/
Makefile
457 lines (414 loc) · 22.6 KB
/
Makefile
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# Set up makefile config
.RECIPEPREFIX = >
MAKEFLAGS += --warn-undefined-variables
MAKEFLAGS += --no-builtin-rules
# export
# Define globally used variables
# Locations are relative unless indicated otherwise
PACKAGE_NAME := spatialprofilingtoolbox
export PYTHON := python
export BUILD_SCRIPTS_LOCATION_ABSOLUTE := ${PWD}/build/build_scripts
SOURCE_LOCATION := ${PACKAGE_NAME}
BUILD_LOCATION := build
BUILD_LOCATION_ABSOLUTE := ${PWD}/build
export TEST_LOCATION := test
export TEST_LOCATION_ABSOLUTE := ${PWD}/${TEST_LOCATION}
LOCAL_USERID := $(shell id -u)
VERSION := $(shell cat version.txt | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+')
export WHEEL_FILENAME := ${PACKAGE_NAME}-${VERSION}-py3-none-any.whl
export MESSAGE := bash ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/verbose_command_wrapper.sh
help:
>@${MESSAGE} print 'The main targets are:'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make release-package'
>@${MESSAGE} print ' Build the Python package wheel and push it to PyPI.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make build-docker-images'
>@${MESSAGE} print ' Build the Docker images.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make build-and-push-docker-images'
>@${MESSAGE} print ' Build the Docker images and push them to DockerHub repositories.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make force-rebuild-data-loaded-images'
>@${MESSAGE} print ' Rebuild the data-preloaded Docker images. This is relatively'
>@${MESSAGE} print ' long-running and so is left out of the typical test target'
>@${MESSAGE} print ' fulfillment process.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make test'
>@${MESSAGE} print ' Do unit and module tests.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make [unit | module]-test-[apiserver | graphs | ondemand | db | workflow]'
>@${MESSAGE} print ' Do only the unit or module tests for the indicated module.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make clean'
>@${MESSAGE} print ' Attempt to remove all build or partial-build artifacts.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make clean-docker-images'
>@${MESSAGE} print ' Aggressively removes the Docker images created here.'
>@${MESSAGE} print ' It makes use `docker system prune`, which might delete other images, so use at your own risk.'
>@${MESSAGE} print ' This target does not attempt to remove external images pulled as base images, however.'
>@${MESSAGE} print ' Note that normal `make clean` does not attempt to remove Docker images at all.'
>@${MESSAGE} print ' '
>@${MESSAGE} print ' make help'
>@${MESSAGE} print ' Show this text.'
>@${MESSAGE} print ' '
>@${MESSAGE} print 'Use VERBOSE=1 to send command outputs to STDOUT rather than log files.'
>@${MESSAGE} print 'Use NOCACHE=1 to cause docker build commands to rebuild each cached layer.'
>@${MESSAGE} print ' '
# Docker and test variables
export DOCKER_ORG_NAME := nadeemlab
export DOCKER_REPO_PREFIX := spt
export DOCKER_SCAN_SUGGEST:=false
SUBMODULES := apiserver graphs ondemand db workflow
DOCKERIZED_SUBMODULES := apiserver db ondemand
DOCKERFILES := $(foreach submodule,$(DOCKERIZED_SUBMODULES),${BUILD_LOCATION}/$(submodule)/Dockerfile)
DOCKER_BUILD_TARGETS := $(foreach submodule,$(DOCKERIZED_SUBMODULES),${BUILD_LOCATION_ABSOLUTE}/$(submodule)/docker.built)
_UNPUSHABLES := db
PUSHABLE_SUBMODULES := $(filter-out ${_UNPUSHABLES},$(DOCKERIZED_SUBMODULES))
DOCKER_PUSH_TARGETS := $(foreach submodule,$(PUSHABLE_SUBMODULES),docker-push-${PACKAGE_NAME}/$(submodule))
DOCKER_PUSH_DEV_TARGETS := $(foreach submodule,$(DOCKERIZED_SUBMODULES),docker-push-dev-${PACKAGE_NAME}/$(submodule))
MODULE_TEST_TARGETS := $(foreach submodule,$(SUBMODULES),module-test-$(submodule))
UNIT_TEST_TARGETS := $(foreach submodule,$(SUBMODULES),unit-test-$(submodule))
SINGLETON_TEST_TARGETS := $(foreach submodule,$(SUBMODULES),singleton-test-$(submodule))
DLI := force-rebuild-data-loaded-image
# Define PHONY targets
.PHONY: help release-package check-for-pypi-credentials print-source-files build-and-push-docker-images ${DOCKER_PUSH_TARGETS} build-docker-images test module-tests ${MODULE_TEST_TARGETS} ${UNIT_TEST_TARGETS} clean clean-files docker-compositions-rm clean-network-environment generic-spt-push-target data-loaded-images-push-target
