diff --git a/.github/actions/ansible/Dockerfile b/.github/actions/ansible/Dockerfile deleted file mode 100644 index ad9558dbc7..0000000000 --- a/.github/actions/ansible/Dockerfile +++ /dev/null @@ -1,10 +0,0 @@ -FROM alpine:3.19.0 -LABEL app=kg-prototypes - -ENV ANSIBLE_HOST_KEY_CHECKING=False - -RUN apk add ansible python3-dev gcc openssh-client - -COPY entrypoint.sh ./entrypoint.sh - -ENTRYPOINT [ "/entrypoint.sh" ] diff --git a/.github/actions/ansible/action.yml b/.github/actions/ansible/action.yml deleted file mode 100644 index 1dc81d1b02..0000000000 --- a/.github/actions/ansible/action.yml +++ /dev/null @@ -1,33 +0,0 @@ -name: Ansible Runner -description: Runs Ansible Playbooks using Github Actions - -inputs: - workspace_dir: - description: Root directory of the Ansible workspace. - required: true - playbook_file_path: - description: Playook path relative to the workspace directory. - required: true - inventory_file_path: - description: Inventory path relative to the workspace directory - required: true - ssh_key: - description: SSH key for remote Ansible connections - required: false - vault_password: - description: Password used for Ansible vault encrypted files - required: false - options: - description: Additional options for Ansible playbook - required: false - -runs: - using: docker - image: Dockerfile - args: - - ${{ inputs.workspace_dir }} - - ${{ inputs.playbook_file_path }} - - ${{ inputs.inventory_file_path }} - - ${{ inputs.ssh_key }} - - ${{ inputs.vault_password }} - - ${{ inputs.options }} diff --git a/.github/actions/ansible/entrypoint.sh b/.github/actions/ansible/entrypoint.sh deleted file mode 100755 index f3da85a0ed..0000000000 --- a/.github/actions/ansible/entrypoint.sh +++ /dev/null @@ -1,62 +0,0 @@ -#!/bin/sh - -set -e - -export WORKSPACE_DIR= -if [ ! -z "$INPUT_WORKSPACE_DIR" ] -then - WORKSPACE_DIR="${INPUT_WORKSPACE_DIR}" -else - echo "No working space directory specified." -fi - -export PLAYBOOK_FILE_PATH= -if [ ! -z "$INPUT_PLAYBOOK_FILE_PATH" ] -then - PLAYBOOK_FILE_PATH="${INPUT_PLAYBOOK_FILE_PATH}" -else - echo "No playbook specified." -fi - -export INVENTORY_FILE_PATH= -if [ ! -z "$INPUT_INVENTORY_FILE_PATH" ] -then - INVENTORY_FILE_PATH="-i ${INPUT_INVENTORY_FILE_PATH}" -else - echo "No inventory specified." -fi - -export SSH_KEY= -if [ ! -z "$INPUT_SSH_KEY" ] -then - mkdir ~/.ssh - echo "$INPUT_SSH_KEY" > ~/.ssh/ansible - chmod 0600 ~/.ssh/ansible - tilde=~ - SSH_KEY_PATH="${tilde}/.ssh/ansible" - SSH_KEY="--key-file ${SSH_KEY_PATH}" -else - echo "No SSH key specified." -fi - -export VAULT_PASSWORD= -if [ ! -z "$INPUT_VAULT_PASSWORD" ] -then - echo "$INPUT_VAULT_PASSWORD" > ~/.vault_secrets_pw - tilde=~ - VAULT_PASSWORD_PATH="${tilde}/.vault_secrets_pw" - VAULT_PASSWORD="--vault-password-file ${VAULT_PASSWORD_PATH}" -else - echo "No vault password specified." -fi - -export OPTIONS= -if [ ! -z "$INPUT_OPTIONS" ] -then - OPTIONS=$(echo "${INPUT_OPTIONS}" | tr "\n" " ") -fi - -cd ${WORKSPACE_DIR} -echo "Running command..." -echo ansible-playbook ${PLAYBOOK_FILE_PATH} ${INVENTORY_FILE_PATH} ${SSH_KEY} ${VAULT_PASSWORD} ${OPTIONS} -ansible-playbook ${PLAYBOOK_FILE_PATH} ${INVENTORY_FILE_PATH} ${SSH_KEY} ${VAULT_PASSWORD} ${OPTIONS} diff --git a/.github/actions/cloud-sql-backup/action.yml b/.github/actions/cloud-sql-backup/action.yml deleted file mode 100644 index 9199899ced..0000000000 --- a/.github/actions/cloud-sql-backup/action.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: Cloud SQL backup -description: Backup a Google Cloud SQL instance - -inputs: - gcp_credentials: - description: Google Cloud Platform credentials - required: true - cloud_sql_instance_name: - description: Google Cloud SQL instance name - required: true - backup_description: - description: Backup description - required: false - default: "" - -outputs: - backup_id: - description: Google Cloud SQL backup ID - value: ${{ steps.fetch-backup-id.outputs.backup_id }} - -runs: - using: composite - steps: - - id: auth - uses: google-github-actions/auth@v0 - with: - credentials_json: "${{ inputs.gcp_credentials }}" - - - uses: google-github-actions/setup-gcloud@v0 - - - run: | - gcloud sql backups create \ - --instance="${{ inputs.cloud_sql_instance_name }}" \ - --description="${{ inputs.backup_description }}" - shell: bash - - - id: fetch-backup-id - run: | - echo ::set-output name=backup_id::$( \ - gcloud sql backups list \ - --instance="${{ inputs.cloud_sql_instance_name }}" \ - --format=json --limit 1 | jq -r ".