diff --git a/.github/.trivyignore b/.github/.trivyignore new file mode 100644 index 000000000..e69de29bb diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 000000000..e2e02646a --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,2 @@ +# Code owners for the .github directory +/.github/ @PilotDataPlatform/indoc-devops diff --git a/.github/workflows/build-and-publish-admin-server.yml b/.github/workflows/build-and-publish-admin-server.yml index ba4707523..7ab5ce112 100644 --- a/.github/workflows/build-and-publish-admin-server.yml +++ b/.github/workflows/build-and-publish-admin-server.yml @@ -14,18 +14,25 @@ jobs: - name: Extract Branch Name id: extract_branch shell: bash - run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})" + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT get-version: runs-on: ubuntu-20.04 outputs: app_version: ${{steps.get-version.outputs.app_version}} steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Get Version id: get-version shell: bash - run: echo "app_version=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json`" >> $GITHUB_OUTPUT + run: | + BRANCH=${GITHUB_REF#refs/heads/} + BASE_VERSION=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json` + if [ $BRANCH == "patched-version" ]; then + echo "app_version=$BASE_VERSION-`git rev-parse --short HEAD`" >> $GITHUB_OUTPUT + else + echo "app_version=$BASE_VERSION" >> $GITHUB_OUTPUT + fi build-and-push-docker-image: needs: [extract-branch-name, get-version] @@ -34,12 +41,12 @@ jobs: runs-on: ubuntu-20.04 steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Set up Docker Buildx id: buildx - uses: docker/setup-buildx-action@v1 + uses: docker/setup-buildx-action@v2 - name: Login to Github Packages - uses: docker/login-action@v1 + uses: docker/login-action@v2 with: registry: pilotdataplatform.azurecr.io username: ${{ secrets.ACR_CLIENT }} @@ -54,12 +61,11 @@ jobs: # generate Docker tags based on the following events/attributes sep-tags: ',' tags: | - type=sha,enable=true,prefix=arranger-admin-server-,suffix=,format=short - type=raw,prefix=arranger-admin-server-,suffix=,value=${{needs.get-version.outputs.app_version}}, enable=${{needs.extract-branch-name.outputs.branch=='patched-version'}} + type=raw,prefix=arranger-admin-server-,suffix=,value=${{needs.get-version.outputs.app_version}} # - name: Image digest # run: echo ${{ steps.meta.outputs.tags }} - name: Build image and push to GitHub Container Registry - uses: docker/build-push-action@v2 + uses: docker/build-push-action@v4 with: # relative path to the place where source code with Dockerfile is located context: . @@ -71,7 +77,7 @@ jobs: target: arranger-admin-server Trigger: - needs: [build-and-push-docker-image, extract-branch-name] + needs: [build-and-push-docker-image, extract-branch-name, get-version] #if: ${{ (github.event.workflow_run.conclusion == 'success' && needs.extract-branch-name.outputs.branch == 'patched-version') || (needs.extract-branch-name.outputs.branch == 'main') }} if: ${{ (needs.extract-branch-name.outputs.branch == 'patched-version') || (needs.extract-branch-name.outputs.branch == 'main') }} name: Trigger jenkins job @@ -99,7 +105,7 @@ jobs: target_release=arranger-admin-server env=${ENV} echo "The CI external URL is ${CI_EXTERNAL_URL}" - curl --silent -i -X POST -m 60 -L -o output.txt --user jenkins:${CI_API_TOKEN} ${CI_EXTERNAL_URL}/job/Infra/job/UpdateAppVersion/buildWithParameters --data TF_TARGET_ENV=$env --data TARGET_RELEASE=$target_release --data NEW_APP_VERSION="${{ env.SHA }}" + curl --silent -i -X POST -m 60 -L -o output.txt --user jenkins:${CI_API_TOKEN} ${CI_EXTERNAL_URL}/job/Infra/job/UpdateAppVersion/buildWithParameters --data TF_TARGET_ENV=$env --data TARGET_RELEASE=$target_release --data NEW_APP_VERSION="${{needs.get-version.outputs.app_version}}" location=$(cat output.txt | grep location | cut -d " " -f2 | sed 's/\r//') link=${location}api/json && echo $link && echo -n "location_link=$link" >> $GITHUB_ENV - name: getting the json diff --git a/.github/workflows/build-and-publish-admin-ui.yml b/.github/workflows/build-and-publish-admin-ui.yml index cc07ee1a7..96c00be76 100644 --- a/.github/workflows/build-and-publish-admin-ui.yml +++ b/.github/workflows/build-and-publish-admin-ui.yml @@ -14,18 +14,25 @@ jobs: - name: Extract Branch Name id: extract_branch shell: bash - run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})" + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT get-version: runs-on: ubuntu-20.04 outputs: app_version: ${{steps.get-version.outputs.app_version}} steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Get Version id: get-version shell: bash - run: echo "app_version=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json`" >> $GITHUB_OUTPUT + run: | + BRANCH=${GITHUB_REF#refs/heads/} + BASE_VERSION=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json` + if [ $BRANCH == "patched-version" ]; then + echo "app_version=$BASE_VERSION-`git rev-parse --short HEAD`" >> $GITHUB_OUTPUT + else + echo "app_version=$BASE_VERSION" >> $GITHUB_OUTPUT + fi build-and-push-docker-image: needs: [extract-branch-name, get-version] @@ -34,12 +41,12 @@ jobs: runs-on: ubuntu-20.04 steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Set up Docker Buildx id: buildx - uses: docker/setup-buildx-action@v1 + uses: docker/setup-buildx-action@v2 - name: Login to Github Packages - uses: docker/login-action@v1 + uses: docker/login-action@v2 with: registry: pilotdataplatform.azurecr.io username: ${{ secrets.ACR_CLIENT }} @@ -54,12 +61,11 @@ jobs: # generate Docker tags based on the following events/attributes sep-tags: ',' tags: | - type=sha,enable=true,prefix=arranger-admin-ui-,suffix=,format=short - type=raw,prefix=arranger-admin-ui-,suffix=,value=${{needs.get-version.outputs.app_version}}, enable=${{needs.extract-branch-name.outputs.branch=='patched-version'}} + type=raw,prefix=arranger-admin-ui-,suffix=,value=${{needs.get-version.outputs.app_version}} # - name: Image digest # run: echo ${{ steps.meta.outputs.tags }} - name: Build image and push to GitHub Container Registry - uses: docker/build-push-action@v2 + uses: docker/build-push-action@v4 with: # relative path to the place where source code with Dockerfile is located context: . @@ -71,7 +77,7 @@ jobs: target: arranger-admin-ui Trigger: - needs: [build-and-push-docker-image, extract-branch-name] + needs: [build-and-push-docker-image, extract-branch-name, get-version] #if: ${{ (github.event.workflow_run.conclusion == 'success' && needs.extract-branch-name.outputs.branch == 'patched-version') || (needs.extract-branch-name.outputs.branch == 'main') }} if: ${{ (needs.extract-branch-name.outputs.branch == 'patched-version') || (needs.extract-branch-name.outputs.branch == 'main') }} name: Trigger jenkins job @@ -99,7 +105,7 @@ jobs: target_release=arranger-admin-ui env=${ENV} echo "The CI external URL is ${CI_EXTERNAL_URL}" - curl --silent -i -X POST -m 60 -L -o output.txt --user jenkins:${CI_API_TOKEN} ${CI_EXTERNAL_URL}/job/Infra/job/UpdateAppVersion/buildWithParameters --data TF_TARGET_ENV=$env --data TARGET_RELEASE=$target_release --data NEW_APP_VERSION="${{ env.SHA }}" + curl --silent -i -X POST -m 60 -L -o output.txt --user jenkins:${CI_API_TOKEN} ${CI_EXTERNAL_URL}/job/Infra/job/UpdateAppVersion/buildWithParameters --data TF_TARGET_ENV=$env --data TARGET_RELEASE=$target_release --data NEW_APP_VERSION="${{needs.get-version.outputs.app_version}}" location=$(cat output.txt | grep location | cut -d " " -f2 | sed 's/\r//') link=${location}api/json && echo $link && echo -n "location_link=$link" >> $GITHUB_ENV - name: getting the json diff --git a/.github/workflows/build-and-publish-server-filter.yml b/.github/workflows/build-and-publish-server-filter.yml index 1602b72b6..b0dec9212 100644 --- a/.github/workflows/build-and-publish-server-filter.yml +++ b/.github/workflows/build-and-publish-server-filter.yml @@ -14,18 +14,25 @@ jobs: - name: Extract Branch Name id: extract_branch shell: bash - run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})" + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT get-version: runs-on: ubuntu-20.04 outputs: app_version: ${{steps.get-version.outputs.app_version}} steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Get Version id: get-version shell: bash - run: echo "app_version=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json`" >> $GITHUB_OUTPUT + run: | + BRANCH=${GITHUB_REF#refs/heads/} + BASE_VERSION=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json` + if [ $BRANCH == "patched-version" ]; then + echo "app_version=$BASE_VERSION-`git rev-parse --short HEAD`" >> $GITHUB_OUTPUT + else + echo "app_version=$BASE_VERSION" >> $GITHUB_OUTPUT + fi build-and-push-docker-image: needs: [extract-branch-name, get-version] @@ -34,12 +41,12 @@ jobs: runs-on: ubuntu-20.04 steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Set up Docker Buildx id: buildx - uses: docker/setup-buildx-action@v1 + uses: docker/setup-buildx-action@v2 - name: Login to Github Packages - uses: docker/login-action@v1 + uses: docker/login-action@v2 with: registry: pilotdataplatform.azurecr.io username: ${{ secrets.ACR_CLIENT }} @@ -54,12 +61,11 @@ jobs: # generate Docker tags based on the following events/attributes sep-tags: ',' tags: | - type=sha,enable=true,prefix=arranger-server-filter-,suffix=,format=short - type=raw,prefix=arranger-server-filter-,suffix=,value=${{needs.get-version.outputs.app_version}}, enable=${{needs.extract-branch-name.outputs.branch=='patched-version'}} + type=raw,prefix=arranger-server-filter-,suffix=,value=${{needs.get-version.outputs.app_version}} # - name: Image digest # run: echo ${{ steps.meta.outputs.tags }} - name: Build image and push to GitHub Container Registry - uses: docker/build-push-action@v2 + uses: docker/build-push-action@v4 with: # relative path to the place where source code with Dockerfile is located context: . @@ -71,7 +77,7 @@ jobs: target: arranger-server Trigger: - needs: [build-and-push-docker-image, extract-branch-name] + needs: [build-and-push-docker-image, extract-branch-name, get-version] #if: ${{ (github.event.workflow_run.conclusion == 'success' && needs.extract-branch-name.outputs.branch == 'patched-version') || (needs.extract-branch-name.outputs.branch == 'main') }} if: ${{ (needs.extract-branch-name.outputs.branch == 'patched-version') || (needs.extract-branch-name.outputs.branch == 'main') }} name: Trigger jenkins job @@ -99,7 +105,7 @@ jobs: target_release=arranger-server-filter env=${ENV} echo "The CI external URL is ${CI_EXTERNAL_URL}" - curl --silent -i -X POST -m 60 -L -o output.txt --user jenkins:${CI_API_TOKEN} ${CI_EXTERNAL_URL}/job/Infra/job/UpdateAppVersion/buildWithParameters --data TF_TARGET_ENV=$env --data TARGET_RELEASE=$target_release --data NEW_APP_VERSION="${{ env.SHA }}" + curl --silent -i -X POST -m 60 -L -o output.txt --user jenkins:${CI_API_TOKEN} ${CI_EXTERNAL_URL}/job/Infra/job/UpdateAppVersion/buildWithParameters --data TF_TARGET_ENV=$env --data TARGET_RELEASE=$target_release --data NEW_APP_VERSION="${{needs.get-version.outputs.app_version}}" location=$(cat output.txt | grep location | cut -d " " -f2 | sed 's/\r//') link=${location}api/json && echo $link && echo -n "location_link=$link" >> $GITHUB_ENV - name: getting the json diff --git a/.github/workflows/pilot-pipeline-admin-server.yml b/.github/workflows/pilot-pipeline-admin-server.yml new file mode 100644 index 000000000..29fbb7c2f --- /dev/null +++ b/.github/workflows/pilot-pipeline-admin-server.yml @@ -0,0 +1,165 @@ +name: CI pipeline admin server + +on: + push: + branches: + - patched-version + paths: + - 'modules/admin/**' + pull_request: + branches: + - patched-version + paths: + - 'modules/admin/**' + +jobs: + + extract-branch-name: + runs-on: ubuntu-20.04 + outputs: + branch: ${{steps.extract_branch.outputs.branch}} + steps: + - name: Extract Branch Name + id: extract_branch + shell: bash + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT + get-version: + runs-on: ubuntu-20.04 + outputs: + app_version: ${{steps.get-version.outputs.app_version}} + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Get Version + id: get-version + shell: bash + run: | + BRANCH=${GITHUB_REF#refs/heads/} + BASE_VERSION=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json` + echo "app_version=$BASE_VERSION" >> $GITHUB_OUTPUT + + build-and-push-docker-image: + needs: [extract-branch-name, get-version] + if: ${{ needs.extract-branch-name.outputs.branch == 'patched-version'}} + name: Build admin server Docker image and push to repositories + runs-on: ubuntu-20.04 + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Set up Docker Buildx + id: buildx + uses: docker/setup-buildx-action@v2 + - name: Login to Github Packages + uses: docker/login-action@v2 + with: + registry: pilotdataplatform.azurecr.io + username: ${{ secrets.ACR_CLIENT }} + password: ${{ secrets.ACR_SECRET }} + - name: Docker metadata + id: meta + uses: docker/metadata-action@v4 + with: + # list of Docker images to use as base name for tags + images: | + pilotdataplatform.azurecr.io/arranger/arranger-admin-server + # generate Docker tags based on the following events/attributes + sep-tags: ',' + tags: | + type=raw,prefix=arranger-admin-server-,suffix=,value=${{needs.get-version.outputs.app_version}} +# - name: Image digest +# run: echo ${{ steps.meta.outputs.tags }} + - name: Image digest + run: echo ${{ steps.meta.outputs.tags }} + - name: Check if Docker image tags exist + shell: bash + run: | + image_tag=$(echo "${{ steps.meta.outputs.tags }}") + if docker manifest inspect $image_tag >/dev/null; then + echo "Docker image with tag already exists. Please update the version." + exit 1 + else + echo "Image tags do not exist, proceeding..." + fi + - name: Check Trivy ignore exceptions + # Check if the Trivy ignorefile has exceptions and the exceptions + # date is defined and less than 90 days. + # + # The ignorefile has the following format: + # CVE-YYYY-XXXXX exp:YYYY-MM-DD + # + # Error out if the format is not respected. + # Given a CVE-YYYY-XXXXX defined in the ignorefile, + # if no exception date is defined, we will error out. + # if the exception date is more than 90 days, we will error out too. + # + # Successfully parsed lines will be ignored, + # if the exception date exist and is less than 90 days, the step will exit with 0. + uses: PilotDataPlatform/shared-ci-tools/.github/actions/trivyignore-checking@main + - name: Build image and push to GitHub Container Registry + uses: docker/build-push-action@v4 + with: + # relative path to the place where source code with Dockerfile is located + context: . + # Note: tags has to be all lower-case + tags: ${{ steps.meta.outputs.tags }} + # build on feature branches, push only on main branch + push: ${{ github.event_name != 'pull_request' }} + # Sets the target stage to build + target: arranger-admin-server + load: true + + - name: Run Trivy vulnerability scanner + uses: aquasecurity/trivy-action@0.20.0 + with: + image-ref: '${{ steps.meta.outputs.tags }}' + format: 'table' + severity: 'CRITICAL' + exit-code: '1' + hide-progress: true + trivyignores: .github/.trivyignore + output: scan-results.txt + env: + TRIVY_IGNORE_STATUS: 'will_not_fix' + + - name: Publish Trivy Scan Results to Summary + if: always() + run: | + if [[ -s scan-results.txt ]]; then + { + echo "### Trivy Scan Results" + echo "
Click to expand" + echo "" + echo '```arranger-admin-server' + cat scan-results.txt + echo '```' + echo "
" + } >> $GITHUB_STEP_SUMMARY + fi + + trigger_pilot_dev_deployment: + needs: [build-and-push-docker-image, get-version] + runs-on: ubuntu-20.04 + if: github.event_name != 'pull_request' + steps: + - name: Checkout helmfile repo + uses: actions/checkout@v2 + with: + repository: PilotDataPlatform/pilot-helmfile + ref: 'main' #always checkout main branch + ssh-key: ${{ secrets.PILOT_HELMFILE_REPO_DEPLOYMENT_KEY }} + + - name: Update service version + run: | + git config user.name "GitHub Actions" + git config user.email "github-actions@users.noreply.indocresearch.org" + BASE_FILE='./helmfile.d/values/shared/lab/shared-services-values.yaml' + + pattern="arranger_admin_server" + + current_version=$(grep -m 1 $pattern $BASE_FILE) + echo "current version is $current_version" + + sed -i "/$pattern/,/charts/ s/$current_version/ $pattern: ${{needs.get-version.outputs.app_version}}/" $BASE_FILE + git add $BASE_FILE + git commit -m "Deploy arranger-admin-server ${{needs.get-version.outputs.app_version}} [app_name:arranger-admin-server, app_version:${{needs.get-version.outputs.app_version}}]" + git push origin main diff --git a/.github/workflows/pilot-pipeline-admin-ui.yml b/.github/workflows/pilot-pipeline-admin-ui.yml new file mode 100644 index 000000000..8e47d2f01 --- /dev/null +++ b/.github/workflows/pilot-pipeline-admin-ui.yml @@ -0,0 +1,165 @@ +name: CI pipeline admin ui + +on: + push: + branches: + - patched-version + paths: + - 'modules/admin-ui/**' + pull_request: + branches: + - patched-version + paths: + - 'modules/admin-ui/**' + +jobs: + + extract-branch-name: + runs-on: ubuntu-20.04 + outputs: + branch: ${{steps.extract_branch.outputs.branch}} + steps: + - name: Extract Branch Name + id: extract_branch + shell: bash + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT + get-version: + runs-on: ubuntu-20.04 + outputs: + app_version: ${{steps.get-version.outputs.app_version}} + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Get Version + id: get-version + shell: bash + run: | + BRANCH=${GITHUB_REF#refs/heads/} + BASE_VERSION=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json` + echo "app_version=$BASE_VERSION" >> $GITHUB_OUTPUT + + build-and-push-docker-image: + needs: [extract-branch-name, get-version] + if: ${{ needs.extract-branch-name.outputs.branch == 'patched-version'}} + name: Build admin ui Docker image and push to repositories + runs-on: ubuntu-20.04 + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Set up Docker Buildx + id: buildx + uses: docker/setup-buildx-action@v2 + - name: Login to Github Packages + uses: docker/login-action@v2 + with: + registry: pilotdataplatform.azurecr.io + username: ${{ secrets.ACR_CLIENT }} + password: ${{ secrets.ACR_SECRET }} + - name: Docker metadata + id: meta + uses: docker/metadata-action@v4 + with: + # list of Docker images to use as base name for tags + images: | + pilotdataplatform.azurecr.io/arranger/arranger-admin-ui + # generate Docker tags based on the following events/attributes + sep-tags: ',' + tags: | + type=raw,prefix=arranger-admin-ui-,suffix=,value=${{needs.get-version.outputs.app_version}} +# - name: