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 <gandhiraja...@gmail.com> 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 <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 > !!!" > >