[0].selfLink" ) - shell: bash diff --git a/.github/actions/cloud-sql-restore/action.yml b/.github/actions/cloud-sql-restore/action.yml deleted file mode 100644 index 7d78d1d270..0000000000 --- a/.github/actions/cloud-sql-restore/action.yml +++ /dev/null @@ -1,29 +0,0 @@ -name: Cloud SQL restore -description: Restore a Google Cloud SQL instance backup - -inputs: - gcp_credentials: - description: Google Cloud Platform credentials - required: true - cloud_sql_backup_id: - description: Google Cloud SQL backup ID to restore - required: true - cloud_sql_restore_instance: - description: Google Cloud SQL instance name to restore backup into - required: true - -runs: - using: composite - steps: - - id: auth - uses: google-github-actions/auth@v0 - with: - credentials_json: "${{ inputs.gcp_credentials }}" - - - uses: google-github-actions/setup-gcloud@v0 - - - run: | - gcloud sql backups restore \ - --restore-instance="${{ inputs.cloud_sql_restore_instance }}" \ - ${{ inputs.cloud_sql_backup_id }} - shell: bash diff --git a/.github/actions/docker-publish.yml b/.github/actions/docker-publish.yml deleted file mode 100644 index 580dd94672..0000000000 --- a/.github/actions/docker-publish.yml +++ /dev/null @@ -1,67 +0,0 @@ -name: 'Docker build and publish' -description: 'Builds and publishes a Docker image into a Docker registry.' - -inputs: - registry: - description: 'Server address of the Docker registry' - default: lifelike.azurecr.io - required: false - image: - description: 'Docker image' - required: true - username: - description: 'Username to log in to a Docker registry' - default: ${{ secrets.AZURE_CR_USERNAME }} - required: false - password: - description: 'Password or PAT to log in to a Docker registry' - default: ${{ secrets.AZURE_CR_PASSWORD }} - required: false - dockerfile: - description: 'Dockerfile to use for building the image' - required: false - default: './Dockerfile' - context: - description: 'Docker build context' - required: false - default: '.' - push: - description: 'Whether to push the image to the registry' - required: false - default: 'true' - -runs: - using: 'composite' - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Docker meta - id: docker_meta - uses: crazy-max/ghaction-docker-meta@v1 - with: - images: ${{ inputs.image }} - - - name: Set up QEMU - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - if: github.event_name != 'pull_request' && inputs.username != '' && inputs.password != '' - uses: docker/login-action@v1 - with: - username: ${{ inputs.username }} - password: ${{ inputs.password }} - - - name: Build and push - uses: docker/build-push-action@v2 - with: - file: ${{ inputs.dockerfile }} - context: ${{ inputs.context }} - tags: ${{ steps.docker_meta.outputs.tags }} - labels: ${{ steps.docker_meta.outputs.labels }} - push: ${{ inputs.push }} - cache-from: type=gha - cache-to: type=gha,mode=max diff --git a/.github/labeler.yml b/.github/labeler.yml index debee6d781..c19e1e9fb8 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -37,6 +37,3 @@ docker: workflow: - .github/* - .github/**/* - -infrastructure: - - deployment diff --git a/.github/workflows/backup-tests.yml b/.github/workflows/backup-tests.yml deleted file mode 100644 index 18e7b9c516..0000000000 --- a/.github/workflows/backup-tests.yml +++ /dev/null @@ -1,284 +0,0 @@ -name: Database backups tests - -on: - workflow_dispatch: - inputs: - force: - description: Force backup tests to run even for backups already tested - type: boolean - default: false - required: false - schedule: - # Run once a week on sunday at 00:00 - - cron: "0 1 * * 0" - -concurrency: - group: ${{ github.workflow }} - cancel-in-progress: false - -jobs: - get-sql-instances: - name: List Cloud SQL instances - runs-on: ubuntu-latest - outputs: - instances: ${{ steps.instances.outputs.json }} - steps: - - uses: actions/checkout@v3 - - - name: Authenticate to Google Cloud - uses: google-github-actions/auth@v0 - id: auth - with: - credentials_json: "${{ secrets.GCE_SA_KEY }}" - - - name: Set up Cloud SDK - uses: google-github-actions/setup-gcloud@v0 - - - name: Get all Cloud SQL instances - id: instances - run: | - INSTANCES=$( \ - gcloud sql instances list \ - --format="value(name.list())" \ - --filter="labels.test-backups=true" \ - | jq -R -s -c 'split("\n") | map(select(.!