Image digest +# run: echo ${{ steps.meta.outputs.tags }} + - name: Image digest + run: echo ${{ steps.meta.outputs.tags }} + - name: Check if Docker image tags exist + shell: bash + run: | + image_tag=$(echo "${{ steps.meta.outputs.tags }}") + if docker manifest inspect $image_tag >/dev/null; then + echo "Docker image with tag already exists. Please update the version." + exit 1 + else + echo "Image tags do not exist, proceeding..." + fi + - name: Check Trivy ignore exceptions + # Check if the Trivy ignorefile has exceptions and the exceptions + # date is defined and less than 90 days. + # + # The ignorefile has the following format: + # CVE-YYYY-XXXXX exp:YYYY-MM-DD + # + # Error out if the format is not respected. + # Given a CVE-YYYY-XXXXX defined in the ignorefile, + # if no exception date is defined, we will error out. + # if the exception date is more than 90 days, we will error out too. + # + # Successfully parsed lines will be ignored, + # if the exception date exist and is less than 90 days, the step will exit with 0. + uses: PilotDataPlatform/shared-ci-tools/.github/actions/trivyignore-checking@main + - name: Build image and push to GitHub Container Registry + uses: docker/build-push-action@v4 + with: + # relative path to the place where source code with Dockerfile is located + context: . + # Note: tags has to be all lower-case + tags: ${{ steps.meta.outputs.tags }} + # build on feature branches, push only on main branch + push: ${{ github.event_name != 'pull_request' }} + # Sets the target stage to build + target: arranger-admin-ui + load: true + + - name: Run Trivy vulnerability scanner + uses: aquasecurity/trivy-action@0.20.0 + with: + image-ref: '${{ steps.meta.outputs.tags }}' + format: 'table' + severity: 'CRITICAL' + exit-code: '1' + hide-progress: true + trivyignores: .github/.trivyignore + output: scan-results.txt + env: + TRIVY_IGNORE_STATUS: 'will_not_fix' + + - name: Publish Trivy Scan Results to Summary + if: always() + run: | + if [[ -s scan-results.txt ]]; then + { + echo "### Trivy Scan Results" + echo "
Click to expand" + echo "" + echo '```arranger-admin-ui' + cat scan-results.txt + echo '```' + echo "
" + } >> $GITHUB_STEP_SUMMARY + fi + + trigger_pilot_dev_deployment: + needs: [build-and-push-docker-image, get-version] + runs-on: ubuntu-20.04 + if: github.event_name != 'pull_request' + steps: + - name: Checkout helmfile repo + uses: actions/checkout@v2 + with: + repository: PilotDataPlatform/pilot-helmfile + ref: 'main' #always checkout main branch + ssh-key: ${{ secrets.PILOT_HELMFILE_REPO_DEPLOYMENT_KEY }} + + - name: Update service version + run: | + git config user.name "GitHub Actions" + git config user.email "github-actions@users.noreply.indocresearch.org" + BASE_FILE='./helmfile.d/values/shared/lab/shared-services-values.yaml' + + pattern="arranger_admin_ui" + + current_version=$(grep -m 1 $pattern $BASE_FILE) + echo "current version is $current_version" + + sed -i "/$pattern/,/charts/ s/$current_version/ $pattern: ${{needs.get-version.outputs.app_version}}/" $BASE_FILE + git add $BASE_FILE + git commit -m "Deploy arranger-admin-ui ${{needs.get-version.outputs.app_version}} [app_name:arranger-admin-ui, app_version:${{needs.get-version.outputs.app_version}}]" + git push origin main diff --git a/.github/workflows/pilot-pipeline-server-filter.yml b/.github/workflows/pilot-pipeline-server-filter.yml new file mode 100644 index 000000000..269f1670e --- /dev/null +++ b/.github/workflows/pilot-pipeline-server-filter.yml @@ -0,0 +1,165 @@ +name: CI pipeline server filter + +on: + push: + branches: + - patched-version + paths: + - 'modules/server-filter/**' + pull_request: + branches: + - patched-version + paths: + - 'modules/server-filter/**' + +jobs: + + extract-branch-name: + runs-on: ubuntu-20.04 + outputs: + branch: ${{steps.extract_branch.outputs.branch}} + steps: + - name: Extract Branch Name + id: extract_branch + shell: bash + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT + get-version: + runs-on: ubuntu-20.04 + outputs: + app_version: ${{steps.get-version.outputs.app_version}} + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Get Version + id: get-version + shell: bash + run: | + BRANCH=${GITHUB_REF#refs/heads/} + BASE_VERSION=`sed -n 's/^ *"version":.*"\([^"]*\)".*/\1/p' package.json` + echo "app_version=$BASE_VERSION" >> $GITHUB_OUTPUT + + build-and-push-docker-image: + needs: [extract-branch-name, get-version] + if: ${{ needs.extract-branch-name.outputs.branch == 'patched-version'}} + name: Build server filter Docker image and push to repositories + runs-on: ubuntu-20.04 + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Set up Docker Buildx + id: buildx + uses: docker/setup-buildx-action@v2 + - name: Login to Github Packages + uses: docker/login-action@v2 + with: + registry: pilotdataplatform.azurecr.io + username: ${{ secrets.ACR_CLIENT }} + password: ${{ secrets.ACR_SECRET }} + - name: Docker metadata + id: meta + uses: docker/metadata-action@v4 + with: + # list of Docker images to use as base name for tags + images: | + pilotdataplatform.azurecr.io/arranger/arranger-server + # generate Docker tags based on the following events/attributes + sep-tags: ',' + tags: | + type=raw,prefix=arranger-server-filter-,suffix=,value=${{needs.get-version.outputs.app_version}} +# - name: Image digest +# run: echo ${{ steps.meta.outputs.tags }} + - name: Image digest + run: echo ${{ steps.meta.outputs.tags }} + - name: Check if Docker image tags exist + shell: bash + run: | + image_tag=$(echo "${{ steps.meta.outputs.tags }}") + if docker manifest inspect $image_tag >/dev/null; then + echo "Docker image with tag already exists. Please update the version." + exit 1 + else + echo "Image tags do not exist, proceeding..." + fi + - name: Check Trivy ignore exceptions + # Check if the Trivy ignorefile has exceptions and the exceptions + # date is defined and less than 90 days. + # + # The ignorefile has the following format: + # CVE-YYYY-XXXXX exp:YYYY-MM-DD + # + # Error out if the format is not respected. + # Given a CVE-YYYY-XXXXX defined in the ignorefile, + # if no exception date is defined, we will error out. + # if the exception date is more than 90 days, we will error out too. + # + # Successfully parsed lines will be ignored, + # if the exception date exist and is less than 90 days, the step will exit with 0. + uses: PilotDataPlatform/shared-ci-tools/.github/actions/trivyignore-checking@main + - name: Build image and push to GitHub Container Registry + uses: docker/build-push-action@v4 + with: + # relative path to the place where source code with Dockerfile is located + context: . + # Note: tags has to be all lower-case + tags: ${{ steps.meta.outputs.tags }} + # build on feature branches, push only on main branch + push: ${{ github.event_name != 'pull_request' }} + # Sets the target stage to build + target: arranger-server + load: true + + - name: Run Trivy vulnerability scanner + uses: aquasecurity/trivy-action@0.20.0 + with: + image-ref: '${{ steps.meta.outputs.tags }}' + format: 'table' + severity: 'CRITICAL' + exit-code: '1' + hide-progress: true + trivyignores: .github/.trivyignore + output: scan-results.txt + env: + TRIVY_IGNORE_STATUS: 'will_not_fix' + + - name: Publish Trivy Scan Results to Summary + if: always() + run: | + if [[ -s scan-results.txt ]]; then + { + echo "### Trivy Scan Results" + echo "
Click to expand" + echo "" + echo '```arranger-server-filter' + cat scan-results.txt + echo '```' + echo "
" + } >> $GITHUB_STEP_SUMMARY + fi + + trigger_pilot_dev_deployment: + needs: [build-and-push-docker-image, get-version] + runs-on: ubuntu-20.04 + if: github.event_name != 'pull_request' + steps: + - name: Checkout helmfile repo + uses: actions/checkout@v2 + with: + repository: PilotDataPlatform/pilot-helmfile + ref: 'main' #always checkout main branch + ssh-key: ${{ secrets.PILOT_HELMFILE_REPO_DEPLOYMENT_KEY }} + + - name: Update service version + run: | + git config user.name "GitHub Actions" + git config user.email "github-actions@users.noreply.indocresearch.org" + BASE_FILE='./helmfile.d/values/development/dev/pilot-versions-values.yaml' + + pattern="arranger_server_filter_service" + + current_version=$(grep -m 1 $pattern $BASE_FILE) + echo "current version is $current_version" + + sed -i "/$pattern/,/service/ s/$current_version/ $pattern: ${{needs.get-version.outputs.app_version}}/" $BASE_FILE + git add $BASE_FILE + git commit -m "Deploy arranger-server-filter ${{needs.get-version.outputs.app_version}} [app_name:arranger-server-filter, app_version:${{needs.get-version.outputs.app_version}}]" + git push origin main diff --git a/Dockerfile b/Dockerfile index 5b1921bce..7c2d58d7b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,11 +1,17 @@ FROM node:14.21-alpine as builder +RUN addgroup --system arranger && \ + adduser -S arranger -G arranger + WORKDIR /app COPY . . +RUN chown -R arranger:arranger /app FROM builder as arranger-server WORKDIR modules/server-filter +RUN chown -R arranger:arranger /app/modules/server-filter +USER arranger RUN npm install ENTRYPOINT ["node","server.js"] @@ -13,11 +19,17 @@ ENTRYPOINT ["node","server.js"] FROM builder as arranger-admin-server WORKDIR modules/admin +RUN chown -R arranger:arranger /app/modules/admin +USER