is strictly prohibited and against the law.
> > >
> > > >
> > >
> > > This email and any files transmitted with it are confidential and
> > intended
> > > solely for the use of the individual or entity to whom they are
> > addressed.
> > > If you are not the named addressee you should not disseminate,
> distribute
> > > or copy this e-mail. Please notify the sender or system manager by
> email
> > > immediately if you have received this e-mail by mistake and delete
> > > this e-mail from your system. If you are not the intended
> > > recipient you are notified that disclosing, copying, distributing
> > > or taking any action in reliance on the contents of this
> > > information is strictly prohibited and against the law.
> > >
> > > --
> > Regards
> > Chahal Arora
> > Software Engineer
> > Raxa
> >
>
Re: Custom Dictionary connected to mysql [EXTERNAL]
Posted by Chahal Arora <ch...@raxa.com>.
Hi Gandhi, Sean, and James
Thank you all for your help.
It ran fine but after some time, I started getting the following error-
ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
The class giving the issue is -
https://github.com/apache/ctakes/blob/bed6cca07743e30aec40aae30af1738a0ba1a93d/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java
It looks like the statement is getting closed by a thread and another
thread is trying to use it.
mysqlUrl entred - jdbc:mysql://
127.0.0.1:3306/umlstest?useUnicode=true&characterEncoding=utf8&useSSL=false&
Is there a MySQL setting I need to change or the code in
JdbcRareWordDictionary.java
like creating a connection pool?
Regards
Chahal Arora
Regards
Chahal Arora
Software Engineer
Raxa
On Sat, Dec 23, 2017 at 8:08 AM, James Masanz <ma...@gmail.com>
wrote:
> 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 <ch...@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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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<ma...@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
> > >
> > > > <ma...@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
> > >
> > > >
> > >
> > > > This email and any files transmitted with it are confidential and
> > >
> > > > intended solely for the use of the individual or entity to whom they
> > are
> > > addressed.
> > >
> > > > If you are not the named addressee you should not disseminate,
> > >
> > > > distribute or copy this e-mail. Please notify the sender or system
> > >
> > > > manager by email immediately if you have received this e-mail by
> > >
> > > > mistake and delete this e-mail from your system. If you are not the
> > >
> > > > intended recipient you are notified that disclosing, copying,
> > >
> > > > distributing or taking any action in reliance on the contents of this
> > >
> > > > information is strictly prohibited and against the law.
> > >
> > > >
> > >
> > > > This email and any files transmitted with it are confidential and
> > >
> > > > intended solely for the use of the individual or entity to whom they
> > are
> > > addressed.
> > >
> > > > If you are not the named addressee you should not disseminate,
> > >
> > > > distribute or copy this e-mail. Please notify the sender or system
> > >
> > > > manager by email immediately if you have received this e-mail by
> > >
> > > > mistake and delete this e-mail from your system. If you are not the
> > >
> > > > intended recipient you are notified that disclosing, copying,
> > >
> > > > distributing or taking any action in reliance on the contents of this
> > >
> > > > information is strictly prohibited and against the law.
> > >
> > > >
> > >
> > > This email and any files transmitted with it are confidential and
> > intended
> > > solely for the use of the individual or entity to whom they are
> > addressed.
> > > If you are not the named addressee you should not disseminate,
> distribute
> > > or copy this e-mail. Please notify the sender or system manager by
> email
> > > immediately if you have received this e-mail by mistake and delete this
> > > e-mail from your system. If you are not the intended recipient you are
> > > notified that disclosing, copying, distributing or taking any action in
> > > reliance on the contents of this information is strictly prohibited and
> > > against the law.
> > >
> > > --
> > Regards
> > Chahal Arora
> > Software Engineer
> > Raxa
> >
>
Re: Custom Dictionary connected to mysql [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
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 <ch...@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<ma...@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
> >
> > > <ma...@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
> >
> > >
> >
> > > This email and any files transmitted with it are confidential and
> >
> > > intended solely for the use of the individual or entity to whom they
> are
> > addressed.
> >
> > > If you are not the named addressee you should not disseminate,
> >
> > > distribute or copy this e-mail. Please notify the sender or system
> >
> > > manager by email immediately if you have received this e-mail by
> >
> > > mistake and delete this e-mail from your system. If you are not the
> >
> > > intended recipient you are notified that disclosing, copying,
> >
> > > distributing or taking any action in reliance on the contents of this
> >
> > > information is strictly prohibited and against the law.
> >
> > >
> >
> > > This email and any files transmitted with it are confidential and
> >
> > > intended solely for the use of the individual or entity to whom they
> are
> > addressed.
> >
> > > If you are not the named addressee you should not disseminate,
> >
> > > distribute or copy this e-mail. Please notify the sender or system
> >
> > > manager by email immediately if you have received this e-mail by
> >
> > > mistake and delete this e-mail from your system. If you are not the
> >
> > > intended recipient you are notified that disclosing, copying,
> >
> > > distributing or taking any action in reliance on the contents of this
> >
> > > information is strictly prohibited and against the law.
> >
> > >
> >
> > This email and any files transmitted with it are confidential and
> intended
> > solely for the use of the individual or entity to whom they are
> addressed.
> > If you are not the named addressee you should not disseminate, distribute
> > or copy this e-mail. Please notify the sender or system manager by email
> > immediately if you have received this e-mail by mistake and delete this
> > e-mail from your system. If you are not the intended recipient you are
> > notified that disclosing, copying, distributing or taking any action in
> > reliance on the contents of this information is strictly prohibited and
> > against the law.
> >
> > --
> Regards
> Chahal Arora
> Software Engineer
> Raxa
>
Re: Custom Dictionary connected to mysql [EXTERNAL]
Posted by Chahal Arora <ch...@raxa.com>.
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<ma...@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
>
> > <ma...@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
>
> >
>
> > This email and any files transmitted with it are confidential and
>
> > intended solely for the use of the individual or entity to whom they are
> addressed.
>
> > If you are not the named addressee you should not disseminate,
>
> > distribute or copy this e-mail. Please notify the sender or system
>
> > manager by email immediately if you have received this e-mail by
>
> > mistake and delete this e-mail from your system. If you are not the
>
> > intended recipient you are notified that disclosing, copying,
>
> > distributing or taking any action in reliance on the contents of this
>
> > information is strictly prohibited and against the law.
>
> >
>
> > This email and any files transmitted with it are confidential and
>
> > intended solely for the use of the individual or entity to whom they are
> addressed.
>
> > If you are not the named addressee you should not disseminate,
>
> > distribute or copy this e-mail. Please notify the sender or system
>
> > manager by email immediately if you have received this e-mail by
>
> > mistake and delete this e-mail from your system. If you are not the
>
> > intended recipient you are notified that disclosing, copying,
>
> > distributing or taking any action in reliance on the contents of this
>
> > information is strictly prohibited and against the law.
>
> >
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> If you are not the named addressee you should not disseminate, distribute
> or copy this e-mail. Please notify the sender or system manager by email
> immediately if you have received this e-mail by mistake and delete this
> e-mail from your system. If you are not the intended recipient you are
> notified that disclosing, copying, distributing or taking any action in
> reliance on the contents of this information is strictly prohibited and
> against the law.
>
> --
Regards
Chahal Arora
Software Engineer
Raxa