Makefile

.PHONY: Pipfile.lock
Pipfile.lock:
	docker compose --progress=plain build
	docker compose --progress=plain run --rm --name de-identifier-shell dev sh -c "rm -f Pipfile.lock && pipenv lock --dev"

build:
	docker compose build --progress plain

.PHONY:shell
shell: build ## Brings up the bash shell in dev docker
	docker compose --progress=plain run --rm --name de-identifier-shell dev sh

.PHONY:update
update: Pipfile.lock  ## Updates all the packages using Pipfile
	make build

# config file format: https://github.com/microsoft/Tools-for-Health-Data-Anonymization/blob/master/docs/FHIR-anonymization.md#fhir-path-rules

.PHONY: run
run:
	docker compose --progress=plain build && \
	rm -rf ./data/output/* && \
	docker compose run --rm --name de-identifier-shell dev ls /data -v && \
	docker compose run --rm --name de-identifier-shell dev anonymize -r -i /data/input/large/ -o /data/output/large/ -c /data/config/config.json -v && \
	make find_text

.PHONY: find_text
find_text:
	python3 find_text_in_files.py data/output/large bailey

.PHONY: up
up: build
	docker compose --progress=plain up

.PHONY: down
down:
	docker compose --progress=plain down