arranger RUN npm install ENTRYPOINT ["node","admin-server.js"] FROM builder as arranger-admin-ui +USER arranger RUN npm ci RUN npm run bootstrap WORKDIR modules/admin-ui +USER root +RUN chown -R arranger:arranger /app/modules/admin-ui +USER arranger ENTRYPOINT ["npm", "run", "start"] diff --git a/modules/admin/config.js b/modules/admin/config.js index f360a8b94..75d1bf9e3 100644 --- a/modules/admin/config.js +++ b/modules/admin/config.js @@ -1,2 +1,2 @@ -export const ADMIN_SERVER_PORT = process.env.ADMIN_SERVER_PORT || 5050; +export const ADMIN_SERVER_PORT = process.env.ADMIN_SERVER_PORT || 5051; export const ELASTICSEARCH = process.env.ELASTICSEARCH || 'http://127.0.0.1:9200'; diff --git a/modules/components/src/Aggs/AggsState.js b/modules/components/src/Aggs/AggsState.js index 2443fede7..5553f22e5 100644 --- a/modules/components/src/Aggs/AggsState.js +++ b/modules/components/src/Aggs/AggsState.js @@ -59,7 +59,6 @@ export default class extends Component { let { data } = await api({ endpoint: `/${this.props.projectId}/graphql/aggsStateQuery`, body: { - project_code: 'indoctestproject', query: `query aggsStateQuery { ${graphqlField} { diff --git a/modules/components/src/Arranger/GetProjects.js b/modules/components/src/Arranger/GetProjects.js index fb1abfbbd..b7489cf7b 100644 --- a/modules/components/src/Arranger/GetProjects.js +++ b/modules/components/src/Arranger/GetProjects.js @@ -1,11 +1,11 @@ import React from 'react'; -import defaultApi from '../utils/api'; +import defaultAdminApi from '../utils/adminAPI'; class GetProjects extends React.Component { state = { projects: [] }; async componentDidMount() { - const { api = defaultApi } = this.props; + const { api = defaultAdminApi } = this.props; let { data } = await api({ endpoint: '/admin/graphql', body: { diff --git a/modules/components/src/DataTable/ColumnsState.js b/modules/components/src/DataTable/ColumnsState.js index f37d20311..86ccf4a72 100644 --- a/modules/components/src/DataTable/ColumnsState.js +++ b/modules/components/src/DataTable/ColumnsState.js @@ -63,7 +63,6 @@ export default class extends Component { let { data } = await api({ endpoint: `/${this.props.projectId}/graphql/columnsStateQuery`, body: { - project_code: 'indoctestproject', query: `query columnsStateQuery { ${graphqlField} { @@ -84,7 +83,6 @@ export default class extends Component { } = await api({ endpoint: `/${this.props.projectId}/graphql`, body: { - project_code: 'indoctestproject', query: ` query{ ${this.props.graphqlField} { diff --git a/modules/components/src/Query.js b/modules/components/src/Query.js index e60f14566..79e061317 100644 --- a/modules/components/src/Query.js +++ b/modules/components/src/Query.js @@ -32,7 +32,7 @@ class Query extends Component { let { data, errors } = await api({ ...options, endpoint: path.join(projectId, 'graphql', name || ''), - body: { query, variables, project_code: 'indoctestproject' }, + body: { query, variables }, }); this.setState({ data, diff --git a/modules/components/src/utils/adminAPI.js b/modules/components/src/utils/adminAPI.js new file mode 100644 index 000000000..12d8865f9 --- /dev/null +++ b/modules/components/src/utils/adminAPI.js @@ -0,0 +1,17 @@ +import { ARRANGER_ADMIN_API } from './config'; +import urlJoin from 'url-join'; + +let alwaysSendHeaders = { 'Content-Type': 'application/json' }; + +let Token = { + Authorization: `Bearer ${process.env.STORYBOOK_TOKEN}`, +}; + +export const defaultAdminApi = ({ endpoint = '', body, headers, method }) => + fetch(urlJoin(ARRANGER_ADMIN_API, endpoint), { + method: method || 'POST', + headers: { ...alwaysSendHeaders, ...headers, ...Token }, + body: JSON.stringify(body), + }).then((r) => r.json()); + +export default defaultAdminApi; diff --git a/modules/components/src/utils/api.js b/modules/components/src/utils/api.js index 8a4fa03c7..db535ce05 100644 --- a/modules/components/src/utils/api.js +++ b/modules/components/src/utils/api.js @@ -21,7 +21,6 @@ export const fetchExtendedMapping = ({ graphqlField, projectId, api = defaultApi api({ endpoint: `/${projectId}/graphql`, body: { - project_code: 'indoctestproject', query: ` { ${graphqlField}{ diff --git a/modules/components/src/utils/config.js b/modules/components/src/utils/config.js index a26dbf077..99597fa0f 100644 --- a/modules/components/src/utils/config.js +++ b/modules/components/src/utils/config.js @@ -16,6 +16,7 @@ export function deleteValue(key) { } export const ARRANGER_API = getValue('ARRANGER_API', 'http://localhost:5050'); +export const ARRANGER_ADMIN_API = getValue('ARRANGER_ADMIN_API', 'http://localhost:5051'); export const ES_HOST = getValue('ES_HOST', 'http://localhost:9200'); export const PROJECT_ID = getValue('PROJECT_ID', null); export const ACTIVE_INDEX = getValue('ACTIVE_INDEX', null); diff --git a/modules/mapping-utils/src/utils/columnsToGraphql.js b/modules/mapping-utils/src/utils/columnsToGraphql.js index bb67681b7..ff9b31d27 100644 --- a/modules/mapping-utils/src/utils/columnsToGraphql.js +++ b/modules/mapping-utils/src/utils/columnsToGraphql.js @@ -27,7 +27,6 @@ export default function columnsToGraphql({ config = {}, sqon, queryName, sort, o .join('\n'); return { - project_code: 'indoctestproject', fields, query: ` query($sort: [Sort], $first: Int, $offset: Int, $score: String, $sqon: JSON) { diff --git a/modules/nf-server-filter/.env.schema b/modules/nf-server-filter/.env.schema new file mode 100644 index 000000000..2088b27fa --- /dev/null +++ b/modules/nf-server-filter/.env.schema @@ -0,0 +1,12 @@ +# ARRANGER SERVER PORT +SERVER_PORT= + +# ARRANGER PROJECT ID SETUP BY ADMIN UI +ARRANGER_PROJECT_ID= + +# ELASTICSEARCH HOST:PORT +ELASTICSEARCH= + +# DOWNLOAD FILE STREAM BUFFER SIZE (export) +DOWNLOAD_STREAM_BUFFER_SIZE= + diff --git a/modules/nf-server-filter/README.md b/modules/nf-server-filter/README.md new file mode 100644 index 000000000..336621a33 --- /dev/null +++ b/modules/nf-server-filter/README.md @@ -0,0 +1,23 @@ +# Nextflow Arranger Server + +### Overview + +This arranger server acts as a proxy to obtain nextflow workflow updates. + +### Prerequisites + +NodeJs version: `v14.21.0`; NPM version: `6.14.17`. Recommended to use node version manager (NVM). + +### Installation + +1. `cd nf-server-filter` +2. `npm install` + +### Start up + +1. Set `.env` to point to desired server port, arranger project ID, and elasticsearch instance. +2. Run `node server.js` + +### Important notes + +1. Export-to-file logic exists under `/export`. diff --git a/modules/nf-server-filter/authFilter.js b/modules/nf-server-filter/authFilter.js new file mode 100644 index 000000000..afe3ea23d --- /dev/null +++ b/modules/nf-server-filter/authFilter.js @@ -0,0 +1,19 @@ +import { BaseSQON } from './sqon/base_sqon.js'; + +/** + * Function will create custom SQON filter + * @returns a JSON encoded SQON filter to apply to graphql query, including aggregations + */ + +export async function arrangerFilter() { + return BaseSQON.generate(); +} + +/** + * Function will process incoming request to obtain SQON filter + * @returns a JSON encoded SQON filter to apply to graphql query, including aggregations + */ + +export async function processRequest() { + return await arrangerFilter(); +} diff --git a/modules/nf-server-filter/config.js b/modules/nf-server-filter/config.js new file mode 100644 index 000000000..c998cd175 --- /dev/null +++ b/modules/nf-server-filter/config.js @@ -0,0 +1,4 @@ +export const SERVER_PORT = process.env.SERVER_PORT || 5050; +export const ARRANGER_PROJECT_ID = process.env.ARRANGER_PROJECT_ID || 'nextflow-runs'; +export const ELASTICSEARCH = process.env.ELASTICSEARCH || 'http://127.0.0.1:9200'; +export const DOWNLOAD_STREAM_BUFFER_SIZE = process.env.DOWNLOAD_STREAM_BUFFER_SIZE || 2000; diff --git a/modules/nf-server-filter/export/export-file.js b/modules/nf-server-filter/export/export-file.js new file mode 100644 index 000000000..346e3c017 --- /dev/null +++ b/modules/nf-server-filter/export/export-file.js @@ -0,0 +1,160 @@ +import express from 'express'; +import zlib from 'zlib'; +import tar from 'tar-stream'; +import pkg from 'lodash'; +const { defaults } = pkg; + +import { getAllData } from './utils/getAllData.js'; +import { dataToExportFormat } from './utils/dataToExportFormat.js'; + +const convertDataToExportFormat = + ({ req, project_info, params, headers, ctx, fileType }) => + async (args) => + ( + await getAllData({ + req, + project_info, + params, + headers, + ctx, + ...args, + }) + ).pipe(dataToExportFormat({ ...args, fileType })); + +const getFileStream = async ({ + req, + project_info, + params, + headers, + chunkSize, + ctx, + file, + fileType, + mock, +}) => { + const exportArgs = defaults(file, { chunkSize, fileType, mock }); + + return convertDataToExportFormat({ req, project_info, params, headers, ctx, fileType })({ + ...exportArgs, + mock, + }); +}; + +const multipleFiles = async ({ + req, + project_info, + params, + headers, + chunkSize, + ctx, + files, + mock, +}) => { + const pack = tar.pack(); + + Promise.all( + files.map((file, i) => { + return new Promise(async (resolve, reject) => { + // pack needs the size of the stream. We don't know that until we get all the data. + // This collects all the data before adding it. + let data = ''; + const fileStream = await getFileStream({ + req, + project_info, + params, + headers, + chunkSize, + ctx, + file, + fileType: file.fileType, + mock, + }); + + fileStream.on('data', (chunk) => (data += chunk)); + fileStream.on('end', () => { + pack.entry({ name: file.fileName || `file-${i + 1}.tsv` }, data, function (err) { + if (err) { + reject(err); + } else { + resolve(null); + } + }); + }); + }); + }), + ).then(() => pack.finalize()); + + /** NOTE from zlib's maintainers: + * (This library) is only intended for small (< 128 KB) data + * that you already have buffered. It is not meant for input/output streams. + * -- Found at: https://www.npmjs.com/package/zlib + * + * TODO: may have to find one that manages larger buffer sizes. + * Must do testing for this + */ + return pack.pipe(zlib.createGzip()); +}; + +export const dataStream = async ({ req, project_info, headers, ctx, params }) => { + const { chunkSize, files, fileName = 'file.tar.gz', fileType = 'tsv', mock } = params; + + if (files?.length > 0) { + return files.length === 1 + ? { + contentType: 'text/plain', + output: await getFileStream({ + req, + project_info, + params, + headers, + chunkSize, + ctx, + file: files[0], + fileType: files[0].fileType || fileType, + mock, + }), + responseFileName: files[0].fileName || fileName, + } + : { + contentType: 'application/gzip', + output: multipleFiles({ req, project_info, headers, chunkSize, ctx, files, mock }), + responseFileName: fileName.replace(/(\.tar(\.gz)?)?$/, '.tar.gz'), // make sure file ends with '.tar.gz' + }; + } + + console.warn('no files defined to download'); + throw new Error('files array was missing or empty'); +}; + +export function downloader(project_info) { + const router = express.Router(); + + router.use(express.json()); + + router.post('/', async function (req, res) { + try { + const data = req.body; + const requestHeaders = { + ...req.headers, + Authorization: req.headers.authorization, + }; + const { output, responseFileName, contentType } = await dataStream({ + req, + project_info, + headers: requestHeaders, + ctx: req.context, + params: data, + }); + + res.set('Content-Type', contentType); + res.set('Content-disposition', `attachment; filename=${responseFileName}`); + output.pipe(res).on('finish', () => {}); + } catch (err) { + console.error(err); + + res.status(400).send(err?.message || err?.details || 'An unknown error occurred.'); + } + }); + + return router; +} diff --git a/modules/nf-server-filter/export/utils/arrangerFilterDownload.js b/modules/nf-server-filter/export/utils/arrangerFilterDownload.js new file mode 100644 index 000000000..abe3b1c33 --- /dev/null +++ b/modules/nf-server-filter/export/utils/arrangerFilterDownload.js @@ -0,0 +1,14 @@ +/** + * Function will return SQON to be passed to download stream + * @param req request that contains sqon generated by arranger filter. + */ +export function arrangerFilterDownload(req) { + try { + // add user-selected identifiers + + // return custom sqon + return req.sqon; + } catch (error) { + console.log(`Error returning download SQON: ${error}`); + } +} diff --git a/modules/nf-server-filter/export/utils/dataToExportFormat.js b/modules/nf-server-filter/export/utils/dataToExportFormat.js new file mode 100644 index 000000000..c3b08086d --- /dev/null +++ b/modules/nf-server-filter/export/utils/dataToExportFormat.js @@ -0,0 +1,323 @@ +import { format, isValid, parseISO } from 'date-fns'; +import jsonPath from 'jsonpath'; +import pkg from 'lodash'; +const { get, flatten, isNil } = pkg; +import through2 from 'through2'; + +const STANDARD_DATE = 'yyyy-MM-dd'; + +const dateHandler = (value, { dateFormat = STANDARD_DATE }) => { + switch (true) { + case isNil(value): + return ''; + + case isValid(new Date(value)): + return format(new Date(value), dateFormat); + + case isValid(parseISO(value)): + return format(parseISO(value), dateFormat); + + case !isNaN(parseInt(value, 10)): + return format(parseInt(value, 10), dateFormat); + + default: { + console.error('unhandled "date"', value, dateFormat); + return value; + } + } +}; + +const getAllValue = (data) => { + if (typeof data === 'object') { + return Object.values(data || {}) + .map(getAllValue) + .reduce((a, b) => a.concat(b), []); + } else { + return data; + } +}; + +const getValue = (row, column) => { + const valueFromExtended = (value) => { + switch (true) { + case column?.extendedDisplayValues?.constructor === Object && + Object.keys(column.extendedDisplayValues).length > 0: + return column.extendedDisplayValues[value]; + + case column.isArray && Array.isArray(value): + return value + .map((each) => valueFromExtended(each)) + .join(';') + .replace(';;', ';'); + + case [column.displayType, column.type].includes('date'): + return dateHandler(value, { dateFormat: column.displayFormat }); + + default: + return value; + } + }; + + if (column.jsonPath) { + return jsonPath + .query(row, column.jsonPath.split('.hits.edges[*].node.').join('[*].')) + .map(getAllValue) + .reduce((a, b) => a.concat(b), []) + .map(valueFromExtended) + .join(', '); + } else if (column.accessor) { + return valueFromExtended(get(row, column.accessor)); + } else { + return ''; + } +}; + +const getRows = (args) => { + const { row, data = row, paths, pathIndex = 0, columns, entities = [] } = args; + if (pathIndex >= paths.length - 1) { + return [ + columns.map((column) => { + const entity = entities + .slice() + .reverse() + .find((entity) => column.field.indexOf(entity.field) === 0); + + if (entity) { + return getValue(entity.data, { + ...column, + jsonPath: column.field.replace(`${entity.path.join('.')}.`, ''), + }); + } else { + return getValue(row, column); + } + }), + ]; + } else { + const currentPath = paths[pathIndex]; + return flatten( + (get(data, currentPath) || []).map((node) => { + return getRows({ + ...args, + data: node, + pathIndex: pathIndex + 1, + entities: [ + ...entities, + { + path: paths.slice(0, pathIndex + 1), + field: paths.slice(0, pathIndex + 1).join(''), + // TODO: don't assume hits.edges.node. + // .replace(/(\.hits.edges(node)?)/g, ''), + data: node, + }, + ], + }); + }), + ); + } +}; + +export const columnsToHeader = ({ columns, fileType = 'tsv' }) => { + return fileType === 'tsv' + ? `${columns.map(({ Header, displayName }) => (displayName ? displayName : Header)).join('\t')}` + : fileType === 'json' + ? columns.reduce((output, { Header, displayName, accessor }) => { + output[[accessor]] = displayName ? displayName : Header; + return output; + }, {}) + : ''; +}; + +export const dataToTSV = ({ isFirst, pipe, columns, ...args }) => { + if (isFirst) { + const headerRow = columnsToHeader({ columns, fileType: 'tsv' }); + pushToStream(headerRow, pipe); + } + + transformData({ + isFirst, + pipe, + columns, + ...args, + dataTransformer: transformDataToTSV, + }); +}; + +/** + * This should ideally stream data as a JSON list using JSONStream + * but as of now; in favor of simplicity; it streams each row as separate JSON object + * and it is left up to consuming application to make a well formatted + * JSON list from individual JSON objects + * See https://github.com/nci-hcmi-catalog/portal/tree/master/api/src/dataExport.js for an example consumer + * @param {*} param0 + */ +export const dataToJSON = ({ isFirst, pipe, columns, ...args }) => { + if (isFirst) { + const headerRow = columnsToHeader({ columns, fileType: 'json' }); + pushToStream(JSON.stringify(headerRow), pipe); + } + + transformData({ + isFirst, + pipe, + columns, + ...args, + dataTransformer: transformDataToJSON, + }); +}; + +export function dataToExportFormat({ + index, + columns, + emptyValue, // kept for backwards compatibility. To be deprecated + uniqueBy, + valueWhenEmpty = emptyValue || '--', + fileType = 'tsv', +}) { + let isFirst = true; + let chunkCounts = 0; + + return through2.obj(function ({ hits, total }, enc, callback) { + const outputStream = this; + dataToStream({ + index, + columns, + uniqueBy, + valueWhenEmpty, + hits, + total, + pipe: outputStream, + isFirst, + fileType, + }); + + if (isFirst) { + isFirst = false; + } + + callback(); + chunkCounts++; + }); +} + +const transformData = ({ + data: { hits, total }, + data, + index, + uniqueBy, + columns, + valueWhenEmpty, + dataTransformer, + pipe, +}) => { + hits + .map((row) => dataTransformer({ row, uniqueBy, columns, valueWhenEmpty })) + .forEach((transformedRow) => { + pushToStream(transformedRow, pipe); + }); +}; + +const transformDataToTSV = ({ row, uniqueBy, columns, valueWhenEmpty }) => { + return getRows({ + row: row._source, + paths: (uniqueBy || '').split('.hits.edges[].node.').filter(Boolean), + columns: columns, + valueWhenEmpty, + }).map((r) => rowToTSV({ row: r, valueWhenEmpty })); +}; + +const transformDataToJSON = ({ row, uniqueBy, columns, valueWhenEmpty }) => { + return JSON.stringify( + rowToJSON({ + row: row._source, + paths: (uniqueBy || '').split('.hits.edges[].node.').filter(Boolean), + columns: columns, + valueWhenEmpty, + }), + ); +}; + +const dataToStream = ({ + index, + columns, + uniqueBy, + valueWhenEmpty = '--', + hits, + total, + pipe, + isFirst, + fileType = 'tsv', +}) => { + const args = { + data: { hits, total }, + index, + uniqueBy, + columns, + valueWhenEmpty, + pipe, + isFirst, + }; + + // transform and stream data + if (fileType === 'tsv') { + dataToTSV(args); + } else if (fileType === 'json') { + dataToJSON(args); + } else { + throw new