Turns out that this problem was indeed due to the fact that package names had changed from v4.x.x to v5.x.x from ...drugner... to ..drug.ner.. But across the sources and typesystem files it had not been completely done and had been left in a halfway state. By reverting the package spec of resources in the drugner jar
from *resources/org/apache/drug/ner/**<typesystem stuff>* to *resources/org/apache/drugner/<**typesystem stuff>* It started working again Peter On Tue, Dec 3, 2024 at 11:50 PM Finan, Sean <sean.fi...@childrens.harvard.edu.invalid> wrote: > Hi Peter, > > This looks like the same problem encountered here: > https://github.com/apache/ctakes/issues/23 > > It was fixed for -standard- ctakes workflows in 6.0.0, but if you don't > use the PiperFileRunner or have a custom reader then you may still see the > problem. > > The root cause is still an open issue in uima, so if anybody out there has > a general solution please share. > https://github.com/apache/uima-uimaj/issues/234 > > > Sean > > ________________________________ > From: Peter Abramowitsch <pabramowit...@gmail.com> > Sent: Tuesday, December 3, 2024 3:29 PM > To: dev@ctakes.apache.org <dev@ctakes.apache.org> > Subject: Question about DrugNerAnnotator [EXTERNAL] > > * External Email - Caution * > > > Hi All > > If anyone has tried using the Drugner in 5.1.0 have they run into this > error when its process() method is run. > > message: JCas type > "org.apache.ctakes.drugner.type.FractionStrengthAnnotation" used in > Java code, but was not declared in the XML type descriptor > > The thing is that this attribute is declared in the annotator's Xml > Type Description, and because FractionStrengthAnnotation is also the > first one that the code attempts to access, I'm assuming that none of > the other attributes are found either. > attribute defs will actually be found > > <typeDescription> > > <name>org.apache.ctakes.drugner.type.FractionStrengthAnnotation</name> > > <description>The fraction portion of dosages strength determination for the > Drug NER profile.</description> > > <supertypeName>uima.tcas.Annotation</supertypeName> > > </typeDescription> > > etc > > I've looked for a rogue > *org.apache.ctakes.drugner.types.TypeSystem.xml* elswhere in my > classpath and there isn't one. But there is an issue that some bits > of the configuration & src of this annotator refer to the package as > *org.apache.ctakes.drugner*. and others as > *org.apache.ctakes.drug.ner.* The use of both "stringifyied package > names" and actual packages in the FIT architecture always confuses me. > This discrepancy is something that crept into certain annotators whose > packages changed in 5.0.x. At that time I fixed all of these so they > would compile, but it seems there are still issues. > > Any thoughts? > > Peter >
