diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml index 01a2e15149..f376fd85cb 100644 --- a/.github/workflows/NightlyBMDB_CLI.yml +++ b/.github/workflows/NightlyBMDB_CLI.yml @@ -117,130 +117,6 @@ jobs: 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@v4 -# 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 "" | awk '{print $3;}') to get image id -# run: | -# # Prepare files -# echo "[]" > ${{ github.workspace }}/total_exec_summary.json -# echo "[]" > ${{ github.workspace }}/full_tracer.json -# # The /* goes on the outside, otherwise bash just interprets a string! -# for file in "$GITHUB_WORKSPACE/set_${{ matrix.sets }}"/*; do -# echo "\"$file\"" -# if [ -f "$file" ]; then -# extensionless_name="${file%.*}" -# base_name="$(basename ${file})" -# base_extless_name="$(basename ${extensionless_name})" -# mkdir "${extensionless_name}_output" -# echo "Running \"${file}\" in output folder \"${base_extless_name}_output\"" -# sim_input="/root/${base_name}" -# sim_output="/root/${base_extless_name}_output" -# vcell_result=$(docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "" | awk '{print $3;}') execute-omex -d -i ${sim_input} -o ${sim_output} --timeout_ms=300000) -# -# echo -e "\n\n\n\n\n" # give ourselves some line separation -# -# # Grab Summary -# if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name exec_summary.json | wc -l) -ne 0 ] -# then -# # Append to master summary in github workspace -# jq '. + [inputs]' ${{ github.workspace }}/total_exec_summary.json $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name exec_summary.json) > temp.json -# mv temp.json ${{ github.workspace }}/total_exec_summary.json -# else -# echo "No summary found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}" -# fi -# -# # Check for individual Failure (a.k.a. if we failed early) -# status=$(cat $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name exec_summary.json) | jq -r '.status') -# if [[ "$status" == "FAILED" ]] || [ ${vcell_result} -ne 0 ] -# then -# # Copy error log to github workspace -# echo "${base_extless_name}" >> $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output/errorLog.txt -# touch ${{ github.workspace }}/errors.report -# cat $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output/errorLog.txt >> ${{ github.workspace }}/errors.report -# else -# echo "Run of ${base_extless_name} succeeded (set_${{ matrix.sets }})" -# fi -# -# # Grab Trace -# # Check for individual Success -# if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name tracer.json | wc -l) -ne 0 ] -# then -# # Append to master trace in github workspace -# jq '. + inputs' ${{ github.workspace }}/full_tracer.json $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name tracer.json) > temp_2.json -# mv temp_2.json ${{ github.workspace }}/full_tracer.json -# else -# echo "No trace found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}" -# fi -# fi -# done -# -# - name: Check For Success -# run: | -# # If the error file exists, then we have failures to report and upload; else, we can just end here; the next job will process results -# if [ $(find ${{ github.workspace }} -name errors.report | wc -l) -eq 0 ] -# then -# exit 0 -# fi -# echo "Models that failed:" -# cat ${{ github.workspace }}/errors.report -# -# - name: Upload failures -# uses: actions/upload-artifact@v3 -# with: -# name: set_${{ 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 @@ -404,26 +280,6 @@ jobs: uses: mxschmitt/action-tmate@v3 if: ${{ failure() }} -# published_results: -# runs-on: ubuntu-20.04 -# needs: published -# -# steps: -# - name: Gather Artifacts -# uses: actions/download-artifact@v3 -# 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=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(sort ${GITHUB_WORKSPACE}/combined.txt)" https://slack.com/api/chat.postMessage - - bmdb_results: runs-on: ubuntu-20.04 needs: bmdb @@ -453,7 +309,4 @@ jobs: run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(sort ${GITHUB_WORKSPACE}/combined.txt)" https://slack.com/api/chat.postMessage - name: Post results to slack part 3 - run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F file=$GITHUB_WORKSPACE/summary.json https://slack.com/api/files.upload - - - name: Post results to slack part 4 - run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F file=$GITHUB_WORKSPACE/tracer.json https://slack.com/api/files.upload \ No newline at end of file + run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="To see detailed logs of the BMDB results, see - ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}. Go see what happened!" https://slack.com/api/chat.postMessage \ No newline at end of file