=""))') - echo ::set-output name=json::$INSTANCES - - restore-and-test: - needs: get-sql-instances - runs-on: ubuntu-latest - continue-on-error: true - strategy: - matrix: - instance: ${{ fromJSON(needs.get-sql-instances.outputs.instances) }} - type: ["AUTOMATED", "ON_DEMAND"] - steps: - - uses: actions/checkout@v3 - - - name: Authenticate to Google Cloud - uses: google-github-actions/auth@v0 - id: auth - with: - credentials_json: "${{ secrets.GCE_SA_KEY }}" - - - name: "Set up Cloud SDK" - uses: google-github-actions/setup-gcloud@v0 - with: - install_components: beta - - - name: Get latest ${{ matrix.type }} backup ID - id: get-backup - run: | - BACKUP=$( \ - gcloud sql backups list \ - --instance="${{ matrix.instance }}" \ - --filter="status=SUCCESSFUL AND type=${{ matrix.type }}" \ - --format="value(id, startTime)" --sort-by="-startTime" \ - | head -n 1) - echo ::set-output name=id::$(echo $BACKUP | cut -d' ' -f1) - echo ::set-output name=date::$(echo $BACKUP | cut -d' ' -f2) - - - name: Retrieve previous results artifact, if any - id: download-artifact - uses: dawidd6/action-download-artifact@v2 - with: - name: backup-test-results-${{ steps.get-backup.outputs.id }} - search_artifacts: true - if_no_artifact_found: ignore - - - name: Check if backup exists and hasn't been tested before - uses: actions/github-script@v6 - with: - script: | - if (!'${{ steps.get-backup.outputs.id }}') { - core.warning('Skipping. No backup found of type ${{ matrix.type }} for Cloud SQL instance: {{ matrix.instance }}') - } else if (!core.getInput('force') && (await (await glob.create('results.txt')).glob()).length > 0) { - core.notice('Skipping. Backup ${{ steps.get-backup.outputs.id }} has already been tested.') - } else { - core.exportVariable('PROCEED', 'true') - } - - - name: Get instance details - if: ${{ env.PROCEED == 'true' }} - id: instance-details - run: | - INSTANCE=$( \ - gcloud sql instances describe \ - --format="value(databaseVersion, settings.tier, region, project)" \ - ${{ matrix.instance }}) - echo ::set-output name=version::$(echo $INSTANCE | cut -d' ' -f1) - echo ::set-output name=tier::$(echo $INSTANCE | cut -d' ' -f2) - echo ::set-output name=region::$(echo $INSTANCE | cut -d' ' -f3) - echo ::set-output name=project::$(echo $INSTANCE | cut -d' ' -f4) - - - name: Create temporary Cloud SQL instance - if: ${{ env.PROCEED == 'true' }} - id: create-temp-instance - run: | - TEMP_INSTANCE_NAME=$(echo "temp-${{ matrix.instance }}-${{ matrix.type }}-${{ github.run_id }}" | sed 's/_/-/g' | awk '{print tolower($0)}') - gcloud beta sql instances create "$TEMP_INSTANCE_NAME" \ - --database-version=${{ steps.instance-details.outputs.version }} \ - --tier=${{ steps.instance-details.outputs.tier }} \ - --region=${{ steps.instance-details.outputs.region }} \ - --labels="temp-instance=true,workflow-run=${{ github.run_id }}" - echo ::set-output name=temp_instance_name::$TEMP_INSTANCE_NAME - - - name: Restore backup into temporary instance - if: ${{ env.PROCEED == 'true' }} - run: | - gcloud sql backups restore --quiet \ - --restore-instance=${{ steps.create-temp-instance.outputs.temp_instance_name }} \ - --backup-instance=${{ matrix.instance }} \ - ${{ steps.get-backup.outputs.id }} - - - name: Reset postgres password - if: ${{ env.PROCEED == 'true' }} - run: | - gcloud sql users set-password \ - --instance=${{ steps.create-temp-instance.outputs.temp_instance_name }} \ - --password=password postgres - - - uses: mattes/gce-cloudsql-proxy-action@v1 - if: ${{ env.PROCEED == 'true' }} - with: - creds: ${{ secrets.GCE_SA_KEY }} - instance: ${{ steps.instance-details.outputs.project }}:${{ steps.instance-details.outputs.region }}:${{ steps.create-temp-instance.outputs.temp_instance_name }} - - - name: Setup PostgreSQL client - if: ${{ env.PROCEED == 'true' }} - run: | - sudo apt-get update - sudo apt-get install --yes --no-install-recommends postgresql-client - - - name: Query temporary instance - if: ${{ env.PROCEED == 'true' }} - env: - PGPASSWORD: password - PGHOST: localhost - run: | - cat < queries.sql - -- ------------------------------------------------------------ - -- Count stats - -- ------------------------------------------------------------ - WITH tbl AS - (SELECT table_schema,TABLE_NAME - FROM information_schema.tables - WHERE TABLE_NAME not like 'pg_%' - AND table_schema in ('public')) - SELECT TABLE_NAME, (xpath('/row/c/text()', query_to_xml(format('select count(*) as c from %I.