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NightlyBMDB_CLI.yml
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name: Nightly CLI Execution Tests (Published + BMDB)
on:
schedule:
- cron: "0 7 * * *"
workflow_dispatch:
env:
python-version: "3.9"
poetry-version: "1.2.1"
jobs:
build:
runs-on: ubuntu-20.04
steps:
- name: Checkout Our Code
uses: actions/checkout@v3
with:
ref: '${{ github.ref }}'
- name: Get GH Reference
run: echo '${{ github.ref }}' >> ~/github.ref
- name: Upload Ref
uses: actions/upload-artifact@v3
with:
name: github_hash
path: ~/github.ref
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ env.python-version }}
- name: Install poetry
run: python3 -m pip install poetry==${{ env.poetry-version }}
- name: Install other python dependencies
run: python3 -m pip install -r requirements.txt
- name: build vcell-cli-utils package
run: |
cd vcell-cli-utils
poetry install
poetry run python -m pytest
- name: build vcell-admin package
run: |
cd docker/swarm/vcell-admin
poetry install
poetry run python -m pytest
- name: build pythonCopasiOpt package
run: |
cd pythonCopasiOpt/vcell-opt
poetry install
poetry run python -m pytest
- name: build pythonVtk package
run: |
cd pythonVtk
poetry install
poetry run python -m pytest
- name: build vcutils package
run: |
cd python-utils
poetry install
poetry run python -m pytest
- name: build python-restclient package
run: |
cd python-restclient
poetry install
poetry run python -m pytest
- name: build vcelldata package
run: |
cd pythonData
poetry install
poetry run python -m pytest
- name: Setup Java for Build
uses: actions/setup-java@v2
with:
java-version: '17'
distribution: 'temurin'
cache: 'maven'
- name: Build VCell Jars
run: mvn clean install dependency:copy-dependencies -DskipTests=True
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
- name: Build and Export
uses: docker/build-push-action@v3
with:
context: .
file: ./Dockerfile
outputs: type=docker,dest=/tmp/image.tar
build-args: | # Max ram for Ubuntu GitHub workflow is 7GB (as of 12/9/22), using MB for precision (0.8 of 7gb)
MAX_JAVA_MEM=5734
- name: Upload Artifact
uses: actions/upload-artifact@v3
with:
name: docker-image
path: /tmp/image.tar
# Report a Problem to Slack
- name: Report Problem to Slack
if: ${{ failure() }}
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Uh-Oh! The *Build Step* of Nightly Execution Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} )! This may need attention..." https://slack.com/api/chat.postMessage
# Tmate just in case
- name: Setup tmate session 3
uses: mxschmitt/action-tmate@v3
if: ${{ failure() }}
published:
runs-on: ubuntu-20.04
needs: build
strategy:
matrix:
sets: ["0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19"]
steps:
- name: Create Docker Image Dir
run: mkdir /tmp/docker
- name: Download Docker Image from `build` Job
uses: actions/download-artifact@v3
with:
name: docker-image
path: /tmp/docker
- name: Load Downloaded Docker Image
run: docker load --input /tmp/docker/$(ls /tmp/docker)
# Get files from BMDB
- name: Checkout Input Files
uses: actions/checkout@v3
with:
repository: virtualcell/vcdb
- name: Prepare sub directory
run: |
SOURCE_DIR="$GITHUB_WORKSPACE/published/biomodel/omex/sbml"
TARGET_DIR="$GITHUB_WORKSPACE/set_${{ matrix.sets }}"
MOD_VALUE=${{ matrix.sets }}
file_index=0
# make target dir
mkdir $TARGET_DIR
# loop through files in directory, increment indexing and separating files
for file in $SOURCE_DIR/*; do
file_index=$((file_index+1))
if [ $((file_index%${{ strategy.job-total }})) -eq $((MOD_VALUE + 0)) ]; then
cp ${file} $TARGET_DIR/
fi
done
# Do the execution
- name: Begin Execution
#$(docker image ls | grep "<none>" | awk '{print $3;}') to get image id
run: docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | awk '{print $3;}') execute -d -i "/root" -o "/root/output" --writeLogFiles # grabs image and runs
- name: Check For Success
run: |
errorSearch=$(find $GITHUB_WORKSPACE/set_${{ matrix.sets }} -name errorLog.txt)
if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }} -name errorLog.txt | wc -l) -eq 0 ]
then
exit 0
else
# Copy error log to github workspace
cp $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }} -name errorLog.txt) ${{ github.workspace }}/errors.report
fi
