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try while IFS loop instead of cat #30

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try while IFS loop instead of cat

try while IFS loop instead of cat #30

Workflow file for this run

.github/workflows/icd_tests_linux.yml at 52f69ae
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: ${{ matrix.runner }}
strategy:
fail-fast: false
matrix:
include:
- os_version: ubuntu-20.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2004-dec2023.sif
- os_version: ubuntu-22.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2204-dec2023.sif
- os_version: rhel-7
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/centos7-dec3023.sif
- os_version: rhel-8
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/almalinux8-dec3023.sif
- os_version: rhel-9
runner: [self-hosted, linux, Apptainer, ICD3]
image: /opt/apptainer/almalinux9-dec3023.sif
steps:
- name: Checkout
uses: actions/checkout@v3
with:
path: source
- name: Build backend
shell: bash
run: |
SRC_DIR=$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: ${{ matrix.runner }}
strategy:
fail-fast: false
matrix:
include:
- os_version: ubuntu-20.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2004-dec2023.sif
port: 9001
- os_version: ubuntu-22.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2204-dec2023.sif
port: 9002
- os_version: rhel-7
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/centos7-dec3023.sif
port: 9003
- os_version: rhel-8
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/almalinux8-dec3023.sif
port: 9004
- os_version: rhel-9
runner: [self-hosted, linux, Apptainer, ICD3]
image: /opt/apptainer/almalinux9-dec3023.sif
port: 9005
needs: Build
steps:
- name: Prepare ICD-RxJS
shell: bash
run: |
BUILD_DIR=$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: ${{ matrix.runner }}
strategy:
fail-fast: false
matrix:
include:
- os_version: ubuntu-20.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2004-dec2023.sif
port: 9001
- os_version: ubuntu-22.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2204-dec2023.sif
port: 9002
- os_version: rhel-7
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/centos7-dec3023.sif
port: 9003
- os_version: rhel-8
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/almalinux8-dec3023.sif
port: 9004
- os_version: rhel-9
runner: [self-hosted, linux, Apptainer, ICD3]
image: /opt/apptainer/almalinux9-dec3023.sif
port: 9005
needs: [Build, Prepare-ICD-RxJS]
steps:
- name: File Browser ICD tests
shell: bash
run: |
SRC_DIR=$GITHUB_WORKSPACE/source
BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
LOG_FILE="/tmp/carta_icd_${{ matrix.os_version }}_${TEST_STAGE}.log"
TEST_FILES="$BUILD_DIR/ICD-RxJS/ICD_test_stages/file_browser.tests"
apptainer exec \
--bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE \
--bind /images:/images \
--pwd $BUILD_DIR \
${{ matrix.image }} /bin/bash -c "\
# Start carta_backend
ASAN_OPTIONS=suppressions=$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 >> $LOG_FILE 2>&1 & \
sleep 5 && \
CARTA_BACKEND_PID=$(pgrep -f carta_backend) && \
echo 'carta_backend started with PID: $CARTA_BACKEND_PID' && \
cat $TEST_FILES && \
while IFS= read -r test_file || [ -n "$test_file" ]; do
CI=true npm test "$test_file"
sleep 3 && pgrep carta_backend
done < "$TEST_FILES" && \
kill $CARTA_BACKEND_PID"
Animator-ICD-Tests:
name: Animator ${{ matrix.os_version }}
runs-on: ${{ matrix.runner }}
strategy:
fail-fast: false
matrix:
include:
- os_version: ubuntu-20.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2004-dec2023.sif
port: 9001
- os_version: ubuntu-22.04
runner: [self-hosted, Linux, Apptainer, ICD1]
image: /opt/apptainer/ubuntu-2204-dec2023.sif
port: 9002
- os_version: rhel-7
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/centos7-dec3023.sif
port: 9003
- os_version: rhel-8
runner: [self-hosted, linux, Apptainer, ICD2]
image: /opt/apptainer/almalinux8-dec3023.sif
port: 9004
- os_version: rhel-9
runner: [self-hosted, linux, Apptainer, ICD3]
image: /opt/apptainer/almalinux9-dec3023.sif
port: 9005
needs: [File-Browser-ICD-Tests, Prepare-ICD-RxJS]
steps:
- name: Animator ICD tests
shell: bash
run: |
SRC_DIR=$GITHUB_WORKSPACE/source
BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
LOG_FILE="/tmp/carta_icd_${{ matrix.os_version }}_${TEST_STAGE}.log"
TEST_FILES="$BUILD_DIR/ICD-RxJS/ICD_test_stages/animator.tests"
apptainer exec \
--bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE \
--bind /images:/images \
--pwd $BUILD_DIR \
${{ matrix.image }} /bin/bash -c "\
# Start carta_backend
ASAN_OPTIONS=suppressions=$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 >> $LOG_FILE 2>&1 & \
sleep 5 && \
CARTA_BACKEND_PID=$(pgrep -f carta_backend) && \
echo 'carta_backend started with PID: $CARTA_BACKEND_PID' && \
cat $TEST_FILES && \
while IFS= read -r test_file || [ -n "$test_file" ]; do
CI=true npm test "$test_file"
sleep 3 && pgrep carta_backend
done < "$TEST_FILES" && \
kill $CARTA_BACKEND_PID"