# Submodule-specific variables
export DB_SOURCE_LOCATION_ABSOLUTE := ${PWD}/${SOURCE_LOCATION}/db
export DB_BUILD_LOCATION_ABSOLUTE := ${PWD}/${BUILD_LOCATION}/db
# Locations can't be relative because these are used by the submodules' Makefiles.
# Fetch all runnable files that will be needed for making
PACKAGE_SOURCE_FILES := pyproject.toml $(shell find ${SOURCE_LOCATION} -type f)
# Redefine what shell to pass to submodule makefiles
export SHELL := ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/status_messages_only_shell.sh
# Adjust verbosity based on how make was called
ifdef VERBOSE
export .SHELLFLAGS := -c -super-verbose
else
export .SHELLFLAGS := -c -not-super-verbose
endif
ifdef NOCACHE
export NO_CACHE_FLAG := --no-cache
else
export NO_CACHE_FLAG :=
endif
release-package: development-image check-for-pypi-credentials
>@${MESSAGE} start "Uploading spatialprofilingtoolbox==${VERSION} to PyPI"
>@cp ~/.pypirc .
>@docker run -u ${LOCAL_USERID} --rm --mount type=bind,src=${PWD},dst=/mount_sources -t ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest /bin/bash -c 'cd /mount_sources; PYTHONDONTWRITEBYTECODE=1 python -m twine upload --config-file .pypirc --repository ${PACKAGE_NAME} dist/${WHEEL_FILENAME} ' ; echo "$$?" > status_code
>@${MESSAGE} end "Uploaded." "Error."
>@rm -f .pypirc
check-for-pypi-credentials:
>@${MESSAGE} start "Checking for PyPI credentials in ~/.pypirc for spatialprofilingtoolbox"
>@${PYTHON} ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/check_for_credentials.py pypi ; echo "$$?" > status_code
>@${MESSAGE} end "Found." "Not found."
development-image-prerequisites-installed: pyproject.toml.unversioned ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/development_prereqs.Dockerfile
>@${MESSAGE} start "Building development image precursor"
>@cp ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/.dockerignore .
>@docker build \
${NO_CACHE_FLAG} \
--rm \
-f ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/development_prereqs.Dockerfile \
-t ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development-prereqs:latest \
. ; echo "$$?" > status_code ; \
status_code=$$(cat status_code); \
if [[ "$$status_code" == "0" ]]; \
then \
touch development-image-prerequisites-installed ; \
fi
>@${MESSAGE} end "Built." "Build failed."
>@rm -f .dockerignore
development-image: ${PACKAGE_SOURCE_FILES} ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/development.Dockerfile development-image-prerequisites-installed
>@${MESSAGE} start "Building development image"
>@cp ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/.dockerignore .
>@docker build \
${NO_CACHE_FLAG} \
--rm \
--no-cache \
--pull=false \
-f ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/development.Dockerfile \
-t ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest \
--build-arg WHEEL_FILENAME=$${WHEEL_FILENAME} \
. ; echo "$$?" > status_code ; \
status_code=$$(cat status_code) ; \
if [[ "$$status_code" == "0" ]]; \
then \
if [ ! -d dist/ ]; then mkdir dist ; fi; \
docker run --rm -v $$(pwd)/dist:/buffer ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development /bin/sh -c "cp dist/${WHEEL_FILENAME} /buffer; chown ${LOCAL_USERID}:${LOCAL_USERID} /buffer/*; "; \
fi
>@status_code=$$(cat status_code); \
if [[ "$$status_code" == "0" ]]; \
then \
touch development-image ; \
fi
>@${MESSAGE} end "Built." "Build failed."
