Re: Unable to get Confidence score for any entity [EXTERNAL]

[Miller, Timothy]

These items are created by a dictionary lookup -- not any kind of probabilistic 
algorithm -- which doesn't set the confidence score. There is nothing really 
like confidence distinguishing different kinds of found dictionary concepts.
Tim



From: Ratan Sharma 
Sent: Thursday, December 28, 2017 2:09 PM
To: dev@ctakes.apache.org
Subject: Unable to get Confidence score for any entity [EXTERNAL]

I am trying to find confidence score for difference section entities like -

ProcedureMention
SignSymptomMention
MedicationMention
DiseaseDisorderMention
AnatomicalSiteMention

But for all entities under any category, the Confidence score is always 0.0

Is there a specific setting I need to turn on to get these results.

Any suggestion / link to understand more would be helpful.

Unable to get Confidence score for any entity

[Ratan Sharma]

I am trying to find confidence score for difference section entities like -

ProcedureMention
SignSymptomMention
MedicationMention
DiseaseDisorderMention
AnatomicalSiteMention

But for all entities under any category, the Confidence score is always 0.0

Is there a specific setting I need to turn on to get these results.

Any suggestion / link to understand more would be helpful.

Re: Custom Dictionary connected to mysql [EXTERNAL]

[Finan, Sean]

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 
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 
> 
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.ar...@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=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=VOGRYBwYyG1zdYg5tgQm1oZ7uLNttyQdSvc7jDT9SV0=4USoFHxgktikbJUwVl1joy0LisnxFzv6M8HGQnlaRVg=

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=truecharacterEncoding=utf8useSSL=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 
>
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 
> >
> 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.fi...@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.natara...@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.ar...@raxa.com]
> > >
> > > Sent: Thursday, December 21, 2017 7:32 PM
> > >