Thanks Sean for your understanding, and I am in hope now. Where is the best place to start looking at regarding "create a collection reader that works similarly to org.apache.ctakes.core.cr. FilesInDirectoryCollectionReader"?
Justin On Wed, Aug 5, 2015 at 7:24 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Justin, > > A shot in the dark: > You could create a collection reader that works similarly to > org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader , but instead of > grabbing all of the files in a directory it grabs all the records parsed > from a single .xml and runs a pipeline per record. Basically, swap a > directory for an .xml, a text file for an xml element containing a record. > Somebody out there might have something that already does as much. > > Sean > > -----Original Message----- > From: Justin Zhang [mailto:justinzhang...@gmail.com] > Sent: Wednesday, August 05, 2015 6:40 PM > To: u...@ctakes.apache.org; dev@ctakes.apache.org > Subject: how to run i2b2 data > > Hello everyone, > > I am running ctakes with i2b2 data > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.i2b2.org_NLP_DataSets_Main.php&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=IygWj6YGkcjofGRbrDiFJacJHMaBveHR9qzY0VD1AAE&s=swpt3QP4-B392iLlJ9wypBwD17tRDOCxPdSZOW1rS8s&e= > > In each xml file, there are multiple patient records. I am able to > separate each patient into single files and process them with "runCPE.sh" > > Is there a way to convert this single xml file into the format "ctakes" > accepted, and process as a single input file, and generate a single output > file (results labelled by patient id). For example, each patient id has a > "smoking status". > > Thanks, > > -- > Justin > -- Justin