>@rm -f .dockerignore
pyproject.toml: pyproject.toml.unversioned ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/create_pyproject.py version.txt
>@${MESSAGE} start "Creating pyproject.toml"
>@${PYTHON} ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/create_pyproject.py; echo "$$?" > status_code
>@${MESSAGE} end "Created." "Failed."
print-source-files:
>@echo "${PACKAGE_SOURCE_FILES}" | tr ' ' '\n'
build-and-push-docker-images: ${DOCKER_PUSH_TARGETS} generic-spt-push-target data-loaded-images-push-target
build-and-push-docker-images-dev: ${DOCKER_PUSH_DEV_TARGETS}
${DOCKER_PUSH_TARGETS}: build-docker-images check-for-docker-credentials
>@submodule_directory=$$(echo $@ | sed 's/^docker-push-//g') ; \
submodule_version=$$(grep '^__version__ = ' $$submodule_directory/__init__.py | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') ;\
submodule_name=$$(echo $$submodule_directory | sed 's/spatialprofilingtoolbox\///g') ; \
repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-$$submodule_name ; \
${MESSAGE} start "Pushing Docker container $$repository_name"
>@submodule_directory=$$(echo $@ | sed 's/^docker-push-//g') ; \
submodule_version=$$(grep '^__version__ = ' $$submodule_directory/__init__.py | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') ;\
echo "$$submodule_version"; \
submodule_name=$$(echo $$submodule_directory | sed 's/spatialprofilingtoolbox\///g') ; \
echo "$$submodule_name"; \
repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-$$submodule_name ; \
echo "$$repository_name"; \
docker push $$repository_name:$$submodule_version ; \
exit_code1=$$?; \
docker push $$repository_name:latest ; \
exit_code2=$$?; \
exit_code=$$(( exit_code1 + exit_code2 )); echo "$$exit_code" > status_code
>@${MESSAGE} end "Pushed." "Not pushed."
${DOCKER_PUSH_DEV_TARGETS}: build-docker-images check-for-docker-credentials
>@submodule_directory=$$(echo $@ | sed 's/^docker-push-dev-//g') ; \
submodule_version=$$(grep '^__version__ = ' $$submodule_directory/__init__.py | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') ;\
submodule_name=$$(echo $$submodule_directory | sed 's/spatialprofilingtoolbox\///g') ; \
repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-$$submodule_name ; \
${MESSAGE} start "Pushing Docker container $$repository_name"
>@submodule_directory=$$(echo $@ | sed 's/^docker-push-dev-//g') ; \
submodule_version=$$(grep '^__version__ = ' $$submodule_directory/__init__.py | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') ;\
echo "$$submodule_version"; \
submodule_name=$$(echo $$submodule_directory | sed 's/spatialprofilingtoolbox\///g') ; \
echo "$$submodule_name"; \
repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-$$submodule_name ; \
echo "$$repository_name"; \
docker push $$repository_name:dev ; \
exit_code1=$$?; \
echo "$$exit_code1" > status_code
>@${MESSAGE} end "Pushed." "Not pushed."
generic-spt-push-target: build-docker-images check-for-docker-credentials
>@repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX} ; \
${MESSAGE} start "Pushing Docker container $$repository_name"
>@repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX} ; \
docker tag ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest $$repository_name:${VERSION} ; \
docker push $$repository_name:${VERSION} ; \
exit_code1=$$?; \
docker tag ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest $$repository_name:latest ; \
docker push $$repository_name:latest ; \
exit_code2=$$?; \
exit_code=$$(( exit_code1 + exit_code2 )); echo "$$exit_code" > status_code
>@${MESSAGE} end "Pushed." "Not pushed."
data-loaded-images-push-target:
>@${MESSAGE} start "Pushing preloaded data Docker containers"
>@repository_name_prefix=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-db-preloaded ; \
codes=0 ; \
for suffix in 1 2 1and2 1small 1smallnointensity; \
do \
existing=$$repository_name_prefix-$$suffix:latest ; \
tag=$$repository_name_prefix-$$suffix:${VERSION} ; \
docker tag $$existing $$tag ; \
docker push $$existing ; \
exitcode="$$?" ; \
codes=$$(( codes + exitcode )) ; \
docker push $$tag ; \
exitcode="$$?" ; \
codes=$$(( codes + exitcode )) ; \
done; \
echo "$$codes" > status_code
>@${MESSAGE} end "Pushed." "Not pushed."