- name: Upload failures
uses: actions/upload-artifact@v3
with:
name: set_${{ matrix.sets }}.report
path: ${{ github.workspace }}/errors.report
# Report a Problem to Slack
- name: Report Problem to Slack
if: ${{ failure() }}
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Oops! The *Published Step* of set ${{ matrix.sets }} in Nightly **Execution** Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} ). Go see what happened!" https://slack.com/api/chat.postMessage
- name: Setup tmate session 3
uses: mxschmitt/action-tmate@v3
if: ${{ failure() }}
bmdb:
runs-on: ubuntu-20.04
needs: build
strategy:
matrix:
sets: ["0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19"]
steps:
- name: Create Docker Image Dir
run: mkdir /tmp/docker
- name: Download Docker Image from `build` Job
uses: actions/download-artifact@v3
with:
name: docker-image
path: /tmp/docker
- name: Load Downloaded Docker Image
run: docker load --input /tmp/docker/$(ls /tmp/docker)
# Get files from BMDB
- name: Checkout Input Files
uses: actions/checkout@v3
with:
repository: sys-bio/temp-biomodels
- name: Prepare sub directory
run: |
SOURCE_DIR="$GITHUB_WORKSPACE/omex_files"
TARGET_DIR="$GITHUB_WORKSPACE/set_${{ matrix.sets }}"
MOD_VALUE=${{ matrix.sets }}
file_index=0
# make target dir
mkdir $TARGET_DIR
# loop through files in directory, increment indexing and separating files
for file in $SOURCE_DIR/*; do
file_index=$((file_index+1))
if [[ $file == *1008* ]]; then
echo -n 'skipping '
echo $file
continue
fi
if [ $((file_index%${{ strategy.job-total }})) -eq $((MOD_VALUE + 0)) ]; then
cp ${file} $TARGET_DIR/
fi
done
# Do the execution
- name: Begin Execution
#$(docker image ls | grep "<none>" | awk '{print $3;}') to get image id
run: docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | awk '{print $3;}') execute -d -i "/root" -o "/root/output" --writeLogFiles # grabs image and runs
- name: Check For Success
run: |
errorSearch=$(find $GITHUB_WORKSPACE/set_${{ matrix.sets }} -name errorLog.txt)
if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }} -name errorLog.txt | wc -l) -eq 0 ]
then
exit 0
else
# Copy error log to github workspace
cp $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }} -name errorLog.txt) ${{ github.workspace }}/errors.report
fi
- name: Upload failures
uses: actions/upload-artifact@v3
with:
name: set_${{ matrix.sets }}.report
path: ${{ github.workspace }}/errors.report
# Report a Problem to Slack
- name: Report Problem to Slack
if: ${{ failure() }}
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Oops! The *BMDB Step* of Nightly **Execution** (set ${{ matrix.sets }}) Testing Action on GitHub Failed ( ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} ). Go see what happened!" https://slack.com/api/chat.postMessage
- name: Setup tmate session 3
uses: mxschmitt/action-tmate@v3
if: ${{ failure() }}
published_results:
runs-on: ubuntu-20.04
needs: published
steps:
- name: Gather Artifacts
uses: actions/download-artifact@v2
with:
path: ${{ github.workspace }}/published-results
- name: Combine .report artifacts into one file
run: cat $(find $GITHUB_WORKSPACE/published-results -name 'errors.report') > $GITHUB_WORKSPACE/combined.txt
- name: Post results to slack part 1
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Here're the $(cat ${GITHUB_WORKSPACE}/combined.txt | wc -l) published models that didn't pass:" https://slack.com/api/chat.postMessage
- name: Post results to slack part 2
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ${GITHUB_WORKSPACE}/combined.txt)" https://slack.com/api/chat.postMessage
bmdb_results:
runs-on: ubuntu-20.04
needs: bmdb
steps:
- name: Gather Artifacts
uses: actions/download-artifact@v2
with:
path: ${{ github.workspace }}/bmdb-results
- name: Combine .report artifacts into one file
run: cat $(find $GITHUB_WORKSPACE/bmdb-results -name 'errors.report') > $GITHUB_WORKSPACE/combined.txt
- name: Post results to slack part 1
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="Here're the $(cat ${GITHUB_WORKSPACE}/combined.txt | wc -l) BMDB models that didn't pass:" https://slack.com/api/chat.postMessage
- name: Post results to slack part 2
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ${GITHUB_WORKSPACE}/combined.txt)" https://slack.com/api/chat.postMessage