GROK-16944: AutoDock: Error when run from context pane from Browse #2125
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| name: Packages | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| packages: | |
| description: 'Packages separated by spaces' | |
| required: true | |
| type: string | |
| push: | |
| paths: | |
| - 'packages/**' | |
| pull_request: | |
| paths: | |
| - 'packages/**' | |
| jobs: | |
| common-check: | |
| name: Common checks | |
| uses: ./.github/workflows/common_check.yaml | |
| with: | |
| run_trigger: ${{ github.event_name }} | |
| matrix: | |
| name: Check changes | |
| runs-on: ubuntu-22.04 | |
| needs: common-check | |
| if: needs.common-check.outputs.continue == 'true' | |
| outputs: | |
| matrix_publish: ${{ steps.generate-matrix.outputs.matrix_publish }} | |
| publish: ${{ steps.generate-matrix.outputs.publish }} | |
| permissions: | |
| pull-requests: read | |
| steps: | |
| - name: Set git fetch depth | |
| run: | | |
| if [[ ${{ github.event_name }} != 'pull_request' ]]; then | |
| echo "FETCH_DEPTH=2" >> "$GITHUB_ENV" | |
| else | |
| echo "FETCH_DEPTH=0" >> "$GITHUB_ENV" | |
| fi | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: ${{ env.FETCH_DEPTH }} | |
| sparse-checkout: | | |
| ./packages | |
| - name: Get changed files | |
| uses: tj-actions/changed-files@v42 | |
| id: changed-files | |
| with: | |
| files: 'packages/**' | |
| separator: "\n" | |
| dir_names: true | |
| safe_output: false | |
| - name: Generate matrix | |
| id: generate-matrix | |
| env: | |
| ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }} | |
| run: | | |
| if [[ "${{ github.event.inputs.packages }}" == "" ]]; then | |
| CHANGED_PACKAGES="$(echo -e "${ALL_CHANGED_FILES}" | awk -F'/' '{print $2}' | sort -u)" | |
| else | |
| CHANGED_PACKAGES="${{ github.event.inputs.packages }}" | |
| fi | |
| MATRIX_PUBLISH_JSON="[" | |
| for PACKAGE in $(echo ${CHANGED_PACKAGES} | sort -u); do | |
| DIR="packages/${PACKAGE}" | |
| if [ -f "${DIR}/package.json" ]; then | |
| MATRIX_PUBLISH_JSON+="{\"package\": \"${PACKAGE}\"" | |
| current_version="$(jq -r '.version' "${DIR}/package.json")" | |
| MATRIX_PUBLISH_JSON+=", \"version\": \"${current_version}\"" | |
| scripts="$(jq '. | select( has("scripts") == true ).scripts' "${DIR}/package.json")" | |
| dependencies="$(jq '(. | select( has("dependencies") == true ).dependencies) * (. | select( has("devDependencies") == true ).devDependencies)' "${DIR}/package.json")" | |
| job_name='Check' | |
| if [ ! -z "$(jq -r '. | select( has("build") == true )' <<< "$scripts")" ]; then | |
| MATRIX_PUBLISH_JSON+=", \"build\": \"build\"" | |
| job_name='Build' | |
| fi | |
| unpublished_deps="$(jq -r '. | to_entries | map(select(.value | match("\\.\\./.*")))[] | "\(.key)=\(.value)"' <<<$dependencies | tr '\n' ' ')" | |
| job_test_env='' | |
| if [ -n "$(jq '. | select( has("test") == true )' <<< "$scripts")" ] && \ | |
| [[ "$(jq -r '. | select( has("skipCI") == true ).skipCI' "${DIR}/package.json")" != "true" ]] && \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" != "docking" ]]; then | |
| MATRIX_PUBLISH_JSON+=", \"test\": \"test\"" | |
| job_name='Build, test' | |
| job_test_env='Datagrok' | |
| grok_deps="$(jq -r '. | select( has("devDependencies") == true ).devDependencies | to_entries[] | .key | select(test("@datagrok/.*")?)' ${DIR}/package.json)" | |
