try to escape the special characters in the apptainer exec command #31

Workflow file for this run

.github/workflows/icd_tests_linux.yml at fc4382c

	name: Linux ICD tests
	on:
	push:
	schedule:
	- cron: '0 0 * * *' # UTC time
	env:
	ICD_RXJS_BRANCH_NAME: ajm/icd-test-stages-lists

	jobs:

	Build:
	name: Build ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2004-dec2023.sif
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2204-dec2023.sif
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/centos7-dec2023.sif
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/almalinux8-dec2023.sif
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD3]
	image: /opt/apptainer/almalinux9-dec2023.sif
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	path: source

	- name: Build backend
	shell: bash
	run: \|
	SRC_DIR=$GITHUB_WORKSPACE/source
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	rm -rf $BUILD_DIR
	mkdir -p $BUILD_DIR
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $SRC_DIR ${{ matrix.image }} /bin/bash -c "\
	git submodule update --init --recursive && \
	cd $BUILD_DIR && \
	cmake $SRC_DIR \
	-Dtest=on \
	-DCMAKE_BUILD_TYPE=Debug \
	-DDevSuppressExternalWarnings=ON \
	-DCMAKE_CXX_FLAGS='-O0 -g -fsanitize=address -fno-omit-frame-pointer' \
	-DCMAKE_EXE_LINKER_FLAGS='-fsanitize=address' && \
	make -j 16"

	- name: Check backend runs
	shell: bash
	run: \|
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "./carta_backend --version"

	Prepare-ICD-RxJS:
	name: Prepare-ICD-RxJS ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2004-dec2023.sif
	port: 9001
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2204-dec2023.sif
	port: 9002
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/centos7-dec2023.sif
	port: 9003
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/almalinux8-dec2023.sif
	port: 9004
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD3]
	image: /opt/apptainer/almalinux9-dec2023.sif
	port: 9005
	needs: Build
	steps:
	- name: Prepare ICD-RxJS
	shell: bash
	run: \|
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	ICD_RXJS_DIR=$BUILD_DIR/ICD-RxJS
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "\
	if [ -d '$ICD_RXJS_DIR' ]; then
	cd $ICD_RXJS_DIR && git pull
	else
	echo 'Cloning ICD-RxJS repository...'
	git clone https://github.com/CARTAvis/ICD-RxJS.git
	cd ICD-RxJS
	fi && \
	git checkout ${{ env.ICD_RXJS_BRANCH_NAME }} && \
	git submodule init && git submodule update && npm install && \
	cd protobuf && \
	./build_proto.sh && \
	cd ../src/test && \
	perl -p -i -e 's/3002/${{ matrix.port }}/' config.json"

	File-Browser-ICD-Tests:
	name: File-Browser ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2004-dec2023.sif
	port: 9001
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2204-dec2023.sif
	port: 9002
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/centos7-dec2023.sif
	port: 9003
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/almalinux8-dec2023.sif
	port: 9004
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD3]
	image: /opt/apptainer/almalinux9-dec2023.sif
	port: 9005
	needs: [Build, Prepare-ICD-RxJS]
	steps:
	- name: File Browser ICD tests
	shell: bash
	run: \|
	SRC_DIR=$GITHUB_WORKSPACE/source
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	TEST_STAGE="$BUILD_DIR/ICD-RxJS/ICD_test_stages/file_browser.tests"
	LOG_FILE="/tmp/carta_icd_${{ matrix.os_version }}_file_browser.log"
	apptainer exec \
	--bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE \
	--bind /images:/images \
	--pwd $BUILD_DIR \
	${{ matrix.image }} /bin/bash -c "\
	# Start the carta_backend
	ASAN_OPTIONS=suppressions=$SRC_DIR/debug/asan/myasan.supp \
	LSAN_OPTIONS=suppressions=$SRC_DIR/debug/asan/myasan-leaks.supp \
	ASAN_SYMBOLIZER_PATH=llvm-symbolizer \
	./carta_backend /images \
	--top_level_folder /images \
	--port ${{ matrix.port }} \
	--omp_threads=4 \
	--debug_no_auth \
	--no_frontend \
	--no_database \
	--verbosity=5 >> $LOG_FILE 2>&1 & \
	CARTA_BACKEND_PID=\$(pgrep -f \"carta_backend.*${{ matrix.port }}\" \| head -n 1) && \
	echo 'carta_backend started with PID' \$CARTA_BACKEND_PID && \
	# Run the ICD tests
	cd $BUILD_DIR/ICD-RxJS && \
	pwd && \
	cat $TEST_STAGE && \
	while IFS= read -r test_file \|\| [[ -n "\$test_file\" ]]; do
	CI=true npm test -- \"\$test_file\"
	done < \"$TEST_STAGE\" && \
	# Stop the carta_backend
	kill \$CARTA_BACKEND_PID"

	Animator-ICD-Tests:
	name: Animator ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2004-dec2023.sif
	port: 9001
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD1]
	image: /opt/apptainer/ubuntu-2204-dec2023.sif
	port: 9002
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/centos7-dec2023.sif
	port: 9003
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD2]
	image: /opt/apptainer/almalinux8-dec2023.sif
	port: 9004
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD3]
	image: /opt/apptainer/almalinux9-dec2023.sif
	port: 9005
	needs: [File-Browser-ICD-Tests, Prepare-ICD-RxJS]
	steps:
	- name: Animator ICD tests
	shell: bash
	run: \|
	SRC_DIR=$GITHUB_WORKSPACE/source
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	TEST_STAGE="$BUILD_DIR/ICD-RxJS/ICD_test_stages/animator.tests"
	LOG_FILE="/tmp/carta_icd_${{ matrix.os_version }}_animator.log"
	PORT_NUMBER=${{ matrix.port }}
	apptainer exec \
	--bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE \
	--bind /images:/images \
	--pwd $BUILD_DIR \
	${{ matrix.image }} /bin/bash -c "\
	# Start the carta_backend
	ASAN_OPTIONS=suppressions=$SRC_DIR/debug/asan/myasan.supp \
	LSAN_OPTIONS=suppressions=$SRC_DIR/debug/asan/myasan-leaks.supp \
	ASAN_SYMBOLIZER_PATH=llvm-symbolizer \
	./carta_backend /images \
	--top_level_folder /images \
	--port ${{ matrix.port }} \
	--omp_threads=4 \
	--debug_no_auth \
	--no_frontend \
	--no_database \
	--verbosity=5 >> $LOG_FILE 2>&1 & \
	CARTA_BACKEND_PID=\$(pgrep -f \"carta_backend.*${{ matrix.port }}\" \| head -n 1) && \
	echo 'carta_backend started with PID' \$CARTA_BACKEND_PID && \
	# Run the ICD tests
	cd $BUILD_DIR/ICD-RxJS && \
	pwd && \
	cat $TEST_STAGE && \
	while IFS= read -r test_file \|\| [[ -n "\$test_file\" ]]; do
	CI=true npm test -- \"\$test_file\"
	done < \"$TEST_STAGE\" && \
	# Stop the carta_backend
	kill \$CARTA_BACKEND_PID"

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try to escape the special characters in the apptainer exec command #31

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try to escape the special characters in the apptainer exec command #31

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