Use the plain wrapper command for the normal STAR run. Leave the pipeline flag out unless the project lead asks for a specific pipeline.

cTAKES USD

Run STAR note batches through the cTAKES USD wrapper.

Run one batch

Install once, run flight_check.sh, copy notes into input/batch1, and run the default wrapper command.

Pipelines, dictionary XML, writer profiles, SQLite output, manifests, offline kits, and validation.

Install once

git clone https://codeberg.org/editnori/Ctakes_USD.git
cd Ctakes_USD

bash scripts/setup.sh
bash scripts/flight_check.sh

Put notes in a batch folder

mkdir -p input/batch1
cp /path/to/site/notes/*.txt input/batch1/

Run cTAKES

bash scripts/run_pipeline.sh -i input/batch1 -o outputs/batch1

Check the output

outputs/batch1/annotations.sqlite
outputs/batch1/run_manifest.json
outputs/batch1/run_pipeline.log

Leave the pipeline flag out for the normal STAR run. The plain command already uses the STAR pipeline.

File	Use
`annotations.sqlite`	Results database.
`run_manifest.json`	Run receipt with pipeline, dictionary, wrapper, Java, and output metadata.
`run_pipeline.log`	File to send if the run fails.