Hi Mike,
Have you tried the getCoveredText() method that IdentifiedAnnotation
inherits from Annotation?
- Jessica
On Tue, Feb 13, 2018 at 2:42 PM, Michael Trepanier <m...@metistream.com>
wrote:
> Hi,
>
> I am attempting to run the default FastPipeline to extract various
> features from clinical text. One of the features I'd like to capture is the
> covered text. However, when running the below scala code, calling
> getOriginalText yields a "null" value for every annotation of type
> IdentifiedAnnotation. Is this by design?
>
> And if so, what would be a better way to extract the covered text? The
> other features I need (subject, polarity, confidence, historyOf, and
> snomed/CUI/TUI/PreferredText) I can acquire just fine. Effectively, the
> goal here is to capture every identified annotation, relevant metadata, and
> the original text (only showing my attempt at getting the covered text
> below).
>
> def main(args: Array[String]) {
> val note =
> """
> ... (Some long example note.)
> """.stripMargin
> val aed = ClinicalPipelineFactory.getDefaultPipeline
> val ae = AnalysisEngineFactory.createEngine(aed)
> val jcas =
> JCasFactory.createJCas("org.apache.ctakes.typesystem.
> types.TypeSystem")
> jcas.setDocumentText(note)
> ae.process(jcas)
> val index = jcas.getAnnotationIndex(IdentifiedAnnotation.`type`)
> val iter = index.iterator()
> while (iter.hasNext) {
> val annotation = iter.next().asInstanceOf[IdentifiedAnnotation]
> val fsArray = annotation.getOriginalText()
> if (fsArray != null) {
> for (featureStructure <- fsArray.toArray()) {
> val featureArray = featureStructure.getType().getFeatures()
> val strings = featureArray.map(x => featureStructure.
> getStringValue(x))
> println(strings)
> }
> }
> }
> }
>
>
> Regards,
>
> Mike Trepanier
> --
> [image: MetiStream Logo - 500]
> Mike Trepanier| Big Data Engineer | MetiStream, Inc. |
> m...@metistream.com | 845 - 270 - 3129 <(845)%20270-3129> (m) |
> www.metistream.com
>
