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From Matthew Vita <matthewvit...@gmail.com>
Subject Re: Batching Queries in Ctakes Web Rest
Date Wed, 23 May 2018 06:52:45 GMT
Hi Zakir,

I would strongly suggest against using MIST/Sharp. This is a fairly bespoke
toolset in de-identifying data for a specific use-case. See "ii) Skip
de-identification." in the Readme.

Also, see the steps near the bottom to get a sense of how to run this in a
reasonable generic way:
https://github.com/tmills/ctakes-docker#running-with-custom-dictionaries

The documentation (and examples) aren't perfect. They should generally
point you in the right direction, but PRs and notes (on your experience)
are appreciated to improve them!

Thanks,


*Matthew Vita*Healthcare Software Engineer
https://www.patreon.com/matthewvita




On Tue, May 22, 2018 at 5:10 AM Zakir Saifi <zakir.saifi@raxa.com> wrote:

> Hi Matthew, I have looked into the ctakes docker. I have followed the
> instructions on the readme file and I am running it on my machine by
> skipping de-identification and run the CVD point to the
> desc/nodeidPipeline.xml. It is giving me the following error
>
> Unexpected error while initializing
> "org.apache.uima.aae.jms_adapter.JmsAnalysisEngineServiceAdapter" from
> descriptor file:/Users/zakirsaifi/ctakes-docker/desc/docker-mist.xml .
>
>
> docker-mist.xml file
>
> <?xml version="1.0" encoding="UTF-8" ?>
> <customResourceSpecifier xmlns="http://uima.apache.org/resourceSpecifier">
>
>
> <resourceClassName>org.apache.uima.aae.jms_adapter.JmsAnalysisEngineServiceAdapter</resourceClassName>
>   <parameters>
>     <parameter name="brokerURL" value="tcp://localhost:61616"/>
>     <parameter name="endpoint"  value="mistQueue"/>
>       <parameter name="binary_serialization" value="false"/>
>       <parameter name="ignore_process_errors" value="false"/>
>   </parameters>
> </customResourceSpecifier>
>
>
>
>
> On Tue, May 22, 2018 at 10:20 AM, Zakir Saifi <zakir.saifi@raxa.com>
> wrote:
>
> > Thanks, Matthew and Gandhi. I look into the docker solution.
> >
> > On Mon, May 21, 2018 at 9:59 PM, Matthew Vita <matthewvita48@gmail.com>
> > wrote:
> >
> >> Hi all,
> >>
> >> It's not using the REST service, but this docker solution allows for
> >> distributed queuing: https://github.com/tmills/ctakes-docker
> >>
> >> This may help with your large text volumes.
> >>
> >>
> >> On Mon, May 21, 2018, 9:02 AM Gandhi Rajan Natarajan <
> >> Gandhi.Natarajan@arisglobal.com> wrote:
> >>
> >> > Even if you send it in batch, the processing will be sequential I
> guess.
> >> > You may have to run multiple instances of REST service to process huge
> >> > volume of records.
> >> >
> >> > Regards,
> >> > Gandhi
> >> >
> >> > -----Original Message-----
> >> > From: Zakir Saifi [mailto:zakir.saifi@raxa.com]
> >> > Sent: Monday, May 21, 2018 4:23 PM
> >> > To: dev@ctakes.apache.org
> >> > Subject: Batching Queries in Ctakes Web Rest
> >> >
> >> > I am using ctakesRestService to process unstructured clinical text. I
> >> have
> >> > a long list of records which I want to be structured. On average
> Ctakes
> >> > service for me is taking 3.6 seconds to process a record. I want to
> >> *batch
> >> > this process* in order to reduce time. Is there any way in which I can
> >> sent
> >> > number of queries to the ctakes web rest service in batch and get the
> >> > appropriate result from it. My Ctakes version is 4.0.1. I have also
> >> changed
> >> > the default piper file and added other annotators for extracting more
> >> > information like BackwardsTimeAnnotator, DocTimeRelAnnotator etc.
> >> > ‚Äč
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