| if [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "chem" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "simpkpd" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "dendrogram" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "cvmtests" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "samples" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "admetica" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"chem"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"simpkpd"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"cvmtests"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"dendrogram"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"admetica"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"samples"* ]]; then | |
| job_test_env+=',JKG' | |
| fi | |
| if [ -d "${DIR}/dockerfiles" ]; then | |
| job_test_env+=',Spawner' | |
| fi | |
| if [[ "${unpublished_deps}" == "" ]] && [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" != *"tests"* ]]; then | |
| job_test_env+=' latest version' | |
| else | |
| job_test_env+=' bleeding-edge version' | |
| fi | |
| fi | |
| runner='ubuntu-22.04' | |
| if [[ "${job_test_env}" == *"JKG"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${PACKAGE})" == "admetica" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"admetica"* ]]; then | |
| runner='ubuntu-latest-m' | |
| fi | |
| name="$(jq -r .name "${DIR}/package.json")" | |
| npm_version="$(curl --retry 3 -s "https://registry.npmjs.org/${name}/${current_version}" | jq -r '.? | select( has("version") == true ).version')" | |
| MATRIX_PUBLISH_JSON+=", \"unpublished_deps\": \"$unpublished_deps\"" | |
| if [[ "${{ github.event_name }}" != "pull_request" ]]; then | |
| if [[ $npm_version != ${current_version} ]]; then | |
| if [ "$(awk -F. '{print $1}' <<<$current_version)" -gt "0" ]; then | |
| if [[ $unpublished_deps == "" ]]; then | |
| if [[ '${{ github.ref }}' == 'refs/heads/master' ]]; then | |
| publish="publish" | |
| MATRIX_PUBLISH_JSON+=", \"publish\": \"publish\"" | |
| job_name+=' and publish to NPM' | |
| else | |
| echo "It is an action for branch other than 'master'. Publish will be skipped." | |
| echo "::notice title=${PACKAGE}::It is an action for branch other than 'master'. Publish will be skipped." | |
| fi | |
| else | |
| echo "Package $PACKAGE version ${current_version} has unpublished dependencies: $unpublished_deps. It is not going to be published" | |
| echo "::notice title=${PACKAGE}::Version ${current_version} has unpublished dependencies and is not going to be published" | |
| fi | |
| else | |
| MATRIX_PUBLISH_JSON+=", \"beta\": \"beta\"" | |
| echo "Package $PACKAGE version ${current_version} is under 1.0.0 and is not going to be published" | |
| echo "::notice title=${PACKAGE}::Version ${current_version} is under 1.0.0 and is not going to be published" | |
| fi | |
| else | |
| echo "Package $PACKAGE version ${current_version} already published" | |
| echo "::notice title=${PACKAGE}::Version ${current_version} is already published" | |
| fi | |
| else | |
| echo "It is an actions for PR. Publish will be skipped." | |
| echo "::notice title=${PACKAGE}::It is an actions for PR. Publish will be skipped." | |
| fi | |
| if [[ -d "${DIR}/dockerfiles" ]]; then | |
| build_docker=false | |
| if [[ $publish == "publish" ]] || [[ "${{ github.event.inputs.packages }}" != "" ]]; then | |
| build_docker=true | |
| else | |
| if [[ "${{ steps.changed-files.outputs.all_changed_files }}" == *"${DIR}/dockerfiles"* ]]; then | |
| build_docker=true | |
| fi | |
| fi | |
| MATRIX_PUBLISH_JSON+=", \"build_docker\": \"$build_docker\"" | |
| MATRIX_PUBLISH_JSON+=", \"docker\": \"$(find ${DIR}/dockerfiles -type f -name Dockerfile | tr '\n' ' ')\"" | |
| fi | |
| if [ -n "${job_test_env}" ]; then | |
| job_name+=": ${job_test_env}" | |
| fi | |
| MATRIX_PUBLISH_JSON+=", \"job_name\": \"${job_name}\"" | |
| MATRIX_PUBLISH_JSON+=", \"runner\": \"${runner}\"" | |
