Nightly Round-Trip Tests (Public) #913

Workflow file for this run

.github/workflows/nightly-model-testing.yml at c71bd3b

	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@v4
	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@v5
	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 17 with maven cache
	uses: actions/setup-java@v4
	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@v4
	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() }}

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Nightly Round-Trip Tests (Public) #913

Workflow file

Nightly Round-Trip Tests (Public) #913

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Workflow file for this run