check-for-docker-credentials:
>@${MESSAGE} start "Checking for Docker credentials in ~/.docker/config.json"
>@${PYTHON} ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/check_for_credentials.py docker ; status="$$?"; echo "$$status" > status_code; if [[ "$$status" == "0" ]]; then touch check-for-docker-credentials; fi;
>@${MESSAGE} end "Found." "Not found."
check-dockerfiles-consistency:
>@${MESSAGE} start "Checking dependency lists in Dockerfiles."
>@${PYTHON} ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/check_dockerfiles_consistency.py ${DOCKERIZED_SUBMODULES}; echo "$$?" > status_code;
>@status_code=$$(cat status_code); if [[ "$$status_code" == "0" && ( ! -f check-dockerfiles-consistency ) ]]; then touch check-dockerfiles-consistency; fi;
>@${MESSAGE} end "Consistent." "Something missing."
build-docker-images: ${DOCKER_BUILD_TARGETS}
# Build the Docker container for each submodule by doing the following:
# 1. Identify the submodule being built
# 2. Emit a message about it
# 3. Copy relevant files to the build folder
# 4. docker build the container
# 5. Remove copied files
${DOCKER_BUILD_TARGETS}: ${DOCKERFILES} development-image check-docker-daemon-running check-for-docker-credentials check-dockerfiles-consistency
>@submodule_directory=$$(echo $@ | sed 's/\/docker.built//g') ; \
dockerfile=$${submodule_directory}/Dockerfile ; \
submodule_name=$$(echo $$submodule_directory | sed 's,${BUILD_LOCATION_ABSOLUTE}\/,,g') ; \
submodule_version=$$(grep '^__version__ = ' ${SOURCE_LOCATION}/$$submodule_name/__init__.py | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') ;\
repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-$$submodule_name ; \
${MESSAGE} start "Building Docker image $$repository_name"
>@submodule_directory=$$(echo $@ | sed 's/\/docker.built//g') ; \
dockerfile=$${submodule_directory}/Dockerfile ; \
submodule_name=$$(echo $$submodule_directory | sed 's,${BUILD_LOCATION_ABSOLUTE}\/,,g') ; \
submodule_version=$$(grep '^__version__ = ' ${SOURCE_LOCATION}/$$submodule_name/__init__.py | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') ;\
repository_name=${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-$$submodule_name ; \
cp dist/${WHEEL_FILENAME} $$submodule_directory ; \
cp $$submodule_directory/Dockerfile ./Dockerfile ; \
cp ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/.dockerignore . ; \
docker build \
${NO_CACHE_FLAG} \
-f ./Dockerfile \
-t $$repository_name:$$submodule_version \
-t $$repository_name:latest \
-t $$repository_name:dev \
--build-arg version=$$submodule_version \
--build-arg service_name=$$submodule_name \
--build-arg WHEEL_FILENAME=$${WHEEL_FILENAME} \
$$submodule_directory ; echo "$$?" > status_code; \
if [[ "$$(cat status_code)" == "0" ]]; \
then \
touch $@ ;\
fi
>@${MESSAGE} end "Built." "Build failed."
>@submodule_directory=$$(echo $@ | sed 's/\/docker.built//g') ; \
rm $$submodule_directory/${WHEEL_FILENAME} ; \
rm ./Dockerfile ; \
rm ./.dockerignore ; \
check-docker-daemon-running:
>@${MESSAGE} start "Checking that Docker daemon is running"
>@docker stats --no-stream ; echo "$$?" > status_code
>@${MESSAGE} end "Running." "Not running."
