Hi Sajit, I m able to find the thread safe pipeline in the latest source code in SVN under https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/
You can rebuild the latest code if it's not available in cTAKES 4.0 Monday, April 8, 2019, Sajit Kumar <kumar.sajit...@gmail.com> wrote: > Hi Gandhi, > > I did go and check Sean's mail on Thread Safe DefaultClinicialPipeline. > > https://markmail.org/message/clv3wgrztgh2swjd > > It mentions of a new ThreadSafe pipeline file suffixed with Ts. I didn't > find it the apache ctakes directory. I also tried manually including the > "threads" command in the piper file and i got a error message saying > unknown command. Can you please tell me if its available in cTakes version > 4.0 on Windows. Looking forward to hearing from you. Thanks for your help. > > Regards, > Sajit > > On Sun, Apr 7, 2019 at 10:50 PM gandhi rajan <gandhiraja...@gmail.com> > wrote: > >> Hi Sajit, >> >> As far as I know you can curtail default clinical pipeline as per your >> needs and it does support batch processing too. Please refer earlier mail >> chains from Sean regarding thread safe default clinical pipeline. >> >> On Sunday, April 7, 2019, Sajit Kumar <kumar.sajit...@gmail.com> wrote: >> >>> Hi, >>> >>> I am trying to batch process the clinical notes from MIMIC database. I >>> tried using the CPE tool provided with cTakes for this.I am only interested >>> in extracting the CUIs from the notes. So i created a CPE file using >>> CuisOnlyUMLSProcessor >>> as the CAS Consumer. The XML output using FileWriterCasConsumer works >>> without a problem. >>> >>> However, I wanted the output as XMI instead of the XML as provided by >>> the standard templates. For this i tried using the writer xml's provided in >>> \desc\ctakes-core\desc\cas_consumer directory. I also tried changing >>> the implementation name in these files to org.apache.uima.tools. >>> components.XmiWriterCasConsumer. I get exceptions and am not able to >>> generate a XMI output. >>> >>> I have seen people suggesting to use the Default Clinical pipeline to do >>> a batch processing. However, this has 2 drawbacks. I am stuck using the >>> standard processors and end up with lot of details that i dont need. Also >>> the CPE configuration file provides a multi-threading option thereby help >>> speed up the process. I have close to 200K files to process. >>> >>> Please help to resolve this issue. Thank you. >>> >>> Regards, >>> Sajit >>> >> >> >> -- >> Regards, >> Gandhi >> >> "The best way to find urself is to lose urself in the service of others >> !!!" >> >> -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
