Chahal, By the way, I was having a similar problem, but I don't think iBoundaryAnnType has to do with offsets, but rather refers to an Annotation type.
when it's set to -1, generateDrugMentionsAndAnnotations throws an exception, which is ArrayOutOfBounds stemming from getNarrativeSpansContainingGivenSpanType: Iterator iter = indexes.getAnnotationIndex(annotType).iterator(); (where annotType is iBoundaryAnnType.) It should be set by passing a string, which is the name of a class, e.g., add org.apache.ctakes.drugner.ae.DrugMentionAnnotator STATUS_BOUNDARY_ANN_TYPE="org.apache.ctakes.typesystem.type.textsem.MedicationMention" (note that you have to use STATUS_BOUNDARY_ANN_TYPE) Also, I think it's fine to leave DISTANCE at -1, as it looks to me like it is more of a maximum than a minimum value. -Taylor On Fri, Dec 1, 2017 at 5:23 AM Chahal Arora <chahal.ar...@raxa.com> wrote: > Hi All, > > While debugging DrugMentionAnnotator.java, I found that the issue was > coming because the value of variables iWindowSize, iBoundaryAnnType have > been set to -1 by default. The value of these variables does not > change because in the following code I get null values for > *windowSize* and *boundaryAnnTypeName > *in the initialize method of DrugMentionAnnotator*.* > > String windowSize = (String)annotCtx.getConfigParameterValue(DISTANCE); > String boundaryAnnTypeName > =(String)annotCtx.getConfigParameterValue(BOUNDARY_ANN_TYPE); > > if(windowSize != null) > iWindowSize = Integer.parseInt(windowSize); > > if(boundaryAnnTypeName != null) > iBoundaryAnnType = JCasUtil.getType(boundaryAnnTypeName); > > > The DrugNer worked for me when I changed the value of *iWindowSize*, > *iBoundaryAnnType* to the length of the input string. > > Does anyone know how can I add this change from piper file and as far I can > see the right way to do it is by changing the values of *DISTANCE* and > *BOUNDARY_ANN_TYPE* but I am not sure about this and don't know how to do > it? > > Can anyone help me with this? > > Regards > Chahal Arora > Software Engineer > Raxa > > Regards > Chahal Arora > Software Engineer > Raxa > > On Thu, Nov 30, 2017 at 6:20 PM, Chahal Arora <chahal.ar...@raxa.com> > wrote: > > > Hi All, > > > > I am trying to use the Drug NER using the pipeline. I am able to get the > > medication mention > (org.apache.ctakes.typesystem.type.textsem.MedicationMention) > > and get the value for drug but the issue is that I am getting null values > > for medication dosage/frequency/strength/duration. > > > > I have looked into some of the solution provided in the mailing list but > > still the same result- > > > > 1) http://mail-archives.apache.org/mod_mbox/ctakes-user/201711.mbox/% > > 3cb7d4354fde864bbba44d2427f281a...@blrkecmbx34.ad.infosys.com%3E > > > > 2) http://dev.ctakes.apache.narkive.com/ixUkpiO5/enabling- > > drugner-pipeline-and-identifying-dates#post14 > > > > Some sample input text that I have tested on - > > > > 1) ASAT 10mg Tablet(Atorvastatin): Take 1 Tablet Four times daily, after > > meals and at bedtime for 5 days. > > > > 2) The patient started study treatment of Thalomid 200mg (days 1-21), and > > Epirubicin, 20 mg /m2 (days 1, 8, and 15) on 06/07/02 for the treatment > of > > hepatocellular carcinoma. > > > > 3) ASAT 10mg Four times daily > > > > 4) paracetamol BID AC 10d PO, aspirin BD > > > > > > Regards > > Chahal Arora > > Software Engineer > > Raxa > > >