>@status_code=$$(cat status_code); \
if [ $$status_code -gt 0 ] ; \
then \
${MESSAGE} start "Attempting to start Docker daemon" ; \
bash ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/start_docker_daemon.sh ; echo "$$?" > status_code ; \
status_code=$$(cat status_code); \
if [ $$status_code -eq 1 ] ; \
then \
${MESSAGE} end "--" "Timed out." ; \
else \
${MESSAGE} end "Started." "Failed to start." ; \
fi ; \
fi ; \
touch check-docker-daemon-running
.initial_time.txt:
>@date +%s > .initial_time.txt
test: unit-tests module-tests
>@${MESSAGE} start " "
>@cp .initial_time.txt .current_time.txt; \
rm .initial_time.txt; \
${MESSAGE} end "Total time:" "Error computing time."
module-tests: ${MODULE_TEST_TARGETS}
${MODULE_TEST_TARGETS}: development-image data-loaded-image-1smallnointensity data-loaded-image-1small data-loaded-image-1 data-loaded-image-1and2 ${DOCKER_BUILD_TARGETS} clean-network-environment .initial_time.txt
>@submodule_directory=$$(echo $@ | sed 's/^module-test-/${BUILD_LOCATION}\//g') ; \
${MAKE} SHELL=$(SHELL) --no-print-directory -C $$submodule_directory module-tests ;
unit-tests: ${UNIT_TEST_TARGETS}
${UNIT_TEST_TARGETS}: development-image data-loaded-image-1smallnointensity data-loaded-image-1small data-loaded-image-1 data-loaded-image-1and2 ${DOCKER_BUILD_TARGETS} clean-network-environment .initial_time.txt
>@submodule_directory=$$(echo $@ | sed 's/^unit-test-/${BUILD_LOCATION}\//g') ; \
${MAKE} SHELL=$(SHELL) --no-print-directory -C $$submodule_directory unit-tests ;
${SINGLETON_TEST_TARGETS}: development-image data-loaded-image-1small data-loaded-image-1 data-loaded-image-1and2 ${DOCKER_BUILD_TARGETS} clean-network-environment .initial_time.txt
>@submodule_directory=$$(echo $@ | sed 's/^singleton-test-/${BUILD_LOCATION}\//g') ; \
${MAKE} SHELL=$(SHELL) --no-print-directory -C $$submodule_directory singleton-tests ;
# The below explicitly checks whether the docker image already exists locally.
# If so, not rebuilt. To trigger rebuild, use "make clean-docker-images" first,
# or directly force-rebuild-data-loaded-images .
data-loaded-image-%: ${BUILD_LOCATION_ABSOLUTE}/db/docker.built ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/import_test_dataset%.sh development-image
>@${MESSAGE} start "Building test-data-loaded spt-db image ($*)"
>@cp ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/.dockerignore .
>@source ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/check_image_exists.sh; \
exists=$$(check_image_exists ${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-db-preloaded-$*); \
if [[ "$$exists" == "no" ]]; \
then \
docker container create --name temporary-spt-db-preloading --network host -e POSTGRES_PASSWORD=postgres -e PGDATA=.postgres/pgdata ${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-db:latest ; \
docker container start temporary-spt-db-preloading && \
bash ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/poll_container_readiness_direct.sh temporary-spt-db-preloading && \
pipeline_cmd="cd /working_dir; cp -r /mount_sources/build .; cp -r /mount_sources/test .; bash build/build_scripts/import_test_dataset$*.sh "; \
docker container run \
--rm \
--network container:temporary-spt-db-preloading \
--mount type=bind,src=${PWD},dst=/mount_sources \
--mount type=tmpfs,destination=/working_dir \
-t ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest \
/bin/bash -c \
"$$pipeline_cmd" ; echo "$$?" > status_code && \
docker commit temporary-spt-db-preloading ${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-db-preloaded-$*:latest && \
docker container rm --force temporary-spt-db-preloading ; \
fi
>@status_code=$$(cat status_code); \
if [[ "$$status_code" == "0" ]]; \
then \
touch data-loaded-image-$* ; \
fi
>@${MESSAGE} end "Built." "Build failed."
>@rm -f .dockerignore
force-rebuild-data-loaded-images: ${DLI}-1 ${DLI}-2 ${DLI}-1and2 ${DLI}-1small ${DLI}-1smallnointensity
force-rebuild-data-loaded-image-%: ${BUILD_LOCATION_ABSOLUTE}/db/docker.built ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/import_test_dataset%.sh
>@${MESSAGE} start "Rebuilding test-data-loaded spt-db image ($*)"
>@cp ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/.dockerignore .
