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nightly-model-testing.yml
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name: Nightly Round-Trip Tests (Public)
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: setup java 17 with maven cache
uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-version: '17'
cache: 'maven'
- name: Build VCell Jars
run: mvn --batch-mode 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 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: ${{ failure() }}
export:
runs-on: ubuntu-20.04
needs: build
steps:
- name: Create Docker Image Dir
run: mkdir /tmp/docker
- name: Download Docker Image from `build` Job
uses: actions/download-artifact@v3
with:
name: docker-image
path: /tmp/docker
- name: Load Downloaded Docker Image
run: docker load --input /tmp/docker/$(ls /tmp/docker)
# Get files from VCDB
- name: Checkout Input Files
uses: actions/checkout@v3
with:
repository: virtualcell/vcdb
- name: Prepare Output Directory
run: mkdir -p $GITHUB_WORKSPACE/export_conversion/output
# Do the conversion
- name: Begin Conversion
#$(docker image ls | grep "<none>" | awk '{print $3;}') to get image id
run: docker run -v $GITHUB_WORKSPACE:/root $(docker image ls | grep "<none>" | awk '{print $3;}') export-omex-batch -i "/root/public/biomodel/vcml" -o "/root/export_conversion/output" -m SBML # grabs image and runs
# Parse the results
- name: Parse Results
run: |
cd $GITHUB_WORKSPACE/export_conversion/output
/bin/echo "biomodels processed $(cat jobLog.txt | grep START | wc -l)" >> ../export_results.txt
/bin/echo "biomodels succeeded $(cat jobLog.txt | grep MODEL,SUCC | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts total $(cat jobLog.txt | grep TEXT | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts failed $(cat jobLog.txt | grep TEXT,FAIL | wc -l)" >> ../import_results.txt
/bin/echo "simcontexts supported that failed $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts math not equivalent $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep equiv | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts divide by zero $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep divide | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts duplicate IDs $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep duplicate | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts null pointer $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep null | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts structure mapping $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep struct | wc -l)" >> ../export_results.txt
/bin/echo "simcontexts other failure $(cat jobLog.txt | grep TEXT,FAIL | grep -v supp | grep -v struct | grep -v null | grep -v duplicate | grep -v divide | grep -v equiv | wc -l)" >> ../export_results.txt
/bin/echo "simulations total $(cat jobLog.txt | grep TION | wc -l)" >> ../export_results.txt
/bin/echo "simulations failed $(cat jobLog.txt | grep TION,FAIL | wc -l)" >> ../export_results.txt
/bin/echo "simulations supported that failed $(cat jobLog.txt | grep TION,FAIL | grep -v supp | wc -l)" >> ../export_results.txt
/bin/echo "simulations orphan overrides $(cat jobLog.txt | grep TION,FAIL | grep -v supp | grep Over | wc -l)" >> ../export_results.txt
/bin/echo "simulations unbound identifier $(cat jobLog.txt | grep TION,FAIL | grep -v supp | grep unbound | wc -l)" >> ../export_results.txt
/bin/echo "simulations other failure $(cat jobLog.txt | grep TION,FAIL | grep -v supp | grep -v Over | grep -v unbound | wc -l)" >> ../export_results.txt
# Create tar of converted files
- name: Compress Converted Files
run: cd $GITHUB_WORKSPACE/export_conversion/output && sudo tar cf omexes.tar --wildcards *.omex
# Upload Converted Files
- name: Upload Converted Files
uses: actions/upload-artifact@v3
with:
name: omexes.tar
path: ~/work/vcell/vcell/export_conversion/output/omexes.tar # Action only has basic ~ based expansion, env variables dont appear to work
# Upload Results
- name: Upload results of round-trip
uses: actions/upload-artifact@v3
with:
name: export_results.txt
path: ~/work/vcell/vcell/export_conversion/output/export_results.txt
- name: Upload original log of export
uses: actions/upload-artifact@v3
with:
name: export_log_original
path: ~/work/vcell/vcell/export_conversion/output/jobLog.txt
# 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 *Export Step* of Nightly 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: ${{ failure() }}
import:
runs-on: ubuntu-20.04
needs: export
steps:
- name: Create working directory
run: mkdir ~/wrk
- name: Download Docker Image from `build` Job
uses: actions/download-artifact@v3
with:
name: docker-image
path: ~/wrk
- name: Load Downloaded Docker Image
run: docker load --input ~/wrk/$(ls ~/wrk)
# Make Input Directory
- name: Make Input and Output Directory
run: mkdir -p ~/input_files/output && mkdir ~/input_files/input
# Get the coverted omexes from before
- name: Download Converted COMBINE Archives
uses: actions/download-artifact@v3
with:
name: omexes.tar
path: ~/input_files/input
- name: Unpack Input Files
run: cd ~/input_files/input && sudo tar xvf $(ls *.tar) && rm $(ls *.tar)
- name: Prepare Output Directory
run: mkdir ~/input_files/input
# Do the round trip
- name: Begin Round-Trip Import
#$(docker image ls | grep "<none>" | awk '{print $3;}') to get image id
run: docker run -v ~/input_files:/root $(docker image ls | grep "<none>" | awk '{print $3;}') import-omex-batch -d -i "/root/input" -o "/root/output"
# Parse the results
- name: Parse Results
run: |
cd ~/input_files/output
/bin/echo "Biomodels processed $(cat jobLog.txt | grep '.omex,SUCC\|.omex,FAIL' | wc -l)" >> ~/import_results.txt
/bin/echo "Biomodels succeeded $(cat jobLog.txt | grep SUCC | wc -l)" >> ~/import_results.txt
/bin/echo "Biomodels that didn't converge $(cat jobLog.txt | grep SUCC | grep -v ',1' | wc -l)" >> ~/import_results.txt
# Upload results
- name: Upload Results of Round-Trip
uses: actions/upload-artifact@v3
with:
name: import_results.txt
path: ~/import_results.txt
- name: Upload Results of Round-Trip
uses: actions/upload-artifact@v3
with:
name: import_log_original
path: ~/input_files/output/jobLog.txt
# 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 *Import Step* of Nightly 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() }}
summarize:
runs-on: ubuntu-20.04
needs: import
steps:
- name: Make Results Directory
run: mkdir -p ~/results && cd ~/results
- name: Download Export Results
uses: actions/download-artifact@v3
with:
name: export_results.txt
path: ~/results
- name: Download Import Results
uses: actions/download-artifact@v3
with:
name: import_results.txt
path: ~/results
- name: Compile Results
run: |
if [ $() -gt 50000] && [ $() -lt 120000 ]; then echo -n 'Good Morning! ' >> ~/results/summary.txt; fi
echo 'Here are the results of the Nightly Testing. Have a great day!' >> ~/results/summary.txt
echo '' >> ~/results/summary.txt
echo '-------- Export Results --------' >> ~/results/summary.txt
cat ~/results/export_results.txt >> ~/results/summary.txt
echo '-------- Import Results --------' >> ~/results/summary.txt
cat ~/results/import_results.txt >> ~/results/summary.txt
echo '' >> ~/results/summary.txt
# Report a Success
- name: Report Results to Slack
run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ~/results/summary.txt)" https://slack.com/api/chat.postMessage
# 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 *Summary Step* of Nightly 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() }}