| MATRIX_PUBLISH_JSON+="}" | |
| fi | |
| done | |
| MATRIX_PUBLISH_JSON="${MATRIX_PUBLISH_JSON//\}\{/\}, \{}" | |
| MATRIX_PUBLISH_JSON+="]" | |
| PUBLISH_JSON="{\"include\": ${MATRIX_PUBLISH_JSON}}" | |
| CONTINUE_PUBLISH_JOB="no" | |
| if [[ "${MATRIX_PUBLISH_JSON}" != "[]" ]]; then | |
| CONTINUE_PUBLISH_JOB="yes" | |
| fi | |
| echo "publish=${CONTINUE_PUBLISH_JOB}" >> $GITHUB_OUTPUT | |
| echo "matrix_publish=${PUBLISH_JSON}" >> $GITHUB_OUTPUT | |
| - name: Output | |
| run: | | |
| echo -e "matrix_publish: ${{ steps.generate-matrix.outputs.matrix_publish }}" | |
| echo -e "publish: ${{ steps.generate-matrix.outputs.publish }}" | |
| publish: | |
| name: "${{ matrix.package }}: ${{ matrix.job_name }}" | |
| needs: | |
| - matrix | |
| - common-check | |
| if: needs.matrix.outputs.publish == 'yes' && needs.common-check.outputs.continue == 'true' | |
| runs-on: ${{ matrix.runner }} | |
| env: | |
| HOST: GitHubAction | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.matrix.outputs.matrix_publish) }} | |
| permissions: | |
| actions: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.WRITE_TOKEN || github.token }} | |
| sparse-checkout: | | |
| ./libraries | |
| ./packages | |
| ./js-api | |
| ./.github | |
| ./docker | |
| - name: Setup Node | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: '18.x' | |
| registry-url: 'https://registry.npmjs.org' | |
| scope: '@datagrok' | |
| cache: 'npm' | |
| cache-dependency-path: | | |
| packages/${{ matrix.package }}/package-lock.json | |
| - name: Upgrade npm | |
| run: npm install -g npm@x | |
| - name: npm version | |
| run: npm version | |
| - name: unpublished dependencies in package-lock.json | |
| id: package-lock | |
| if: ${{ matrix.unpublished_deps == '' }} | |
| run: grep -q '\.\./\.\./' package-lock.json && rm -f package-lock.json || true | |
| working-directory: packages/${{ matrix.package }} | |
| - name: npm install | |
| run: npm install | |
| id: install | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Get build info | |
| id: info | |
| run: | | |
| commit_sha=$(echo ${{ github.sha }} | cut -c1-8) | |
| echo "commit_sha=$commit_sha" >> $GITHUB_OUTPUT | |
| - name: Run datagrok stand | |
| id: datagrok-image | |
| if: ${{ matrix.test == 'test' }} | |
| run: | | |
| echo "Find grok dependencies packages" | |
| grok_deps="$(jq -r '. | select( has("devDependencies") == true ).devDependencies | to_entries[] | .key | select(test("@datagrok/.*")?)' packages/${{ matrix.package }}/package.json)" | |
| # if [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "chem" ]] || | |
| # [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"chem"* ]] || | |
| # [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "ketchersketcher" ]] || | |
| # [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"ketchersketcher"* ]]; then | |
| # if [[ "${{ matrix.unpublished_deps }}" == "" ]]; then | |
| # echo 'Use test stand for tests' | |
| # apiUrl='https://test.datagrok.ai/api' | |
| # alias=test | |
| # else | |
| # echo 'Use dev stand for tests' | |
| # apiUrl='https://dev.datagrok.ai/api' | |
| # alias=dev | |
| # fi | |
| # else | |
| profiles='--profile datagrok --profile db' | |
| echo "Check if Grok Connect is required for the package" | |
| if [ -d "packages/${{ matrix.package }}/connections" ] || [[ -n $(find packages/${{ matrix.package }}/node_modules/@datagrok -type d -name connections) ]] || \ | |
| [ -d "packages/${{ matrix.package }}/queries" ] || [[ -n $(find packages/${{ matrix.package }}/node_modules/@datagrok -type d -name queries) ]]; then | |
| profiles+=' --profile grok_connect' | |
| fi | |