>@source ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/check_image_exists.sh; \
docker container create --name temporary-spt-db-preloading --network host -e POSTGRES_PASSWORD=postgres -e PGDATA=.postgres/pgdata ${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-db:latest ; \
docker container start temporary-spt-db-preloading && \
bash ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/poll_container_readiness_direct.sh temporary-spt-db-preloading && \
pipeline_cmd="cd /working_dir; cp -r /mount_sources/build .; cp -r /mount_sources/test .; bash build/build_scripts/import_test_dataset$*.sh "; \
docker run \
--rm \
--network container:temporary-spt-db-preloading \
--mount type=bind,src=${PWD},dst=/mount_sources \
--mount type=tmpfs,destination=/working_dir \
-t ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest \
/bin/bash -c \
"$$pipeline_cmd" ; echo "$$?" > status_code && \
docker commit temporary-spt-db-preloading ${DOCKER_ORG_NAME}/${DOCKER_REPO_PREFIX}-db-preloaded-$*:latest && \
docker container rm --force temporary-spt-db-preloading ;
>@status_code=$$(cat status_code); \
if [[ "$$status_code" == "0" ]]; \
then \
touch data-loaded-image-$* ; \
fi
>@${MESSAGE} end "Rebuilt." "Rebuild failed."
>@rm -f .dockerignore
clean: clean-files clean-network-environment
clean-files:
>@rm -rf ${PACKAGE_NAME}.egg-info/
>@rm -rf dist/
>@rm -f .initiation_message_size
>@rm -f .current_time.txt
>@rm -f .initial_time.txt
>@rm -f ${BUILD_LOCATION}/*/.initiation_message_size
>@rm -f ${BUILD_LOCATION}/*/.current_time.txt
>@for submodule in ${SUBMODULES} ; do \
submodule_directory=${BUILD_LOCATION}/$$submodule ; \
${MAKE} SHELL=$(SHELL) --no-print-directory -C $$submodule_directory clean ; \
rm -rf $$submodule_directory/docker.built ; \
done
>@rm -f Dockerfile
>@rm -f .dockerignore
>@rm -rf spatialprofilingtoolbox.egg-info/
>@rm -rf __pycache__/
>@rm -f development-image
>@rm -f development-image-prerequisites-installed
>@rm -f pyproject.toml
>@rm -f data-loaded-image-1
>@rm -f data-loaded-image-2
>@rm -f data-loaded-image-1and2
>@rm -f data-loaded-image-1small
>@rm -f data-loaded-image-1smallnointensity
>@rm -f file_manifest.tsv.bak
>@rm -f .nextflow.log; rm -f .nextflow.log.*; rm -rf .nextflow/; rm -f configure.sh; rm -f run.sh; rm -f main.nf; rm -f nextflow.config; rm -rf work/; rm -rf results/
>@rm -f status_code
>@rm -f check-docker-daemon-running
>@rm -f check-dockerfiles-consistency
>@rm -f check-for-docker-credentials
>@rm -rf ${BUILD_LOCATION}/lib
>@rm -f build/*/log_of_build.log
>@rm -f log_of_build.log
docker-compositions-rm: check-docker-daemon-running
>@${MESSAGE} start "Running docker compose rm (remove)"
>@docker compose --project-directory ./build/apiserver/ rm --force --stop ; status_code1="$$?" ; \
docker compose --project-directory ./build/ondemand/ rm --force --stop ; status_code2="$$?" ; \
docker compose --project-directory ./build/db/ rm --force --stop ; status_code3="$$?" ; \
status_code=$$(( status_code1 + status_code2 + status_code3 + status_code4 + status_code5 )) ; echo $$status_code > status_code
>@docker container rm --force temporary-spt-db-preloading
>@${MESSAGE} end "Down." "Error."
clean-network-environment: docker-compositions-rm
clean-docker-images:
>@docker system prune -f
>@for tag in $$(docker image ls | grep ${DOCKER_ORG_NAME} | awk '{print $$1":"$$2}'); \
do \
docker image rm $$tag; \
done;
>@docker system prune -f