hivfacts/Makefile at main · hivdb/hivfacts · GitHub

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data/drms_*.csv: scripts/build_drms.py data/drugs.json

data/drms_hiv1.csv: data/algorithms/HIVDB_latest.xml data/drug-classes_hiv1.json data/genes_hiv1.json
	@pipenv run python scripts/build_drms.py HIV1 data/

# data/drms_hiv2.csv: data/algorithms/HIVDB-HIV2_9.0.xml data/drug-classes_hiv2.json data/genes_hiv2.json
# 	@pipenv run python scripts/build_drms.py HIV2 data/

data/drms_*.json: scripts/drms_csv2json.py
data/drms_%.json: data/drms_%.csv
	@pipenv run python scripts/drms_csv2json.py $<

data/mutation-type-pairs_*.json: scripts/csv2json.py
data/mutation-type-pairs_%.json: data/mutation-type-pairs_%.csv
	@pipenv run python scripts/csv2json.py $<

data/apobec*/apobecs.json: scripts/csv2json.py
data/apobec%/apobecs.json: data/apobec%/apobecs.csv
	@pipenv run python scripts/csv2json.py $<

data/apobec*/apobec_drms.json: scripts/csv2json.py
data/apobec%/apobec_drms.json: data/apobec%/apobec_drms.csv
	@pipenv run python scripts/csv2json.py $<

data/aapcnt/rx-all_subtype-*.json: scripts/csv2json.py
data/aapcnt/rx-all_subtype-%.json: data/aapcnt/rx-all_subtype-%.csv
	@pipenv run python scripts/csv2json.py $<

data/patterns_hiv1.csv: scripts/export_patterns.py
	@pipenv run python scripts/export_patterns.py $@

data/patterns_%.json: data/patterns_%.csv
	@pipenv run python scripts/csv2json.py $<

data/%.json: data/%.yml
	@pipenv run python scripts/yaml2json.py $<

data/conditional-comments_%.json: data/conditional-comments_%.csv scripts/condcmts_csv2json.py
	@pipenv run python scripts/condcmts_csv2json.py HIV1 $< $@

data/conditional-comments_hiv2.json: data/conditional-comments_hiv2.csv scripts/condcmts_csv2json.py
	@pipenv run python scripts/condcmts_csv2json.py HIV2 $< $@

ASI_FILES := $(wildcard data/algorithms/*.xml)
ASI_FILES := $(filter-out data/algorithms/HIVDB_latest.xml, $(ASI_FILES))

$(ASI_FILES):
	@dos2unix -q $@
	@echo $@

data/algorithms/HIVDB_latest.xml: data/algorithms/versions.json
	@rm -f data/algorithms/HIVDB_latest.xml
	@ln -s HIVDB_$(shell cat data/algorithms/versions.json | jq '.HIVDB[-1][0]' --raw-output).xml data/algorithms/HIVDB_latest.xml

data: data/*csv data/*.json data/algorithms/*.xml data/algorithms/*.json data/apobecs/*.json data/apobecs-hiv2/*.json data/aapcnt/*.json data/genotypes/*.json

refresh-yamls:
	@pipenv run python scripts/yaml2json.py

refresh-csvs:
	@scripts/update-csvs.sh

refresh-drmlist:
	@scripts/update-drmlist.sh

refresh-sdrmlist:
	@scripts/update-sdrmlist.sh

refresh-tsmlist:
	@scripts/update-tsmlist.sh

refresh-muttypepairs:
	@scripts/update-muttypepairs.sh

refresh-aapcnt:
	@scripts/update-aapcnt.sh

refresh-codonpcnt:
	@scripts/update-codonpcnt.sh

refresh-condcomments:
	@scripts/update-condcomments.sh

refresh-apobec:
	@scripts/prepare-apobec-data.sh
	@scripts/update-apobec.sh

refresh-data: refresh-drmlist refresh-sdrmlist refresh-tsmlist refresh-muttypepairs

build-java:
	@cd hivfacts-java; ./gradlew build

release-java:
	@cd hivfacts-java; ./gradlew build bintrayUpload

build-python:
	@cd hivfacts-python; ./setup.py copy_data sdist bdist_wheel

release-python:
	@cd hivfacts-python; ./setup.py copy_data sdist bdist_wheel upload

.PHONY: release-java