| echo "Check if CVM is required for the package" | |
| if [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "chem" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "simpkpd" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "dendrogram" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "cvmtests" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" == "samples" ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"chem"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"simpkpd"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"cvmtests"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"dendrogram"* ]] || \ | |
| [[ "$(tr '[:upper:]' '[:lower:]' <<<${grok_deps})" == *"samples"* ]]; then | |
| echo "Add Scripting as dependency for package ${{ matrix.package }}" | |
| profiles+=' --profile scripting' | |
| fi | |
| echo "Check if Grok Spawner is required for the package" | |
| if [ -d "packages/${{ matrix.package }}/dockerfiles" ]; then | |
| profiles+=' --profile grok_spawner' | |
| fi | |
| echo "Run datagrok stand with profiles ${profiles}" | |
| # docker system prune -af --volumes | |
| if [[ "${{ matrix.unpublished_deps }}" == "" ]] && [[ "$(tr '[:upper:]' '[:lower:]' <<<${{ matrix.package }})" != *"tests"* ]]; then | |
| DATAGROK_VERSION='latest' | |
| else | |
| DATAGROK_VERSION='bleeding-edge' | |
| export GROK_SPAWNER_VERSION='bleeding-edge' | |
| export GROK_JUPYTER_KERNEL_GATEWAY_VERSION='bleeding-edge' | |
| fi | |
| export DATAGROK_VERSION | |
| # Skip initial setup in CI | |
| sed -i '/"dbServer": "database"/a\ \ \ \ \ \ \ \ \ \ "initialSetupCompleted": true,' docker/localhost.docker-compose.yaml | |
| docker compose -p datagrok -f "docker/localhost.docker-compose.yaml" ${profiles} up -d | |
| echo "Set docker_sha" | |
| docker_sha=$(docker images --quiet "datagrok/datagrok:$DATAGROK_VERSION") | |
| echo "docker_sha=$docker_sha" >> $GITHUB_OUTPUT | |
| echo "Notify about version used for tests" | |
| echo "::notice title=${{ matrix.package }}::datagrok/datagrok:$DATAGROK_VERSION SHA=$docker_sha docker version was used for tests" | |
| df -h | |
| apiUrl='http://127.0.0.1:8080/api' | |
| alias=${HOST} | |
| # fi | |
| echo "apiUrl=$apiUrl" >> $GITHUB_OUTPUT | |
| echo "alias=$alias" >> $GITHUB_OUTPUT | |
| - id: datagrok-tools | |
| run: npm install -g datagrok-tools@latest | |
| - if: ${{ matrix.unpublished_deps != '' }} | |
| run: grok link | |
| working-directory: packages/${{ matrix.package }} | |
| - name: webpack cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: packages/${{ matrix.package }}/node_modules/.cache/webpack/ | |
| key: ${{ matrix.package }}-${{ github.ref_name }}-webpack-build | |
| restore-keys: | | |
| ${{ matrix.package }}-master-webpack-build | |
| - name: Remove GPU from docker configuration | |
| if: matrix.docker != '' && steps.datagrok-image.outcome == 'success' | |
| run: | | |
| for dockerfile in $(echo -e ${{ matrix.docker }}); do | |
| docker_config_file="$(dirname $dockerfile)/container.json" | |
| if [ -f "${docker_config_file}" ]; then | |
| jq 'del(.gpu)' ${docker_config_file} > temp.json && mv temp.json ${docker_config_file} | |
| fi | |
| done | |
| - name: Build package | |
| if: ${{ matrix.build == 'build' }} | |
| id: build | |
| run: | | |
| if [[ $(jq -r '. | select( has("scripts") == true ).scripts | select( has("build") == true ).build' "package.json") == "webpack" ]]; then | |
| npm run build -- --mode=production | |
| else | |
| npm run build | |
| fi | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Wait for Datagrok to become available | |
| if: ${{ matrix.test == 'test' }} | |
| timeout-minutes: 5 | |
| run: | | |