Error('Unsupported file type specified for export.'); + } +}; + +const rowToTSV = ({ row, valueWhenEmpty }) => row.map((r) => r || valueWhenEmpty).join('\t'); + +/* +example args: +{ row: [250/1767] + { name: 'HCM-dddd-0000-C00', + type: '2-D: Conditionally reprogrammed cells', + growth_rate: 5, + files: [], + clinical_diagnosis: { clinical_tumor_diagnosis: 'Colorectal cancer' }, + variants: [ [Object], [Object], [Object] ] + }, + paths: [], + columns: + [ { field: 'name', + accessor: 'name', + show: true, + type: 'entity', + sortable: true, + canChangeShow: true, + query: null, + jsonPath: null, + Header: 'Name', + extendedType: 'keyword', + extendedDisplayValues: {}, + hasCustomType: true, + minWidth: 140 }, + { field: 'split_ratio', + accessor: 'split_ratio', + show: true, + type: 'string', + sortable: true, + canChangeShow: true, + query: null, + jsonPath: null, + Header: 'Split Ratio', + extendedType: 'keyword', + extendedDisplayValues: {}, + hasCustomType: false } ], + valueWhenEmpty: '--' } +*/ +const rowToJSON = (args) => { + const { row, data = row, paths, pathIndex = 0, columns, valueWhenEmpty, entities = [] } = args; + return (columns || []) + .filter((col) => col.show) + .reduce((output, col) => { + output[[col.accessor]] = row[col.accessor] || valueWhenEmpty; + return output; + }, {}); +}; + +const pushToStream = (line, stream) => { + stream.push(`${line}\n`); +}; diff --git a/modules/nf-server-filter/export/utils/getAllData.js b/modules/nf-server-filter/export/utils/getAllData.js new file mode 100644 index 000000000..2e5aa0973 --- /dev/null +++ b/modules/nf-server-filter/export/utils/getAllData.js @@ -0,0 +1,107 @@ +import { PassThrough } from 'stream'; +import { buildQuery, esToSafeJsInt } from '@arranger/middleware'; +import { DOWNLOAD_STREAM_BUFFER_SIZE } from '../../config.js'; +import { graphql } from 'graphql'; +import { arrangerFilterDownload } from './arrangerFilterDownload.js'; + +export function runQuery({ project_id, esClient, query, schema, variables }) { + return graphql({ + schema, + contextValue: { + schema, + es: esClient, + projectId: project_id, + }, + source: query, + variableValues: variables, + }); +} + +export async function getAllData({ + req, + project_info, + params, + headers, + index, + columns = [], + sort = [], + sqon, + chunkSize = DOWNLOAD_STREAM_BUFFER_SIZE, + ...rest +}) { + const stream = new PassThrough({ objectMode: true }); + const toHits = ({ + body: { + hits: { hits }, + }, + }) => hits; + const esSort = sort.map(({ field, order }) => ({ [field]: order })).concat({ _id: 'asc' }); + + const { esIndex, esType, extended } = await project_info.es + .search({ + index: `arranger-projects-${project_info.projectId}`, + }) + .then(toHits) + .then((hits) => hits.map(({ _source }) => _source)) + .then( + (hits) => + hits + .map(({ index: esIndex, name, esType, config: { extended } }) => ({ + esIndex, + name, + esType, + extended, + })) + .filter(({ name }) => name === index)[0], + ); + + const nestedFields = extended.filter(({ type }) => type === 'nested').map(({ field }) => field); + + const es_schema = project_info.arranger_schema['schema']; + sqon = arrangerFilterDownload(req, params, sqon); + const query = buildQuery({ nestedFields, filters: sqon }); + + runQuery({ + project_id: project_info.projectId, + esClient: project_info.es, + query: ` + query ($sqon: JSON) { + ${index} { + hits(filters: $sqon) { + total + } + } + } + `, + schema: es_schema, + variables: { sqon }, + }) + .then(({ data }) => { + const total = data[index].hits.total; + const steps = Array(Math.ceil(total / chunkSize)).fill(); + // async reduce because each cycle is dependent on result of the previous + return steps.reduce(async (previous) => { + const previousHits = await previous; + const hits = await project_info.es + .search({ + index: esIndex, + size: chunkSize, + body: { + sort: esSort, + ...(previousHits + ? { + search_after: previousHits[previousHits.length - 1].sort.map(esToSafeJsInt), + } + : {}), + ...(Object.entries(query).length ? { query } : {}), + }, + }) + .then(toHits); + stream.write({ hits, total }); + return hits; + }, Promise.resolve()); + }) + .then(() => stream.end()) + .catch(console.error); + return stream; +} diff --git a/modules/nf-server-filter/package-lock.json b/modules/nf-server-filter/package-lock.json new file mode 100644 index 000000000..df1bbc1de --- /dev/null +++ b/modules/nf-server-filter/package-lock.json @@ -0,0 +1,2753 @@ +{ + "name": "server-filter", + "version": "1.0.0", + "lockfileVersion": 1, + "requires": true, + "dependencies": { + "@apollo/protobufjs": { + "version": "1.2.2", + "resolved": "https://registry.npmjs.org/@apollo/protobufjs/-/protobufjs-1.2.2.tgz", + "integrity": "sha512-vF+zxhPiLtkwxONs6YanSt1EpwpGilThpneExUN5K3tCymuxNnVq2yojTvnpRjv2QfsEIt/n7ozPIIzBLwGIDQ==", + "requires": { + "@protobufjs/aspromise": "^1.1.2", + "@protobufjs/base64": "^1.1.2", + "@protobufjs/codegen": "^2.0.4", + "@protobufjs/eventemitter": "^1.1.0", + "@protobufjs/fetch": "^1.1.0", + "@protobufjs/float": "^1.0.2", + "@protobufjs/inquire": "^1.1.0", + "@protobufjs/path": "^1.1.2", + "@protobufjs/pool": "^1.1.0", + "@protobufjs/utf8": "^1.1.0", + "@types/long": "^4.0.0", + 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b/modules/nf-server-filter/package.json new file mode 100644 index 000000000..f1a4511c9 --- /dev/null +++ b/modules/nf-server-filter/package.json @@ -0,0 +1,31 @@ +{ + "name": "server-filter", + "version": "1.0.0", + "description": "", + "main": "index.js", + "type": "module", + "scripts": {}, + "keywords": [], + "author": "", + "license": "ISC", + "dependencies": { + "@arranger/schema": "^2.19.4", + "@arranger/server": "2.19.3", + "@elastic/elasticsearch": "^7.17.0", + "@types/express-serve-static-core": "4.17.24", + "apollo-server-express": "^2.14.2", + "axios": "^1.3.4", + "cors": "^2.8.5", + "date-fns": "^2.29.2", + "express": "^4.18.2", + "graphql": "^14.5.3", + "graphql-playground-middleware-express": "^1.7.12", + "jsonpath": "^1.0.0", + "jwt-decode": "^3.1.2", + "kind-of": "^6.0.3", + "lodash": "^4.17.20", + "memoizee": "^0.4.15", + "minimist": "^1.2.5", + "through2": "^2.0.3" + } +} diff --git a/modules/nf-server-filter/server.js b/modules/nf-server-filter/server.js new file mode 100644 index 000000000..1d549adfd --- /dev/null +++ b/modules/nf-server-filter/server.js @@ -0,0 +1,104 @@ +import express from 'express'; +import cors from 'cors'; +import { Client } from '@elastic/elasticsearch'; +import { ApolloServer } from 'apollo-server-express'; +import { downloader } from './export/export-file.js'; +import { processRequest } from './authFilter.js'; +import { ARRANGER_PROJECT_ID, ELASTICSEARCH, SERVER_PORT } from './config.js'; + +// We need to pull the createProjectSchema method out of the arranger server dist because this gives us access to the `getServerSideFilter` method +import { createProjectSchema } from '@arranger/server/dist/startProject.js'; + +// Manually create ES Client, as we need to give arranger access to it directly +const esClient = new Client({ + node: ELASTICSEARCH, +}); + +/** + * Execute server filter on the incoming request + * @param req request from express server + * @param res response from express server + * @param next next middleware function from express server + */ + +async function serverFilter(req, res, next) { + try { + req.sqon = await processRequest(); + } catch (error) { + console.error(`Failed to execute server filter: ${error.message} `); + } + next(); +} + +/** + * Retrieve sqon from RBAC filter + * @param context The context provided by the ApolloServer based on the incoming request + * @returns a SQON filter to apply to the entire request and to all aggregations + */ +function SQONFilter(context) { + return context.req.sqon; +} + +// Schema for server-side filtering +const arrangerSchema = await createProjectSchema({ + es: esClient, + id: ARRANGER_PROJECT_ID, + graphqlOptions: {}, + enableAdmin: false, + getServerSideFilter: SQONFilter, +}); + +// Schema for download functionality +const arrangerSchemaDownload = await createProjectSchema({ + es: esClient, + id: ARRANGER_PROJECT_ID, + graphqlOptions: {}, + enableAdmin: false, +}); + +// Setup Apollo Server +const server = new ApolloServer({ + schema: arrangerSchema['schema'], + context: ({ req }) => { + return { + es: esClient, + req, + projectId: ARRANGER_PROJECT_ID, + }; + }, +}); + +// Setup express server +const app = express(); +app.use(express.json()); // support json encoded bodies + +// Use serverFilter for incoming requests +app.use(serverFilter); + +// Enable all CORS requests +app.use(cors()); + +// Add Arranger middleware +server.applyMiddleware({ + app, + path: `/${ARRANGER_PROJECT_ID}/graphql`, +}); +server.applyMiddleware({ + app, + path: `/${ARRANGER_PROJECT_ID}/graphql/*`, +}); + +// Enable export file +app.use( + `/${ARRANGER_PROJECT_ID}/download`, + downloader({ + projectId: ARRANGER_PROJECT_ID, + es: esClient, + arranger_schema: arrangerSchemaDownload, + }), +); + +// Start express server +app.listen(SERVER_PORT, () => { + console.log(`Arranger server running on ${SERVER_PORT}`); +}); diff --git a/modules/nf-server-filter/sqon/base_sqon.js b/modules/nf-server-filter/sqon/base_sqon.js new file mode 100644 index 000000000..78465573f --- /dev/null +++ b/modules/nf-server-filter/sqon/base_sqon.js @@ -0,0 +1,19 @@ +/** + * Class to manage base SQONs + */ +export class BaseSQON { + /** + * Create base SQON + */ + static generate() { + return { + op: 'and', + content: [ + { + op: 'or', + content: [], + }, + ], + }; + } +} diff --git a/modules/server-filter/.env.schema b/modules/server-filter/.env.schema index d16e3e4aa..8e5a62e89 100644 --- a/modules/server-filter/.env.schema +++ b/modules/server-filter/.env.schema @@ -13,6 +13,13 @@ AUTH_SERVICE= # AUTH SERVICE PAGE SIZE AUTH_SERVICE_PAGE_SIZE= +# METADATA SERVICE HOST:PORT +METADATA_SERVICE= + +# METADATA SERVICE PAGE SIZE +METADATA_SERVICE_PAGE_SIZE= + + # DOWNLOAD FILE STREAM BUFFER SIZE (export) DOWNLOAD_STREAM_BUFFER_SIZE= diff --git a/modules/server-filter/README.md b/modules/server-filter/README.md index bb2353975..21be1cb16 100644 --- a/modules/server-filter/README.md +++ b/modules/server-filter/README.md @@ -12,7 +12,7 @@ NodeJs version: `v14.21.0`; NPM version: `6.14.17`. Recommended to use node vers 1. ``cd server-filter`` 2. ``npm install`` -### Start-up +### Start up 1. Set ``.env`` to point to desired server port, arranger project ID, and elasticsearch instance. 