Just an update for anyone following this project. @andremillet is setting up the software on his machine and we discussed the need for running the pipeline via AWS. The idea is that one would submit clinical text to an endpoint and the output would be either the iml file or text printed to the screen via org.apache.ctakes.core.cc.pretty.plaintext.PrettyTextWriterUima.
I will hold on doing this work at the moment because we need to test out the software to see if we are happy with the results.
One potential block is that I don't think the pipeline is using ICD10 by default. I'll have to look into how to get it to produce ICD10 along with the SNOMED, RXNORM, etc.