| until .github/scripts/check-output.sh "curl -s ${{ steps.datagrok-image.outputs.apiUrl }}/info/server" '"Http Server"' | |
| do | |
| sleep 1 | |
| if [[ "${{ steps.datagrok-image.outputs.apiUrl }}" == *"127.0.0.1"* ]]; then | |
| docker compose -p datagrok logs --no-color --timestamps datagrok | |
| fi | |
| echo -e "\nRetrying..." | |
| done | |
| curl -s ${{ steps.datagrok-image.outputs.apiUrl }}/info/server | |
| curl -s ${{ steps.datagrok-image.outputs.apiUrl }}/admin/health | |
| token=$(curl -s -X POST ${{ steps.datagrok-image.outputs.apiUrl }}/users/login/dev/admin | jq -r .token) | |
| curl -s -H "Authorization: $token" -H "Content-Type": "application/json" '${{ steps.datagrok-image.outputs.apiUrl }}/admin/plugins/admin/settings' -X POST -d '{"#type":"AdminPluginSettings", "agreementDate":null}' | |
| - name: Create configuration for grok command-line tool | |
| if: ${{ matrix.test == 'test' }} | |
| id: grok-config | |
| env: | |
| DEV_TEST_DEV_KEY: ${{ secrets.DEV_TEST_DEV_KEY }} | |
| TEST_TEST_DEV_KEY: ${{ secrets.TEST_TEST_DEV_KEY }} | |
| run: | | |
| if [[ "${{ steps.datagrok-image.outputs.alias }}" == "test" ]]; then | |
| key="$TEST_TEST_DEV_KEY" | |
| elif [[ "${{ steps.datagrok-image.outputs.alias }}" == "dev" ]]; then | |
| key="$DEV_TEST_DEV_KEY" | |
| else | |
| key='admin' | |
| fi | |
| grok config add --default --alias ${{ steps.datagrok-image.outputs.alias }} --server '${{ steps.datagrok-image.outputs.apiUrl }}' --key "$key" | |
| - name: Install Grok Dependencies before package publish to Datagrok | |
| if: ${{ matrix.test == 'test' }} | |
| run: | | |
| grok_deps="$(jq -r '. | select( has("devDependencies") == true ).devDependencies | to_entries[] | .key | select(test("@datagrok/.*")?)' package.json)" | |
| if [ -n "$grok_deps" ]; then | |
| for dep in $grok_deps; do | |
| current_dir=$(pwd) | |
| cd node_modules/$dep | |
| count=0 | |
| retries=5 | |
| echo "Publishing $dep to ${{ steps.datagrok-image.outputs.alias }}..." | |
| until grok publish ${{ steps.datagrok-image.outputs.alias }}; do | |
| exit=$? | |
| wait=$((2 ** count)) | |
| count=$((count + 1)) | |
| if [ $count -lt "$retries" ]; then | |
| echo "Retry $count/$retries exited $exit, retrying 'grok publish ${{ steps.datagrok-image.outputs.alias }}' for $dep in $wait seconds..." | |
| sleep $wait | |
| else | |
| echo "Retry $count/$retries exited $exit, no more retries left for 'grok publish ${{ steps.datagrok-image.outputs.alias }}' for $dep." | |
| exit $exit | |
| fi | |
| done | |
| cd $current_dir | |
| done | |
| fi | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Publish package to Datagrok | |
| if: ${{ matrix.test == 'test' }} | |
| run: | | |
| count=0 | |
| retries=5 | |
| until grok publish ${{ steps.datagrok-image.outputs.alias }}; do | |
| exit=$? | |
| if [[ "${{ steps.datagrok-image.outputs.apiUrl }}" == *"127.0.0.1"* ]]; then | |
| docker compose -p datagrok logs --no-color --timestamps datagrok | |
| fi | |
| wait=$((2 ** count)) | |
| count=$((count + 1)) | |
| if [ "$count" -lt "$retries" ]; then | |
| echo "Retry $count/$retries exited $exit, retrying 'grok publish ${{ steps.datagrok-image.outputs.alias }}' in $wait seconds..." | |
| sleep $wait | |
| else | |
| echo "Retry $count/$retries exited $exit, no more retries left for 'grok publish ${{ steps.datagrok-image.outputs.alias }}'." | |
| exit $exit | |
| fi | |
| done | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Set required credentials | |
| if: ${{ matrix.test == 'test' }} | |
| env: | |
| CHEMSPACE_APIKEY: ${{ secrets.CHEMSPACE_APIKEY }} | |
| run: | | |
| if [[ "${{ steps.datagrok-image.outputs.apiUrl }}" == *"127.0.0.1"* ]]; then | |