%I', table_schema, TABLE_NAME), FALSE, TRUE, '')))[1]::text::int AS rows - FROM tbl - ORDER BY rows DESC; - -- ------------------------------------------------------------ - -- Alembic - -- ------------------------------------------------------------ - SELECT version_num as current_alembic_version FROM alembic_version; - -- ------------------------------------------------------------ - -- Date stats - -- ------------------------------------------------------------ - CREATE OR REPLACE FUNCTION get_min_max_modified_date() - RETURNS TABLE (table_name text, - max_modified_daye timestamp, - min_modified_daye timestamp) - LANGUAGE plpgsql - AS \$\$ - DECLARE - r record; - BEGIN - FOR r IN - SELECT i.table_name, i.table_schema - FROM information_schema.tables i - WHERE i.table_name in ( - SELECT c.table_name - FROM information_schema.columns c - WHERE c.table_schema = 'public' - AND c.column_name = 'modified_date' - GROUP BY c.table_name - ) - LOOP - execute format ( - 'SELECT min(modified_date) FROM %I.%I', - r.table_schema, r.table_name - ) INTO min_modified_daye; - execute format ( - 'SELECT max(modified_date) FROM %I.%I', - r.table_schema, r.table_name - ) INTO max_modified_daye; - table_name := r.table_name; - RETURN next; - END LOOP; - END - \$\$; - SELECT * FROM get_min_max_modified_date(); - EOF - - # Query the restored database - psql -U postgres -d postgres -f queries.sql > results.txt - - # Export results to variable - echo "RESULTS<> $GITHUB_ENV - echo $(cat results.txt) >> $GITHUB_ENV - echo "EOF" >> $GITHUB_ENV - - results=$(> $GITHUB_STEP_SUMMARY - ## Backup details - - - Cloud SQL instance name: **${{ matrix.instance }}** - - Backup date: **${{ steps.get-backup.outputs.date }}** - - Backup type: **${{ matrix.type }}** - - Backup ID: **${{ steps.get-backup.outputs.id }}** - - Workflow run ID: [**${{ github.run_id }}**](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}) - - ## Results - \`\`\` - $results - \`\`\` - EOF - - - name: Upload results artifact - if: ${{ env.PROCEED == 'true' }} - uses: actions/upload-artifact@v3 - with: - name: backup-test-results-${{ steps.get-backup.outputs.id }} - path: results.txt - retention-days: 90 - - - name: Delete temporary instance - if: ${{ env.PROCEED == 'true' }} - run: | - gcloud sql instances delete --quiet \ - ${{ steps.create-temp-instance.outputs.temp_instance_name }} - - - name: Notify results by email - if: ${{ env.PROCEED == 'true' }} - uses: licenseware/send-email-notification@v1 - with: - api-key: "***REMOVED***" - # api-key: ${{ secrets.SENDGRID_API_KEY }} - from-email: no-reply@lifelike.bio - to-email: darede@biosustain.dtu.dk - # to-email: ${{ secrets.BACKUP_TEST_NOTIFY_EMAILS }} - subject: "Lifelike DB backup test passed for ${{ matrix.instance }} - ${{ matrix.type }}" - markdown-body: | - # Lifelike PostgreSQL backup test results - - ## Test result: ✅ PASSED - - ## Details - - - Cloud SQL instance name: **${{ matrix.instance }}** - - Backup date: **${{ steps.get-backup.outputs.date }}** - - Backup type: **${{ matrix.type }}** - - Backup ID: **${{ steps.get-backup.outputs.id }}** - - Workflow run ID: [**${{ github.run_id }}**](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}) - - ## Database queries - - ``` - $(cat results.txt) - ``` - - --- - - See the workflow run [at GitHub](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}). diff --git a/.github/workflows/cloud-sql-backup-ondemand.yml b/.github/workflows/cloud-sql-backup-ondemand.yml deleted file mode 100644 index 890dc9461e..0000000000 --- a/.github/workflows/cloud-sql-backup-ondemand.yml +++ /dev/null @@ -1,36 +0,0 @@ -name: Backup Cloud SQL on-demand - -on: - workflow_dispatch: - inputs: - cloud_sql_instance_name: - description: Google Cloud SQL instance name - required: true - type: string - backup_description: - description: Backup description - required: false - default: On-demand backup from GitHub workflow - type: string - secrets: - GCE_SA_KEY: - required: true - -jobs: - backup: - name: Backup Cloud SQL instance - runs-on: ubuntu-latest - outputs: - backup_id: ${{ steps.backup.outputs.backup_id }} - - steps: - - uses: actions/checkout@v3 - - name: Create a new Clod SQL instance backup - id: backup - uses: ./.github/actions/cloud-sql-backup - with: - gcp_credentials: "${{ secrets.GCE_SA_KEY }}" - cloud_sql_instance_name: "${{ github.event.inputs.cloud_sql_instance_name }}" - backup_description: "${{ github.event.inputs.backup_description }}" - - run: | - echo "## Backup created: ${{ steps.backup.outputs.backup_id }}" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/deployment-az-public.yml b/.github/workflows/deployment-az-public.yml deleted file mode 100644 index 0347495991..0000000000 --- a/.github/workflows/deployment-az-public.