Hello,
I am using cTAKES 4.0.0 on Windows 8 behind a proxy server as part of a
restricted network.
We are trying to incorporate cTAKES as part of our Clinical document processing
pipeline.
I have been attempting to add Temporal analysis as part of Default Clinical
pipeline and that has not been successful. (Using RunPiperFile.bat to execute
the piper)
Please see the piper file below:
"
// InputDirectory Directory for all input files.
reader org.apache.ctakes.core.cr.FileTreeReader
InputDirectory=C:\Users\prakhar.gaur\Documents
load DefaultTokenizerPipeline.piper
// Add non-core annotators
add ContextDependentTokenizerAnnotator
addDescription POSTagger
// Add Chunkers
load ChunkerSubPipe.piper
// Default fast dictionary lookup
add DefaultJCasTermAnnotator
// Add Cleartk Entity Attribute annotators
load AttributeCleartkSubPipe.piper
// Add Time Annotator
package org.apache.ctakes.temporal
add org.apache.ctakes.temporal.ae.TimeAnnotator
// addDescription org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
modelPath=org/apache/ctakes/temporal/ae/timeannotator/model.jar
// XMI Writer
// Writes XMI files with full representation of input text and all extracted
information.
# OutputDirectory Output directory to write xmi files
addLast org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
OutputDirectory=C:\Users\prakhar.gaur\Documents
" EOF.
Now I have tried two different ways to get a Time annotator to work.
By adding a line to piper file as given above.
1. Line added to Piper file - "add org.apache.ctakes.temporal.ae.TimeAnnotator"
I get error:
24 Oct 2017 11:40:56 ERROR PiperFileRunner - Initialization of annotator
class "org.apache.ctakes.temporal.ae.TimeAnnotator" failed. (Descript
or: <unknown>)
2. Line added to Piper file - "addDescription
org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
modelPath=org/apache/ctakes/temporal/ae/timeannotator/model.jar"
I get error:
24 Oct 2017 11:37:40 ERROR PiperFileReader - No createAnnotatorDescription
method in org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
24 Oct 2017 11:37:40 ERROR PiperFileRunner -
3. I tried using the default Temporal Aggregate
Pipeline(TemporalAggregatePipeline.xml) inside CVD and get error
Output from Stack trace (Only the important part):
11:48:03.680 - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526):
SEVERE: Initialization of annotator class
"org.apache.ctakes.temporal.ae.DocTimeRelAnnotator" failed. (Descriptor:
file:/C:/Users/prakhar.gaur/apache-ctakes-4.0.0/desc/ctakes-temporal/desc/analysis_engine/TemporalAggregatePipeline.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class "org.apache.ctakes.temporal.ae.DocTimeRelAnnotator" failed.
(Descriptor:
file:/C:/Users/prakhar.gaur/apache-ctakes-4.0.0/desc/ctakes-temporal/desc/analysis_engine/TemporalAggregatePipeline.xml)
Caused by: java.lang.IllegalArgumentException: Please specify
PARAM_IS_TRAINING - unable to infer it from context
Please help me in getting the Temporal annotation working for my pipeline.
Pointers, Comments and actual solutions are all welcome.
Thank you,
