This repository contains the configuration to build the ChemDataExtractor app for GATE Cloud. The app is in two parts, an ELG-compatible service that does the actual Python NER, and a thin GATE application that uses the ELG client PR to call the tagger.
docker buildx build -t chemdataextractor:latest .
The image is also built automatically and pushed to ghcr.io when changes are pushed, see the "packages" section to the right for details.
To aid reproducability we use fixed versions for all dependencies. This includes both within the conda environent and the python modules
conda lock -p linux-64 -f environment.yaml
docker run -it --rm --entrypoint /bin/bash ghcr.io/gatenlp/chemdataextractor:main
/env/bin/pip freeze -l | grep ==
The GATE Cloud pipeline is then a thin wrapper which calls the ELG endpoint using the ELG client PR. To build this, run ./gradlew cloudZip in the cloud-pipeline directory and the zip file will be created under build/distributions.
The code in this repository is licenced under the MIT licence, as is ChemDataExtractor itself.