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: Azure Public Deployment - -on: - workflow_dispatch: - push: - tags: [public] - branches: [public/**] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-az.yml - with: - environment_name: public - client_config: production - cloud_sql_instance_name: lifelike-public - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-az-staging.yml b/.github/workflows/deployment-az-staging.yml deleted file mode 100644 index d7e2c2525e..0000000000 --- a/.github/workflows/deployment-az-staging.yml +++ /dev/null @@ -1,20 +0,0 @@ -name: Azure Staging Deployment - -on: - workflow_dispatch: - push: - tags: [staging-az] - branches: [staging-az/**] - -jobs: - call-deployment-az: - uses: ./.github/workflows/deployment-az.yml - with: - environment_name: staging-az - client_config: production - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-az.yml b/.github/workflows/deployment-az.yml deleted file mode 100644 index f2cb12a9bd..0000000000 --- a/.github/workflows/deployment-az.yml +++ /dev/null @@ -1,111 +0,0 @@ -name: Lifelike Azure deployment - -on: - workflow_call: - inputs: - environment_name: - description: Environment name (prod, staging, qa or demo) - required: true - type: string - client_config: - description: Client Runtime configuration preset - required: true - default: production - type: string - container_registry: - description: Container registry name - required: false - default: lifelike.azurecr.io - type: string - secrets: - CONTAINER_REGISTRY_USERNAME: - required: true - CONTAINER_REGISTRY_PASSWORD: - required: true - VAULT_PASSWORD: - required: true - SSH_KEY: - required: true - INFRA_PAT: - required: true - -jobs: - # ------------------------------------------------------------- - # JOB: Build Docker images - # ------------------------------------------------------------- - build: - name: Build - runs-on: ubuntu-latest - strategy: - matrix: - include: - - image: kg-webserver - path: ./client - build_extra_args: --build-arg ANGULAR_CONFIG=${{ inputs.client_config }} --build-arg CLIENT_VERSION=${{ github.sha }} - - image: kg-appserver - path: ./appserver - - image: kg-cache-service - path: ./cache-invalidator - - image: kg-statistical-enrichment - path: ./statistical-enrichment - - image: filebeat - path: ./filebeat - - image: metricbeat - path: ./metricbeat - - steps: - - uses: actions/checkout@v3 - - name: Build and push ${{ matrix.image }} image - uses: whoan/docker-build-with-cache-action@v5 - with: - context: ${{ matrix.path }} - image_name: ${{ matrix.image }} - image_tag: ${{ github.sha }},${{ inputs.environment_name }},latest - build_extra_args: ${{ matrix.build_extra_args }} - registry: ${{ inputs.container_registry }} - username: ${{ secrets.CONTAINER_REGISTRY_USERNAME }} - password: ${{ secrets.CONTAINER_REGISTRY_PASSWORD }} - dockerfile: ./Dockerfile - - # ------------------------------------------------------------- - # JOB: Deploy to AZ environment using Ansible playbook - # pointed by the Git submodule: /deployment - # ------------------------------------------------------------- - deploy: - name: Deploy - needs: - - build - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v3 - with: - token: ${{ secrets.INFRA_PAT }} - submodules: recursive - - - name: Set git metadata - id: git-meta - run: | - echo ::set-output name=commit_timestamp::$(git log -1 --format=%cI) - echo ::set-output name=build_number::$(git rev-list --count HEAD) - echo ::set-output name=build_version::$(echo "${GITHUB_REF#refs/*/}") - - - name: Run Ansible deployment action - uses: ./.github/actions/ansible - with: - workspace_dir: deployment/ansible - playbook_file_path: playbooks/deploy-azure.yml - inventory_file_path: inventories/hosts-az.yml - vault_password: ${{ secrets.VAULT_PASSWORD }} - ssh_key: ${{ secrets.SSH_KEY }} - options: | - --extra-vars environment_name=${{ inputs.environment_name }} - --extra-vars