TODAY := $(shell date --iso --utc) CORDDATE := $(TODAY) SHELL = /bin/bash .SHELLFLAGS = -o pipefail -c .PHONY: help help: ## Print info about all commands @echo "Commands:" @echo @grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf " \033[01;32m%-20s\033[0m %s\n", $$1, $$2}' .PHONY: test test: ## Run all tests and lints pipenv run pytest .PHONY: dev dev: ## Run web interface locally pipenv run ./covid19_tool.py webface --debug .PHONY: update-i18n update-i18n: ## Re-extract and re-compile translation files pipenv run pybabel update -i extra/i18n/web_interface.pot -d fatcat_covid19/translations pipenv run pybabel compile -d fatcat_covid19/translations metadata/$(CORDDATE)/cord19.csv: mkdir -p metadata/$(CORDDATE) @#wget -c "https://archive.org/download/s2-cord19-dataset/cord19.$(CORDDATE).csv" -O /tmp/cord19.$(CORDDATE).csv wget -c "https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/latest/metadata.csv" -O /tmp/cord19.$(CORDDATE).csv mv /tmp/cord19.$(CORDDATE).csv $@ metadata/$(CORDDATE)/cord19.json: metadata/$(CORDDATE)/cord19.csv pipenv run ./covid19_tool.py parse-cord19 metadata/$(CORDDATE)/cord19.csv > $@.wip mv $@.wip $@ metadata/$(CORDDATE)/cord19.enrich.json: metadata/$(CORDDATE)/cord19.json cat metadata/$(CORDDATE)/cord19.json | pipenv run parallel -j10 --linebuffer --round-robin --pipe ./covid19_tool.py enrich-fatcat - | pv -l > $@.wip mv $@.wip $@ metadata/$(CORDDATE)/cord19.missing.json: metadata/$(CORDDATE)/cord19.enrich.json cat metadata/$(CORDDATE)/cord.enrich.json | jq 'select(.release_id == null) | .cord19_paper' -c > $@.wip mv $@.wip $@ metadata/$(TODAY)/fatcat_hits.enrich.json: mkdir -p metadata/$(TODAY) pipenv run ./covid19_tool.py query-fatcat | pv -l > $@ mv $@.wip $@ metadata/$(TODAY)/combined.enrich.json: metadata/$(CORDDATE)/cord19.enrich.json metadata/$(TODAY)/fatcat_hits.enrich.json cat metadata/$(TODAY)/fatcat_hits.enrich.json metadata/$(CORDDATE)/cord19.enrich.json| pipenv run ./covid19_tool.py dedupe | pv -l > $@.wip mv $@.wip $@ metadata/$(TODAY)/fatcat_web.log: metadata/$(TODAY)/combined.enrich.json cat metadata/$(TODAY)/combined.enrich.json | jq .fatcat_release -c | pipenv run parallel -j20 --linebuffer --round-robin --pipe ./bin/deliver_file2disk.py --disk-dir fulltext_web - | pv -l > $@.wip mv $@.wip $@ metadata/$(TODAY)/derivatives.stamp: metadata/$(TODAY)/fatcat_web.log pipenv run ./bin/make_dir_derivatives.sh fulltext_web touch $@ metadata/$(TODAY)/combined.fulltext.json: metadata/$(TODAY)/derivatives.stamp metadata/$(TODAY)/combined.enrich.json ./covid19_tool.py enrich-derivatives metadata/$(TODAY)/combined.enrich.json --base-dir fulltext_web/ | pv -l > $@.wip mv $@.wip $@ .PHONY: corpus corpus: metadata/$(TODAY)/combined.fulltext.json ## Run ingest, resulting in combined fulltext JSON corpus on disk @echo "Successfully built corpus for date (UTC): $(TODAY)" .PHONY: create-es-index create-es-index: http put :9200/covid19_fatcat_fulltext < schema/fulltext_schema.v00.json .PHONY: load-es load-es: metadata/$(TODAY)/combined.fulltext.json ## Push current corpus into elasticsearch index pipenv run ./covid19_tool.py metadata/$(TODAY)/combined.fulltext.json | pv -l | esbulk -verbose -size 1000 -id fatcat_ident -w 8 -index covid19_fatcat_fulltext -type release .PHONY: daily-update daily-update: load-elasticsearch ## Command to run every day: fetch corpus, load to elasticsearch