| if [[ "${{ matrix.package }}" == "Chemspace" ]]; then | |
| token=$(curl -s -X POST ${{ steps.datagrok-image.outputs.apiUrl }}/users/login/dev/admin | jq -r .token) | |
| curl -s -H "Authorization: $token" -H "Content-Type": "application/json" '${{ steps.datagrok-image.outputs.apiUrl }}/credentials/for/Chemspace.Chemspace' -X POST -d "{\"apiKey\": \"$CHEMSPACE_APIKEY\"}" | |
| fi | |
| fi | |
| - name: Wait for published docker to become available | |
| id: docker-wait | |
| if: matrix.docker != '' && steps.datagrok-image.outcome == 'success' | |
| env: | |
| DEV_TEST_DEV_KEY: ${{ secrets.DEV_TEST_DEV_KEY }} | |
| TEST_TEST_DEV_KEY: ${{ secrets.TEST_TEST_DEV_KEY }} | |
| timeout-minutes: 10 | |
| run: | | |
| if [[ "${{ steps.datagrok-image.outputs.alias }}" == "test" ]]; then | |
| key="$TEST_TEST_DEV_KEY" | |
| elif [[ "${{ steps.datagrok-image.outputs.alias }}" == "dev" ]]; then | |
| key="$DEV_TEST_DEV_KEY" | |
| else | |
| key='admin' | |
| fi | |
| token=$(curl -s -X POST ${{ steps.datagrok-image.outputs.apiUrl }}/users/login/dev/$key | jq -r .token) | |
| until .github/scripts/check-output.sh "curl -s -H 'Authorization: $token' '${{ steps.datagrok-image.outputs.apiUrl }}/docker/containers'" '${{ matrix.package }}' | |
| do | |
| sleep 1 | |
| echo -e "\nContainer for ${{ matrix.package }} did not start yet..." | |
| echo -e "\nRetrying '/api/docker/containers'..." | |
| done | |
| if [[ "${{ steps.datagrok-image.outputs.apiUrl }}" == *"127.0.0.1"* ]]; then | |
| until .github/scripts/check-output.sh "docker ps" '${{ matrix.package }}' | |
| do | |
| sleep 1 | |
| echo -e "\nContainer for ${{ matrix.package }} did not start yet..." | |
| echo -e "\nRetrying 'docker ps'..." | |
| done | |
| fi | |
| - name: Test Package | |
| if: ${{ matrix.test == 'test' }} | |
| continue-on-error: ${{ contains(matrix.package, 'Tests') || matrix.package == 'Chemspace' }} | |
| timeout-minutes: 30 | |
| id: test-package | |
| run: npm run test -- --skip-build --skip-publish --record --csv --host ${{ steps.datagrok-image.outputs.alias }} | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Upload Artifact | |
| if: always() && steps.test-package.outcome != 'skipped' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.package }}.test-results | |
| path: | | |
| packages/${{ matrix.package }}/test-record.mp4 | |
| packages/${{ matrix.package }}/test-report.csv | |
| packages/${{ matrix.package }}/test-console-output.log | |
| retention-days: 14 | |
| if-no-files-found: warn | |
| - name: Create error notification | |
| if: failure() && (steps.test-package.outcome == 'failure' || steps.docker-wait.outcome == 'failure') | |
| run: | | |
| if [[ "${{ steps.datagrok-image.outputs.apiUrl }}" == *"127.0.0.1"* ]]; then | |
| docker compose -p datagrok logs --no-color --timestamps | |
| else | |
| echo 'Check dev logs' | |
| fi | |
| echo "::error title=${{ matrix.package }}: failed tests::Check job output for details" | |
| echo "status=error" >> $GITHUB_OUTPUT | |
| - name: Get docker image version | |
| if: matrix.build_docker == 'true' | |
| id: docker_name_ver | |
| working-directory: packages/${{ matrix.package }} | |
| run: | | |
| image_ver=$(jq -r .version package.json) | |
| if [[ "${{ matrix.publish }}" != "publish" ]]; then | |
| image_ver+="-${{ steps.info.outputs.commit_sha }}" | |
| fi | |
| echo "image_ver=$image_ver" >> $GITHUB_OUTPUT | |
| echo "package_name=$(jq -r .name package.json | sed -e 's,@datagrok/,,g')" >> $GITHUB_OUTPUT | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| if: steps.docker_name_ver.outcome == 'success' | |
| - name: Build package Docker image | |
| if: steps.docker_name_ver.outcome == 'success' | |
