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Makefile
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Makefile
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.DEFAULT_GOAL := all
# ORG input default to the shortest one to run
ORG ?= msf
ifdef IMAGE_REPO_NAME
WEB_IMAGE := ${IMAGE_REPO_NAME}
else
WEB_IMAGE := uk.ac.wellcome/reach
endif
EPMC_METADATA_KEY = s3://datalabs-staging/airflow/output/open-research/epmc-metadata/epmc-metadata.json.gz
SCRAPER_DST := s3://datalabs-dev/scraper/split-container/${ORG}/
PARSER_DST := s3://datalabs-dev/parser/split-container/${ORG}/policy_docs_normalized.json.gz
EXTRACTER_PARSED_DST := s3://datalabs-dev/extracter/split-container/${ORG}/extracted-refs-${ORG}.json.gz
EXTRACTER_SPLIT_DST := s3://datalabs-dev/extracter-split/split-container/${ORG}/split-refs-${ORG}.json.gz
FUZZYMATCHER_DST := s3://datalabs-dev/fuzzymatcher/split-container/${ORG}/fuzzymatched-refs-${ORG}.json.gz
GOLD_EVAL_SRC := s3://datalabs-data/reach_evaluation/data/sync/2019.10.8-fuzzy-matched-gold-refs-manually-verified.jsonl
DEEP_REFERENCE_PARSER_WHEEL := deep_reference_parser-2020.4.5-py3-none-any.whl
DEEP_REFERENCE_PARSER_URL := https://github.com/wellcometrust/deep_reference_parser/releases/download/2020.4.29/$(DEEP_REFERENCE_PARSER_WHEEL)
# This is only available on Mac at the time, linux users need to change it to localhost
DOCKER_LOCALHOST := host.docker.internal
ECR_ARN := 160358319781.dkr.ecr.eu-west-1.amazonaws.com/uk.ac.wellcome
WEB_ECR_ARN := 160358319781.dkr.ecr.eu-west-1.amazonaws.com
VERSION := build-$(shell date +%Y%m%dT%H%M%SZ)
LATEST_TAG := latest
.PHONY: aws-docker-login
aws-docker-login:
aws ecr get-login-password --region eu-west-1 | docker login --username AWS --password-stdin 160358319781.dkr.ecr.eu-west-1.amazonaws.com
# _____________
# TODO:
# When we're done with testing the splitter, we should run docker tasks demonized.
# Also all the pipeline related images are meant to be run in Argo, not just like that.
# _____________
.PHONY: base-image
base-image:
docker build \
-t reach.base \
-f base/Dockerfile \
./base
#################
# Reach Scraper #
#################
.PHONY: scraper-image
scraper-image: base-image
docker build \
-t $(ECR_ARN)/reach-scraper:$(VERSION) \
-t $(ECR_ARN)/reach-scraper:$(LATEST_TAG) \
-f pipeline/reach-scraper/Dockerfile \
./pipeline/reach-scraper
.PHONY: push-scraper
push-scraper: aws-docker-login scraper-image
docker push $(ECR_ARN)/reach-scraper:$(LATEST_TAG) && \
docker push $(ECR_ARN)/reach-scraper:$(VERSION)
################
# Reach Parser #
################
.PHONY: parser-image
parser-image: base-image
docker build \
-t $(ECR_ARN)/reach-parser:$(VERSION) \
-t $(ECR_ARN)/reach-parser:$(LATEST_TAG) \
-f pipeline/reach-parser/Dockerfile \
./pipeline/reach-parser
.PHONY: push-parser
push-parser: aws-docker-login parser-image
docker push $(ECR_ARN)/reach-parser:$(LATEST_TAG) && \
docker push $(ECR_ARN)/reach-parser:$(VERSION)
###################
# Reach Extractor #
###################
.PHONY: es-extracter-image
es-extracter-image: base-image
docker build \
-t $(ECR_ARN)/reach-es-extractor:$(VERSION) \
-t $(ECR_ARN)/reach-es-extractor:$(LATEST_TAG) \
-f pipeline/reach-es-extractor/Dockerfile \
./pipeline/reach-es-extractor
.PHONY: push-extracter
push-extracter: aws-docker-login es-extracter-image
docker push $(ECR_ARN)/reach-es-extractor:$(LATEST_TAG) && \
docker push $(ECR_ARN)/reach-es-extractor:$(VERSION)
#################
# Reach Indexer #
#################
.PHONY: indexer-image
indexer-image: base-image
docker build \
-t $(ECR_ARN)/reach-es-indexer:$(VERSION) \
-t $(ECR_ARN)/reach-es-indexer:$(LATEST_TAG) \
-f pipeline/reach-es-indexer/Dockerfile \
./pipeline/reach-es-indexer
.PHONY: push-indexer
push-indexer: aws-docker-login indexer-image
docker push $(ECR_ARN)/reach-es-indexer:$(LATEST_TAG) && \
docker push $(ECR_ARN)/reach-es-indexer:$(VERSION)
######################
# Reach FuzzyMatcher #
######################
.PHONY: fuzzymatcher-image
fuzzymatcher-image: base-image
docker build \
-t $(ECR_ARN)/reach-fuzzy-matcher:$(VERSION) \