client_config=${{ inputs.client_config }} - --extra-vars docker_img_hash=${{ github.sha }} - --extra-vars git_timestamp=${{ steps.git-meta.outputs.commit_timestamp }} - --extra-vars app_build_number=${{ steps.git-meta.outputs.build_number }} - --extra-vars app_version=${{ steps.git-meta.outputs.build_version }} - --extra-vars github_run_id=${{ github.run_id }} - --user ansible - --verbose diff --git a/.github/workflows/deployment-contabo-ucsd.yml b/.github/workflows/deployment-contabo-ucsd.yml deleted file mode 100644 index 2251acc3ee..0000000000 --- a/.github/workflows/deployment-contabo-ucsd.yml +++ /dev/null @@ -1,20 +0,0 @@ -name: Contabo UCSD Deployment - -on: - workflow_dispatch: - push: - tags: [ucsd] - branches: [ucsd/**] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-contabo.yml - with: - environment_name: ucsd - client_config: production - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-contabo.yml b/.github/workflows/deployment-contabo.yml deleted file mode 100644 index 041064b423..0000000000 --- a/.github/workflows/deployment-contabo.yml +++ /dev/null @@ -1,113 +0,0 @@ -name: Lifelike Contabo deployment - -on: - workflow_call: - inputs: - environment_name: - description: Environment name - required: true - type: string - client_config: - description: Client Runtime configuration preset - required: true - default: production - type: string - container_registry: - description: Container registry name - required: false - default: lifelike.azurecr.io - type: string - secrets: - CONTAINER_REGISTRY_USERNAME: - required: true - CONTAINER_REGISTRY_PASSWORD: - required: true - VAULT_PASSWORD: - required: true - SSH_KEY: - required: true - GCP_CREDENTIALS: - required: true - INFRA_PAT: - required: true - -jobs: - # ------------------------------------------------------------- - # JOB: Build Docker images - # ------------------------------------------------------------- - build: - name: Build - runs-on: ubuntu-latest - strategy: - matrix: - include: - - image: kg-webserver - path: ./client - build_extra_args: --build-arg ANGULAR_CONFIG=${{ inputs.client_config }} --build-arg CLIENT_VERSION=${{ github.sha }} - - image: kg-appserver - path: ./appserver - - image: kg-cache-service - path: ./cache-invalidator - - image: kg-statistical-enrichment - path: ./statistical-enrichment - - image: filebeat - path: ./filebeat - - image: metricbeat - path: ./metricbeat - - steps: - - uses: actions/checkout@v3 - - name: Build and push ${{ matrix.image }} image - uses: whoan/docker-build-with-cache-action@v5 - with: - context: ${{ matrix.path }} - image_name: ${{ matrix.image }} - image_tag: ${{ github.sha }},${{ inputs.environment_name }},latest - build_extra_args: ${{ matrix.build_extra_args }} - registry: ${{ inputs.container_registry }} - username: ${{ secrets.CONTAINER_REGISTRY_USERNAME }} - password: ${{ secrets.CONTAINER_REGISTRY_PASSWORD }} - dockerfile: ./Dockerfile - - # ------------------------------------------------------------- - # JOB: Deploy to Contabo environment using Ansible playbook - # pointed by the Git submodule: /deployment - # ------------------------------------------------------------- - deploy: - name: Deploy - needs: - - build - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v3 - with: - token: ${{ secrets.INFRA_PAT }} - submodules: recursive - - - name: Set git metadata - id: git-meta - run: | - echo ::set-output name=commit_timestamp::$(git log -1 --format=%cI) - echo ::set-output name=build_number::$(git rev-list --count HEAD) - echo ::set-output name=build_version::$(echo "${GITHUB_REF#refs/*/}") - - - name: Run Ansible deployment action - uses: ./.github/actions/ansible - with: - workspace_dir: deployment/ansible - playbook_file_path: playbooks/deploy-contabo.yml - inventory_file_path: inventories/hosts-contabo.yml - vault_password: ${{ secrets.VAULT_PASSWORD }} - ssh_key: ${{ secrets.SSH_KEY }} - options: | - --extra-vars environment_name=${{ inputs.environment_name }} - --extra-vars client_config=${{ inputs.client_config }} - --extra-vars docker_img_hash=${{ github.sha }} - --extra-vars git_timestamp=${{ steps.git-meta.outputs.commit_timestamp }} - --extra-vars app_build_number=${{ steps.git-meta.outputs.build_number }} - --extra-vars app_version=${{ steps.git-meta.outputs.build_version }} - --extra-vars github_run_id=${{ github.run_id }} - --user ansible - --verbose diff --git a/.github/workflows/deployment-gcp-demo.yml b/.github/workflows/deployment-gcp-demo.yml deleted file mode 100644 index b673c5c93d..0000000000 --- a/.github/workflows/deployment-gcp-demo.