| id: build-docker | |
| run: | | |
| for dockerfile in $(echo -e ${{ matrix.docker }}); do | |
| image_name=${{ steps.docker_name_ver.outputs.package_name }} | |
| if [[ $(dirname $dockerfile) != *"dockerfiles" ]]; then | |
| image_name+="-$(dirname $dockerfile | awk -F/ '{print $NF}')" | |
| fi | |
| cache_args="--cache-from type=registry,ref=datagrok/${image_name}:cache" | |
| if [ '${{ github.ref }}' == 'refs/heads/master' ]; then | |
| cache_args+=" --cache-to type=registry,ref=datagrok/${image_name}:cache" | |
| fi | |
| docker buildx create --use | |
| docker buildx build $(dirname $dockerfile) --load \ | |
| --tag datagrok/${image_name}:${{ steps.docker_name_ver.outputs.image_ver }} \ | |
| $cache_args | |
| images+=" datagrok/${image_name}:${{ steps.docker_name_ver.outputs.image_ver }}" | |
| done | |
| echo "images=$images" >> $GITHUB_OUTPUT | |
| - name: General checks | |
| run: | | |
| if [[ "$(jq '.name' package.json | sed -E 's/(^"|"$)//g')" != "@datagrok/"* ]]; then | |
| echo "::error title=${{ matrix.package }}: failed properties check::Package should be in '@datagrok' scope. Change package name to '@datagrok/<name>' in ${{ matrix.package }}/package.json" | |
| exit 1 | |
| fi | |
| if [ ! -z "$(jq '. | select( has("beta") == true ).beta' package.json)" ]; then | |
| echo "::error title=${{ matrix.package }}: failed properties check::Remove beta property in ${{ matrix.package }}/package.json. It is deprecated." | |
| exit 1 | |
| fi | |
| id: gen_checks | |
| working-directory: packages/${{ matrix.package }} | |
| - run: grok check | |
| if: ${{ !contains(matrix.package, 'Tests') && !contains(matrix.package, 'Meta') && matrix.beta != 'true' }} | |
| id: check | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Publish to npm | |
| run: npm publish --access public | |
| id: publish | |
| working-directory: packages/${{ matrix.package }} | |
| env: | |
| NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }} | |
| if: matrix.publish == 'publish' && (steps.build.outcome == 'success' || steps.build.outcome == 'skipped') && steps.gen_checks.outcome == 'success' && (steps.check.outcome == 'success' || steps.check.outcome == 'skipped') && steps.install.outcome == 'success' && (steps.test-package.outcome == 'success' || steps.test-package.outcome == 'skipped' || (contains(matrix.package, 'Tests') || matrix.package == 'Chemspace')) | |
| - name: Get actors slack | |
| id: actor | |
| uses: ./.github/actions/slack-user-action | |
| with: | |
| slack-token: ${{ secrets.SLACKBOT_TOKEN }} | |
| email-mapping: ${{ secrets.EMAIL_SLACK_ID }} | |
| - name: Get owner email | |
| run: echo "owner=$(jq -r .author.email package.json)" >> $GITHUB_OUTPUT | |
| id: owner-email | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Get owners slack | |
| id: owner | |
| uses: ./.github/actions/slack-user-action | |
| with: | |
| slack-token: ${{ secrets.SLACKBOT_TOKEN }} | |
| emails: ${{ steps.owner-email.outputs.owner }} | |
| - name: Get QA slack | |
| id: qa | |
| uses: ./.github/actions/slack-user-action | |
| if: ${{ (matrix.package == 'Tutorials' || matrix.package == 'Chem' || matrix.package == 'DiffStidio' || matrix.package == 'PowerPack') }} | |
| with: | |
| slack-token: ${{ secrets.SLACKBOT_TOKEN }} | |
| emails: "[email protected]" | |
| - name: Prepare Slack Message | |
| id: slack-prepare | |
| if: ${{ steps.publish.outcome == 'success' && !contains(matrix.package, 'Meta') }} | |
| shell: bash | |
| run: | | |
| mentions=$(echo -e "${{ steps.actor.outputs.user-ids }}\n${{ steps.owner.outputs.user-ids }}\n${{ steps.qa.outputs.user-ids }}" | sort -u) | |
