Updating to use new command

virtualcell · Dec 19, 2024 · cdff88a · cdff88a
1 parent e9b055a
commit cdff88a
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Showing 2 changed files with 100 additions and 12 deletions.
diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml
@@ -163,6 +163,9 @@ jobs:
       - name: Begin Execution
         #$(docker image ls | grep "<none>" | 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\""
@@ -174,17 +177,41 @@ jobs:
               echo "Running \"${file}\" in output folder \"${base_extless_name}_output\""
               sim_input="/root/${base_name}"
               sim_output="/root/${base_extless_name}_output"
-              docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | awk '{print $3;}') execute -d -i ${sim_input} -o ${sim_output} --writeLogFiles --guaranteeGoodReturnCode
-          
+              vcell_result=$(docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | 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
-              # Check for individual Success
-              if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name errorLog.txt | wc -l) -ne 0 ]
+
+              # 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 $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name errorLog.txt) >> ${{ 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 errors found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}"
+                echo "No trace found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}"
               fi
             fi
           done
@@ -271,10 +298,16 @@ jobs:
               fi
           done
 
+      - name: Install JQ
+        run: sudo apt update && sudo apt install jq -y
+
         # Do the execution
       - name: Begin Execution
         #$(docker image ls | grep "<none>" | 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\""
@@ -286,22 +319,45 @@ jobs:
               echo "Running \"${file}\" in output folder \"${base_extless_name}_output\""
               sim_input="/root/${base_name}"
               sim_output="/root/${base_extless_name}_output"
-              docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | awk '{print $3;}') execute -d -i ${sim_input} -o ${sim_output} --writeLogFiles --guaranteeGoodReturnCode
+              vcell_result=$(docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "<none>" | 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
-              # Check for individual Success
-              if [ $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name errorLog.txt | wc -l) -ne 0 ]
+          
+              # Grab Summary
+              if [ -f "${GITHUB_WORKSPACE}/set_${{ matrix.sets }}/${base_extless_name}_output/exec_summary.json" ]
               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=$(cat "${GITHUB_WORKSPACE}/set_${{ matrix.sets }}/${base_extless_name}_output/exec_summary.json" | jq -r '.status')
+              echo "${status}"
+              if [ "${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 $(find $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output -name errorLog.txt) >> ${{ github.workspace }}/errors.report
+                cat $GITHUB_WORKSPACE/set_${{ matrix.sets }}/${base_extless_name}_output/errorLog.txt >> ${{ github.workspace }}/errors.report
               else
-                echo "No errors found in set $GITHUB_WORKSPACE/set_${{ matrix.sets }}"
+                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
 
-        #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: |
@@ -319,6 +375,18 @@ jobs:
           name: set_${{ matrix.sets }}.report
           path: ${{ github.workspace }}/errors.report
 
+      - name: Upload summary
+        uses: actions/upload-artifact@v3
+        with:
+          name: set_${{ matrix.sets }}.summary
+          path: ${{ github.workspace }}/total_exec_summary.json
+
+      - name: Upload tracer
+        uses: actions/upload-artifact@v3
+        with:
+          name: set_${{ matrix.sets }}.tracer
+          path: ${{ github.workspace }}/full_tracer.json
+
       # Report a Problem to Slack
       - name: Report Problem to Slack
         if: ${{ failure() }}
@@ -358,11 +426,26 @@ jobs:
         with:
           path: ${{ github.workspace }}/bmdb-results
 
+      - name: Install JQ
+        run: sudo apt update && sudo apt install jq -y
+
       - name: Combine .report artifacts into one file
         run: cat $(find $GITHUB_WORKSPACE/bmdb-results -name 'errors.report') > $GITHUB_WORKSPACE/combined.txt
 
+      - name: Combine .summary artifacts into one file
+        run: jq -s 'add' $(find $GITHUB_WORKSPACE/bmdb-results -name 'total_exec_summary.json') > $GITHUB_WORKSPACE/summary.json
+
+      - name: Combine .summary artifacts into one file
+        run: jq -s 'add' $(find $GITHUB_WORKSPACE/bmdb-results -name 'full_tracer.json') > $GITHUB_WORKSPACE/tracer.json
+
       - name: Post results to slack part 1
         run: curl -X POST -F token="${{ 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="$(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=$GITHUB_WORKSPACE/tracer.json https://slack.com/api/files.upload
diff --git a/docker_run.sh b/docker_run.sh
@@ -47,6 +47,11 @@ case "$rawCommand" in
     command="execute"
     shift
     ;;
+  "execute-omex")
+      echo 'special testing execution mode requested'
+      command="execute-omex"
+      shift
+      ;;
   "validate")
     echo 'validate mode requested'
     command="validate"