2. Run `node server.js` @@ -23,3 +23,4 @@ NodeJs version: `v14.21.0`; NPM version: `6.14.17`. Recommended to use node vers 3. Export file logic exists under `/export`. + diff --git a/modules/server-filter/authFilter.js b/modules/server-filter/authFilter.js index 58ba715fb..c85dd1faf 100644 --- a/modules/server-filter/authFilter.js +++ b/modules/server-filter/authFilter.js @@ -6,9 +6,13 @@ import memoize from 'memoizee'; import { AUTH_SERVICE, AUTH_SERVICE_PAGE_SIZE, - MEMOIZE_TIMEOUT + MEMOIZE_TIMEOUT, METADATA_SERVICE, METADATA_SERVICE_PAGE_SIZE } from './config.js'; +import { + ProjectFolder +} from './sqonModels.js' + /** * Function will read sqon json files * @param path The path to sqon file @@ -26,7 +30,8 @@ async function readFile(path) { }); } catch (error) { - console.error(`Failed to read sqon model: ${error}`); + console.error(error) + throw Error('Failed to read sqon model') } } @@ -38,8 +43,14 @@ async function readFile(path) { */ export function decodeToken(request) { try { - // get user roles + // decode token const decoded = jwt_decode(request.headers.authorization); + + if ((!decoded['preferred_username']) || (!decoded['realm_access']['roles'])) { + throw Error('Invalid decoded token format') + } + + // get user roles const user_roles = decoded['realm_access']['roles']; // get username @@ -51,7 +62,8 @@ export function decodeToken(request) { } } catch (error) { - console.error(`Failed to decode token: ${error}`); + console.error(error) + throw Error('Failed to decode token') } } @@ -80,11 +92,63 @@ function UserRoleCheck(project_code, user_roles) { } } catch (error) { - console.error(`Failed to check realm roles against project: ${error}`) + console.error(error) + throw Error(`Failed to check realm roles against project ${project_code}`) + } } +/** + * Function will call metadata service to obtain project folder names that can be accessed by user + * @param project_code project code to query project folders from + * @param token user-specific bearer token + * @param page The page number used for pagination + * @param data The resulting data for a single api call + * @returns An array of non user-accessible project folders for a project + */ + +const getProjectFolders = async (project_code = '', token = '',page = 0, data = []) => { + try { + const zones = {0:'greenroom', 1:'core'} + const request_data = { + params: { + type: 'project_folder', + container_code: project_code, + status: 'ACTIVE', + parent_path: 'shared', + page: page, + page_size: METADATA_SERVICE_PAGE_SIZE + }, + paramsSerializer: { + indexes: null // by default: false + }, + headers: { + "Authorization" : `${token}` + + } + } + + const url = `${METADATA_SERVICE}/v1/items/search`; + const response = await axios.get(url, request_data); + page++; + if (response.data.result.length !== 0){ + for (const entry of response.data.result) { + data.push({"name":entry.name, "zone":zones[entry.zone]}); + } + } + if (response.data.num_of_pages > page) { + return getProjectFolders(project_code, token, page, data); + } + return data; + } catch (error) { + console.error(error.message) + throw Error(`Failed to call metadata service`); + } +}; + + + /** * Function will call auth service to obtain rbac permissions for a project * @param project_code The project code for a project @@ -104,7 +168,8 @@ const getPermissions = async (project_code, page = 0, data = []) => { } return data; } catch (error) { - console.error(`Failed to call auth service: ${error}`); + console.error(error.message) + throw Error(`Failed to call auth service`); } }; @@ -112,15 +177,17 @@ const getPermissions = async (project_code, page = 0, data = []) => { * Function will obtain rbac permissions for a project and filter based on realm role * @param project_code The project code for a project * @param user_roles The realm roles obtained by decoded token + * @param token Bearer token of user * @returns Role and respective RBAC permissions for a project */ -const getRBAC = async (project_code, user_roles) => { +const getRBAC = async (project_code, user_roles, token) => { try { // define base RBAC const permitted = { file_in_own_namefolder: [], - file_any: [] + file_any: [], + project_folders_accessible: [] }; // check if user has role associated with project @@ -141,13 +208,23 @@ const getRBAC = async (project_code, user_roles) => { } } } + + // obtain project folders a user has access to + const projectFolders = await getProjectFolders(project_code, token); + if (projectFolders.length !== 0) { + for (const folder of projectFolders) { + permitted['project_folders_accessible'].push(folder) + } + } + return { "role": validated_role, "permissions": permitted }; } catch (error) { - console.log(`Failed to get RBAC info for project ${project_code}: ${error}`) + console.error(error) + throw Error(`Cannot retrieve RBAC info for project ${project_code}`) } }; @@ -170,7 +247,7 @@ const buildSQON = async (role_metadata, project_code, username) => { const base_sqon = await readFile('./models/base_sqon.json'); // if user does not have any permissions, return no data - if (permissions['file_any'].length === 0 && permissions['file_in_own_namefolder'].length === 0) { + if (permissions['file_any'].length === 0 && permissions['file_in_own_namefolder'].length === 0 && permissions['project_folders_accessible'].length === 0) { base_sqon['content'][0]['content']['field'] = 'no_permissions' return base_sqon } @@ -185,25 +262,36 @@ const buildSQON = async (role_metadata, project_code, username) => { if (permissions['file_any'].length !== 0) { for (const p of permissions['file_any']) { let others_sqon = await readFile('./models/others_sqon.json'); - others_sqon['content']['value'] = [p]; + others_sqon['content'][1]['content']['value'] = [p]; base_sqon['content'][1]['content'].push(others_sqon); } } if (permissions['file_in_own_namefolder'].length !== 0) { for (const p of permissions['file_in_own_namefolder']) { let owner_sqon = await readFile('./models/owner_sqon.json'); - owner_sqon['content'][0]['content']['value'] = [`${username}*`]; + owner_sqon['content'][0]['content']['value'] = [`users/${username}*`]; owner_sqon['content'][1]['content']['value'] = [p]; base_sqon['content'][1]['content'].push(owner_sqon); } } + + // project folders accessible, select these only. User does not have access to all name folders in any zone + if (permissions['project_folders_accessible'].length !== 0) { + const projectFolder = new ProjectFolder(); + for (const p of permissions['project_folders_accessible']){ + const sqon = projectFolder.generateAccessibleSQON(p.zone, p.name); + base_sqon['content'][1]['content'].push(sqon); + } + } + // return sqon with user permissions in place return base_sqon; } catch (error) { - console.error(`Failed to build SQON for project ${project_code}: ${error}`) + console.error(error) + throw Error(`Cannot build SQON for project ${project_code}`) } }; @@ -214,23 +302,16 @@ const buildSQON = async (role_metadata, project_code, username) => { * @param project_code project code for faceted search interface * @param username username of requester * @param user_roles user realm roles + * @param token bearer token of user * @returns a JSON encoded SQON filter to apply to graphql query, including aggregations */ -export async function arrangerAuthFilter(project_code, username, user_roles) { - try { - - // get rbac permissions (if any) - const rbac = await getRBAC(project_code, user_roles); - - // build sqon - return await buildSQON(rbac, project_code, username); - - - } catch (error) { - console.error(`Failed to execute auth filter: ${error} `) +export async function arrangerAuthFilter(project_code, username, user_roles, token) { + // get rbac permissions (if any) + const rbac = await getRBAC(project_code, user_roles, token); - } + // build sqon + return await buildSQON(rbac, project_code, username); } @@ -240,17 +321,12 @@ export async function arrangerAuthFilter(project_code, username, user_roles) { * @param username username of requester * @param request_body JSON of the incoming request body * @param realm_roles keycloak realm roles for user + * @param token