Hi John,
Just out of curiosity, if you have one method that works then why do you want
to use a different method to do the same thing?
I personally use the PIpelineBuilder as you have in your second example when I
need to work with code - though that is extremely rare as piper files can
handle everything that I normally want to do.
If you want an example of how to build a pipeline using only code (no piper
file) then check the ctakes-examples module, class ProcessDirBuilderRunner. It
recreates the default clinical pipeline without dictionary lookup. Adding in
the lookup is fairly simple:
builder
...
.set( UmlsUserApprover.KEY_PARAM, "my-umls-key" )
.add( DefaultJCasTermAnnotator.class )
...
or the single line
.add( DefaultJCasTermAnnotator.class, Collections.emptyList(),
UmlsUserApprover.KEY_PARAM, "my-umls-key" )
The code above is just off the top of my head, so I apologize for any typos or
slight misdirection. Hopefully it is enough to point a way for you.
Sean
________________________________________
From: John Doe <lucanus...@gmail.com>
Sent: Thursday, April 22, 2021 1:09 PM
To: dev@ctakes.apache.org
Subject: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
* External Email - Caution *
Hello,
I'm having trouble running the default clinical pipeline from code. It
keeps giving me the error message that I have an invalid UMLS License.
However, I know my license is valid and I have managed to get the default
pipeline to run using the PiperFileReader with the same credentials.
This is the code that doesn't work that I would like to get working:
System.setProperty(UmlsUserApprover.KEY_PARAM, "my-umls-key");
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText("My text");
AnalysisEngineDescription aed =
ClinicalPipelineFactory.getDefaultPipeline();
SimplePipeline.runPipeline(jCas, aed);
This is the code that I managed to get to work. This just demonstrates to
me that it isn't really a credential issue.
PiperFileReader piperReader = new PiperFileReader();
PipelineBuilder builder = piperReader.getBuilder();
builder.set( UmlsUserApprover.KEY_PARAM , "the-same-umls-key");
piperReader.loadPipelineFile("path/to/default.piper");
builder.run("test text");
default.piper just loads the default pipeline:
load
./resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
Does anyone know what the issue might be here?