| header="Package *${{ matrix.package }}* version *${{ matrix.version }}* published to <https://www.npmjs.com/package/$(jq -r .name "packages/${{ matrix.package }}/package.json")/v/${{ matrix.version }}|NPM>\n$(for value in $mentions; do echo -n "<@$value> "; done) FYI" | |
| echo "SLACK_MESSAGE_HEADER=$header" >> $GITHUB_ENV | |
| - name: Send to Slack | |
| id: slack | |
| if: steps.slack-prepare.outcome == 'success' | |
| uses: ./.github/actions/slack-post-action | |
| with: | |
| channel: '#build' | |
| slack-token: ${{ secrets.SLACKBOT_TOKEN }} | |
| message: ${{ env.SLACK_MESSAGE_HEADER }} | |
| - name: Save package Docker image to tar archive | |
| if: steps.build-docker.outcome == 'success' && (steps.publish.outcome == 'failure' || steps.publish.outcome == 'skipped') | |
| id: save-docker | |
| run: | | |
| docker save -o /tmp/${{ matrix.package }}.docker.tar ${{ steps.build-docker.outputs.images }} | |
| - uses: actions/upload-artifact@v4 | |
| if: steps.save-docker.outcome == 'success' | |
| with: | |
| path: /tmp/${{ matrix.package }}.docker.tar | |
| name: ${{ matrix.package }}.docker.tar | |
| retention-days: 14 | |
| if-no-files-found: warn | |
| - name: Publish package Docker image | |
| if: steps.publish.outcome == 'success' && steps.build-docker.outcome == 'success' | |
| id: publish-docker | |
| run: | | |
| for image in $(echo -e ${{ steps.build-docker.outputs.images }}); do | |
| docker push $image | |
| done | |
| - name: Commit package-lock.json | |
| id: git | |
| continue-on-error: true | |
| if: steps.publish.outcome == 'success' || steps.package-lock.outcome == 'success' | |
| run: | | |
| git config --global user.name 'github-actions[bot]' | |
| git config --global user.email 'github-actions[bot]@users.noreply.github.com' | |
| git pull | |
| continue=false | |
| if [ -n "$(git status -s packages/${{ matrix.package }}/package-lock.json)" ]; then | |
| git add packages/${{ matrix.package }}/package-lock.json | |
| skip_ci="" | |
| if [ ${{ github.ref }} == 'refs/heads/master' ]; then | |
| skip_ci="[skip ci]" | |
| fi | |
| git commit -m "GitHub Actions: Update packages/${{ matrix.package }}/package-lock.json $skip_ci | |
| Workflow ${{ github.workflow }} ${{ github.run_number }} | |
| https://github.com/datagrok-ai/public/actions/runs/${{ github.run_id }}" | |
| continue=true | |
| fi | |
| if [[ "${continue}" == "true" ]]; then | |
| count=0 | |
| retries=10 | |
| until git push; do | |
| exit=$? | |
| wait=$((2 ** count)) | |
| count=$((count + 1)) | |
| if [ $count -lt "$retries" ]; then | |
| echo "Retry $count/$retries exited $exit, retrying 'git push' in $wait seconds..." | |
| sleep $wait | |
| git pull --rebase | |
| else | |
| echo "Retry $count/$retries exited $exit, no more retries left for 'git push'." | |
| exit $exit | |
| fi | |
| done | |
| fi | |
| - name: Trigger help update | |
| continue-on-error: true | |
| if: steps.publish.outcome == 'success' | |
| run: gh workflow run docusaurus.yaml --ref ${{ github.ref }} | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| # - name: Slack Notification | |
| # uses: act10ns/[email protected] | |
| # with: | |
| # status: ${{ steps.publish.outcome }} | |
| # steps: ${{ toJson(steps) }} | |
| # matrix: ${{ toJson(matrix) }} | |
| # config: ".github/config/slack.yml" | |
| # webhook-url: ${{ secrets.SLACK_WEBHOOK_REPORT }} | |
| # - name: Slack Failed-Cancelled Notification | |
| # if: failure() || cancelled() | |
| # uses: act10ns/[email protected] | |
| # with: | |
| # status: ${{ job.status }} | |
| # steps: ${{ toJson(steps) }} | |
| # config: ".github/config/slack.yml" | |
| # webhook-url: ${{ secrets.SLACK_WEBHOOK_REPORT }} |