Hi Sajit, Could you post the error trace so that it will easy to figure out the problem.
On Thursday, April 11, 2019, Sajit Kumar <[email protected]> wrote: > Hi Gandhi, > > I tried building ctakes on my local computer. I used the maven build > command to build it. The build fails for the ctakes ytex module. Any > suggestions to fix it. Thank you, > > Regards, > Sajit > > On Mon, Apr 8, 2019 at 9:24 PM gandhi rajan <[email protected]> > wrote: > >> 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 <[email protected]> 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 <[email protected]> >>> 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 <[email protected]> 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 >> !!!" >> >> -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