-t $(ECR_ARN)/reach-fuzzy-matcher:$(LATEST_TAG) \
-f pipeline/reach-fuzzy-matcher/Dockerfile \
./pipeline/reach-fuzzy-matcher
.PHONY: push-fuzzymatcher
push-fuzzymatcher: aws-docker-login fuzzymatcher-image
docker push $(ECR_ARN)/reach-fuzzy-matcher:$(LATEST_TAG) && \
docker push $(ECR_ARN)/reach-fuzzy-matcher:$(VERSION)
#############
# Reach Web #
#############
.PHONY: web-image
web-image: base-image
docker build \
-t $(WEB_ECR_ARN)/${WEB_IMAGE}:$(VERSION) \
-t $(WEB_ECR_ARN)/${WEB_IMAGE}:$(LATEST_TAG) \
-f web/Dockerfile \
./web
.PHONY: push-web
push-web: aws-docker-login web-image
docker push $(WEB_ECR_ARN)/${WEB_IMAGE}:$(LATEST_TAG) && \
docker push $(WEB_ECR_ARN)/${WEB_IMAGE}:$(VERSION)
##############
# Local runs #
##############
.PHONY: run-scraper
run-scraper: scraper-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
${ECR_ARN}/reach-scraper \
${SCRAPER_DST} \
${ORG}
.PHONY: run-parser
run-parser: parser-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
${ECR_ARN}/reach-parser \
${SCRAPER_DST} \
${PARSER_DST} \
${ORG}
.PHONY: run-extracter
run-extracter: es-extracter-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
${ECR_ARN}/reach-es-extractor \
${PARSER_DST} \
${EXTRACTER_PARSED_DST} \
${EXTRACTER_SPLIT_DST}
.PHONY: run-indexer-fulltexts
run-indexer-fulltexts: indexer-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
-e ES_HOST=${DOCKER_LOCALHOST} \
--network=host \
${ECR_ARN}/reach-es-indexer \
${PARSER_DST} \
${ORG} \
fulltexts
.PHONY: run-indexer-epmc
run-indexer-epmc: indexer-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
-e ES_HOST=${DOCKER_LOCALHOST} \
--network=host \
${ECR_ARN}/reach-es-indexer \
${EPMC_METADATA_KEY} \
${ORG} \
epmc \
--max_items=10000
.PHONY: run-fuzzymatcher
run-fuzzymatcher: fuzzymatcher-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
-e ES_HOST=${DOCKER_LOCALHOST} \
--network=host \
${ECR_ARN}/reach-fuzzy-matcher \
${EXTRACTER_SPLIT_DST} \
${FUZZYMATCHER_DST} \
${ORG} \
epmc_metadata
.PHONY: run-indexer-citations
run-indexer-citations: indexer-image
docker run \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
-e SENTRY_DSN="${SENTRY_DSN}" \
-e ES_HOST=${DOCKER_LOCALHOST} \
--network=host \
${ECR_ARN}/reach-es-indexer \
${FUZZYMATCHER_DST} \
${ORG} \
citations
.PHONY: docker-run
docker-run: docker-build run-scraper run-parser run-extracter run-indexer-epmc run-indexer-citations
##################
# Testing images #
##################
.PHONY: scraper-tests-image
scraper-tests-image: base-image
docker build \
-t $(ECR_ARN)/test-reach-scraper:$(LATEST_TAG) \
-f pipeline/reach-scraper/Dockerfile.test \
./pipeline/reach-scraper
.PHONY: test-scraper
test-scraper: scraper-tests-image
docker run -u root \
-e SENTRY_DSN="${SENTRY_DSN}" \
--rm $(ECR_ARN)/test-reach-scraper:latest \
sh -c "pip install pytest && pytest /opt/reach/"
.PHONY: parser-tests-image
parser-tests-image: base-image
docker build \
-t $(ECR_ARN)/test-reach-parser:$(LATEST_TAG) \
-f pipeline/reach-parser/Dockerfile.test \
./pipeline/reach-parser
.PHONY: test-parser
test-parser: parser-tests-image
docker run -u root \
-e SENTRY_DSN="${SENTRY_DSN}" \
--rm $(ECR_ARN)/test-reach-parser:latest \
sh -c "pip install pytest && pytest /opt/reach/"
.PHONY: extractor-tests-image
extractor-tests-image: base-image
docker build \
-t $(ECR_ARN)/test-reach-extractor:$(LATEST_TAG) \
-f pipeline/reach-es-extractor/Dockerfile.test \
./pipeline/reach-es-extractor
.PHONY: test-extractor
test-extractor: extractor-tests-image
docker run -u root \
-e SENTRY_DSN="${SENTRY_DSN}" \
--rm $(ECR_ARN)/test-reach-extractor:latest \
sh -c "pip install pytest && pytest /opt/reach/"
###################
# General recipes #
###################
.PHONY: docker-test
docker-test: test-scraper test-parser test-extractor
.PHONY: docker-build
docker-build: base-image scraper-image parser-image es-extracter-image indexer-image fuzzymatcher-image
.PHONY: docker-push-all
docker-push-all: docker-test push-fuzzymatcher push-extracter push-indexer push-parser push-scraper
.PHONY: all
all: docker-build