bearer token of user * @returns a JSON encoded SQON filter to apply to graphql query, including aggregations */ -export async function processRequest(project_code, username, request_body, realm_roles) { - - try { - return await arrangerAuthFilter(project_code, username, realm_roles) - - } catch (error) { - console.log(`Failed to process request: ${error}`) - } +export async function processRequest(project_code, username, request_body, realm_roles, token) { + return await arrangerAuthFilter(project_code, username, realm_roles, token) } diff --git a/modules/server-filter/config.js b/modules/server-filter/config.js index 121614df7..18efb9057 100644 --- a/modules/server-filter/config.js +++ b/modules/server-filter/config.js @@ -3,5 +3,7 @@ export const ARRANGER_PROJECT_ID = process.env.ARRANGER_PROJECT_ID || 'pilotdev' export const ELASTICSEARCH = process.env.ELASTICSEARCH || 'http://127.0.0.1:9200'; export const AUTH_SERVICE = process.env.AUTH_SERVICE || 'http://127.0.0.1:5061'; export const AUTH_SERVICE_PAGE_SIZE = process.env.AUTH_SERVICE_PAGE_SIZE || 80; +export const METADATA_SERVICE = process.env.METADATA_SERVICE || 'http://127.0.0.1:5066'; +export const METADATA_SERVICE_PAGE_SIZE = process.env.METADATA_SERVICE_PAGE_SIZE || 80; export const DOWNLOAD_STREAM_BUFFER_SIZE = process.env.DOWNLOAD_STREAM_BUFFER_SIZE || 2000; export const MEMOIZE_TIMEOUT = process.env.MEMOIZE_TIMEOUT || 10000; diff --git a/modules/server-filter/export/utils/authFilterDownload.js b/modules/server-filter/export/utils/authFilterDownload.js index 024cccb82..a599badaa 100644 --- a/modules/server-filter/export/utils/authFilterDownload.js +++ b/modules/server-filter/export/utils/authFilterDownload.js @@ -6,9 +6,8 @@ */ export function arrangerAuthFilterDownload(req, params, sqon) { try { - // add user-selected identifiers - if (params['identifiers'].length > 0) { + if (params['identifiers'] && params['identifiers'].length > 0) { const sqon_id = { "op": "in", "content": { @@ -21,6 +20,17 @@ export function arrangerAuthFilterDownload(req, params, sqon) { } req.sqon.content.push(sqon_id) } + if (sqon !== null) { + if (sqon.content){ + // add facet selections to sqon + for (const filter of sqon.content){ + req.sqon.content.push(filter) + + } + } + + } + // return custom sqon return req.sqon diff --git a/modules/server-filter/models/others_sqon.json b/modules/server-filter/models/others_sqon.json index 47d5be19e..296f58af6 100755 --- a/modules/server-filter/models/others_sqon.json +++ b/modules/server-filter/models/others_sqon.json @@ -1,9 +1,23 @@ { - "op":"in", - "content":{ - "field":"zonefilter", - "value":[ - "zone" - ] - } + "op":"and", + "content":[ + { + "op":"in", + "content":{ + "field":"parent_path", + "value":[ + "users/*" + ] + } + }, + { + "op":"in", + "content":{ + "field":"zonefilter", + "value":[ + "zone" + ] + } + } + ] } diff --git a/modules/server-filter/models/owner_sqon.json b/modules/server-filter/models/owner_sqon.json index 5ea04745b..c83c8e6a9 100644 --- a/modules/server-filter/models/owner_sqon.json +++ b/modules/server-filter/models/owner_sqon.json @@ -6,7 +6,7 @@ "content":{ "field":"parent_path", "value":[ - "user*" + "users/user*" ] } }, diff --git a/modules/server-filter/package.json b/modules/server-filter/package.json index f38393683..f1a4511c9 100644 --- a/modules/server-filter/package.json +++ b/modules/server-filter/package.json @@ -15,6 +15,7 @@ "@types/express-serve-static-core": "4.17.24", "apollo-server-express": "^2.14.2", "axios": "^1.3.4", + "cors": "^2.8.5", "date-fns": "^2.29.2", "express": "^4.18.2", "graphql": "^14.5.3", diff --git a/modules/server-filter/server.js b/modules/server-filter/server.js index 565109c36..30f095408 100644 --- a/modules/server-filter/server.js +++ b/modules/server-filter/server.js @@ -1,4 +1,5 @@ import express from 'express'; +import cors from 'cors'; import { Client } from '@elastic/elasticsearch'; import { ApolloServer } from 'apollo-server-express'; import { downloader } from './export/export-file.js'; @@ -9,7 +10,9 @@ import { ARRANGER_PROJECT_ID, ELASTICSEARCH, SERVER_PORT } from './config.js'; import { createProjectSchema } from '@arranger/server/dist/startProject.js'; // Manually create ES Client, as we need to give arranger access to it directly -const esClient = new Client({node: ELASTICSEARCH}); +const esClient = new Client({ + node: ELASTICSEARCH +}); /** * Execute server filter on the incoming request @@ -18,13 +21,33 @@ const esClient = new Client({node: ELASTICSEARCH}); * @param next next middleware function from express server */ -async function serverFilter (req, res, next) { - const decoded = decodeToken(req) - const project_code = req.body['project_code']; - const username = decoded['username'] - const realm_roles = decoded['roles'] - req.sqon = await memoizedProcess(project_code, username, JSON.stringify(req.body), realm_roles) - next() +async function serverFilter(req, res, next) { + const invalid_sqon = { + "op": "and", + "content": [{ + "op": "in", + "content": { + "field": "container_code", + "value": ["no_permissions"] + } + }] + } + try { + if ((!req.headers.authorization) || (!req.body.project_code)) { + req.sqon = invalid_sqon; + } else { + const decoded = decodeToken(req) + const project_code = req.body['project_code']; + const username = decoded['username'] + const realm_roles = decoded['roles'] + req.sqon = await memoizedProcess(project_code, username, JSON.stringify(req.body), realm_roles, req.headers.authorization) + + } + } catch (error) { + console.error(`Failed to execute server filter: ${error.message} `) + req.sqon = invalid_sqon + } + next() } /** @@ -32,49 +55,69 @@ async function serverFilter (req, res, next) { * @param context The context provided by the ApolloServer based on the incoming request * @returns a SQON filter to apply to the entire request and to all aggregations */ -function SQONFilter(context){ - return context.req.sqon +function SQONFilter(context) { + return context.req.sqon } // Schema for server-side filtering const arrangerSchema = await createProjectSchema({ - es: esClient, - id: ARRANGER_PROJECT_ID, - graphqlOptions: {}, - enableAdmin: false, - getServerSideFilter: SQONFilter, + es: esClient, + id: ARRANGER_PROJECT_ID, + graphqlOptions: {}, + enableAdmin: false, + getServerSideFilter: SQONFilter, }) // Schema for download functionality const arrangerSchemaDownload = await createProjectSchema({ - es: esClient, - id: ARRANGER_PROJECT_ID, - graphqlOptions: {}, - enableAdmin: false, + es: esClient, + id: ARRANGER_PROJECT_ID, + graphqlOptions: {}, + enableAdmin: false, }) // Setup Apollo Server const server = new ApolloServer({ - schema: arrangerSchema['schema'], - context: ({ req }) => { - return {es: esClient, req, projectId: ARRANGER_PROJECT_ID}; - } + schema: arrangerSchema['schema'], + context: ({ + req + }) => { + return { + es: esClient, + req, + projectId: ARRANGER_PROJECT_ID + }; + } }) // Setup express server const app = express(); app.use(express.json()); // support json encoded bodies + +// Use serverFilter for incoming requests app.use(serverFilter) +// Enable all CORS requests +app.use(cors()) + // Add Arranger middleware -server.applyMiddleware({ app, path: `/${ARRANGER_PROJECT_ID}/graphql`}); -server.applyMiddleware({ app, path: `/${ARRANGER_PROJECT_ID}/graphql/*`}); +server.applyMiddleware({ + app, + path: `/${ARRANGER_PROJECT_ID}/graphql` +}); +server.applyMiddleware({ + app, + path: `/${ARRANGER_PROJECT_ID}/graphql/*` +}); // Enable export file -app.use(`/${ARRANGER_PROJECT_ID}/download`, downloader({ projectId: ARRANGER_PROJECT_ID, es: esClient, -arranger_schema: arrangerSchemaDownload})) +app.use(`/${ARRANGER_PROJECT_ID}/download`, downloader({ + projectId: ARRANGER_PROJECT_ID, + es: esClient, + arranger_schema: arrangerSchemaDownload +})) // Start express server app.listen(SERVER_PORT, () => { - console.log(`Arranger server running on ${SERVER_PORT}`); + console.log(`Arranger server running on ${SERVER_PORT}`); }); diff --git a/modules/server-filter/sqonModels.js b/modules/server-filter/sqonModels.js new file mode 100644 index 000000000..f1f3e9ced --- /dev/null +++ b/modules/server-filter/sqonModels.js @@ -0,0 +1,57 @@ +/** + * Class to manage and create shared project folder SQONs + */ +export class ProjectFolder { + /** + * Generate SQON for project folders and their respective files/folders that are user accessible + * @param zone zone of project folder + * @param folderName name of project folder + */ + generateAccessibleSQON(zone, folderName){ + return { + 'op': 'and', + 'content': [{ + 'op': 'in', + 'content': { + 'field': 'zonefilter', + 'value': [ + zone, + ], + }, + }, { + 'op': 'or', + 'content': [{ + 'op': 'in', + 'content': { + 'field': 'parent_path.keyword', + 'value': [ + `shared/${folderName}*`, + ], + }, + }, + { + "op":"and", + "content":[ + { + "op":"in", + "content":{ + "field":"type", + "value":[ + "project_folder" + ] + } + }, + { + "op":"in", + "content":{ + "field":"name", + "value":[ + `${folderName}` + ] + } + } + ] + }]}], + }; + } +} diff --git a/package.json b/package.json index b46439c41..21d159106 100644 --- a/package.json +++ b/package.json @@ -1,5 +1,5 @@ { - "version": "1.0.0", + "version": "1.0.6", "repository": { "type": "git", "url": "https://github.com/overture-stack/arranger.git"