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: GCP Demo Deployment - -on: - workflow_dispatch: - push: - tags: [demo] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-gcp.yml - with: - environment_name: demo - client_config: demo - cloud_sql_instance_name: kg-demo - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - GCP_CREDENTIALS: ${{ secrets.GCE_SA_KEY }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-gcp-prod.yml b/.github/workflows/deployment-gcp-prod.yml deleted file mode 100644 index 4d86fab703..0000000000 --- a/.github/workflows/deployment-gcp-prod.yml +++ /dev/null @@ -1,23 +0,0 @@ -name: GCP Prod Deployment - -on: - workflow_dispatch: - release: - types: [released] - push: - tags: [prod] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-gcp.yml - with: - environment_name: prod - client_config: production - cloud_sql_instance_name: lifelike-prod - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - GCP_CREDENTIALS: ${{ secrets.GCE_SA_KEY }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-gcp-public.yml b/.github/workflows/deployment-gcp-public.yml deleted file mode 100644 index cfaf35aa95..0000000000 --- a/.github/workflows/deployment-gcp-public.yml +++ /dev/null @@ -1,22 +0,0 @@ -name: GCP Public Deployment - -on: - workflow_dispatch: - push: - tags: [public] - branches: [public/**] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-gcp.yml - with: - environment_name: public - client_config: production - cloud_sql_instance_name: lifelike-public - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - GCP_CREDENTIALS: ${{ secrets.GCE_SA_KEY }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-gcp-qa.yml b/.github/workflows/deployment-gcp-qa.yml deleted file mode 100644 index af46d79f4e..0000000000 --- a/.github/workflows/deployment-gcp-qa.yml +++ /dev/null @@ -1,22 +0,0 @@ -name: GCP QA Deployment - -on: - workflow_dispatch: - push: - branches: [master] - tags: [qa] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-gcp.yml - with: - environment_name: qa - client_config: qa - cloud_sql_instance_name: lifelike-qa - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - GCP_CREDENTIALS: ${{ secrets.GCE_SA_KEY }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-gcp-staging.yml b/.github/workflows/deployment-gcp-staging.yml deleted file mode 100644 index f90e923c57..0000000000 --- a/.github/workflows/deployment-gcp-staging.yml +++ /dev/null @@ -1,22 +0,0 @@ -name: GCP Staging Deployment - -on: - workflow_dispatch: - push: - tags: [staging] - branches: [staging/**] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/deployment-gcp.yml - with: - environment_name: staging - client_config: staging - cloud_sql_instance_name: kg-staging - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} - CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - GCP_CREDENTIALS: ${{ secrets.GCE_SA_KEY }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-gcp.yml b/.github/workflows/deployment-gcp.yml deleted file mode 100644 index a5ab0c6ce9..0000000000 --- a/.github/workflows/deployment-gcp.yml +++ /dev/null @@ -1,159 +0,0 @@ -name: Lifelike GCP deployment - -on: - workflow_call: - inputs: - environment_name: - description: Environment nme (prod, staging, qa or demo) - required: true - type: string - client_config: - description: Client Runtime configuration preset - required: true - default: production - type: string - container_registry: - description: Container registry name - required: false - default: lifelike.azurecr.io - type: string - cloud_sql_instance_name: - description: Google Cloud SQL instance name - required: true - type: string - cloud_sql_force_backup: - description: Backup before deploying even if no migrations need to be run - required: false - default: false - type: boolean - secrets: - CONTAINER_REGISTRY_USERNAME: - required: true - CONTAINER_REGISTRY_PASSWORD: - required: true - VAULT_PASSWORD: - required: true - SSH_KEY: - required: true - GCP_CREDENTIALS: - required: true - INFRA_PAT: - required: true - -jobs: - # ------------------------------------------------------------- - # JOB: Build Docker images - # ------------------------------------------------------------- - build: - name: Build - runs-on: ubuntu-latest - strategy: - matrix: - include: - - image: kg-webserver - path: ./client - build_extra_args: --build-arg ANGULAR_CONFIG=${{ inputs.client_config }} --build-arg CLIENT_VERSION=${{ github.sha }} - - image: kg-appserver - path: ./appserver - - image: kg-cache-service - path: ./cache-invalidator - - image: kg-statistical-enrichment - path: ./statistical-enrichment - - image: filebeat - path: ./filebeat - - image: metricbeat - path: ./metricbeat - - steps: - - uses: actions/checkout@v3 - - name: Build and push ${{ matrix.image }} image - uses: whoan/docker-build-with-cache-action@v5 - with: - context: ${{ matrix.path }} - image_name: ${{ matrix.image }} - image_tag: ${{ github.sha }},${{ inputs.environment_name }},latest - build_extra_args: ${{ matrix.build_extra_args }} - registry: ${{ inputs.container_registry }} - username: ${{ secrets.CONTAINER_REGISTRY_USERNAME }} - password: ${{ secrets.CONTAINER_REGISTRY_PASSWORD }} - dockerfile: ./Dockerfile - - # --------------------------------------------- - # JOB: Backup DB - # --------------------------------------------- - cloud-sql-backup: - name: Backup Cloud SQL instance - needs: build - outputs: - backup_id: ${{ steps.backup.outputs.backup_id }} - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v3 - - name: Create a new Clod SQL instance backup - id: backup - uses: ./.github/actions/cloud-sql-backup - with: - gcp_credentials: "${{ secrets.GCP_CREDENTIALS }}" - cloud_sql_instance_name: "${{ inputs.cloud_sql_instance_name }}" - backup_description: "Automated backup from GitHub workflow. Run ID: ${{ github.run_id }}" - - # ------------------------------------------------------------- - # JOB: Deploy to GCP environment using Ansible playbook - # pointed by the Git submodule: /deployment - # ------------------------------------------------------------- - deploy: - name: Deploy - needs: - - build - - cloud-sql-backup - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v3 - with: - token: ${{ secrets.INFRA_PAT }} - submodules: recursive - - - name: Set git metadata - id: git-meta - run: | - echo ::set-output name=commit_timestamp::$(git log -1 --format=%cI) - echo ::set-output name=build_number::$(git rev-list --count HEAD) - echo ::set-output name=build_version::$(echo "${GITHUB_REF#refs/*/}") - - - name: Authenticate to GCP - id: auth - uses: google-github-actions/auth@v0 - with: - credentials_json: "${{ secrets.GCP_CREDENTIALS }}" - - uses: google-github-actions/setup-gcloud@v0 - - - name: Get Cloud SQL instance private IP address - id: database-host - run: | - echo ::set-output name=ip_address::$( \ - gcloud sql instances describe --format=json \ - ${{ inputs.cloud_sql_instance_name }} \ - | jq -r '.ipAddresses[] | select(.type == "PRIVATE").ipAddress') - - - name: Run Ansible deployment action - uses: ./.github/actions/ansible - with: - workspace_dir: deployment/ansible - playbook_file_path: playbooks/deploy-gcloud.yml - inventory_file_path: inventories/hosts.yml - vault_password: ${{ secrets.VAULT_PASSWORD }} - ssh_key: ${{ secrets.SSH_KEY }} - options: | - --extra-vars environment_name=${{ inputs.environment_name }} - --extra-vars client_config=${{ inputs.client_config }} - --extra-vars docker_img_hash=${{ github.sha }} - --extra-vars git_timestamp=${{ steps.git-meta.outputs.commit_timestamp }} - --extra-vars app_build_number=${{ steps.git-meta.outputs.build_number }} - --extra-vars app_version=${{ steps.git-meta.outputs.build_version }} - --extra-vars github_run_id=${{ github.run_id }} - --extra-vars postgres_host=${{ steps.database-host.outputs.ip_address }} - --user ansible - -vvvv diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml deleted file mode 100644 index ac173f1076..0000000000 --- a/.github/workflows/docker.yml +++ /dev/null @@ -1,69 +0,0 @@ -name: Docker images - -on: - push: - branches: - - main - tags: - - v* - pull_request: - branches: - - main -env: - REGISTRY: ghcr.io - REPOSITORY: ${{ github.repository }} - -jobs: - publish-images: - name: Publish ${{ matrix.name }} Docker image - runs-on: ubuntu-latest - - strategy: - fail-fast: false - matrix: - include: - - name: appserver - path: appserver - - name: frontend - path: client - # - name: elasticsearch - # path: docker - # file: docker/elasticsearch.Dockerfile - # - name: Grap data migrator - # path: graph-db - # image: lifelike-graph-db - - permissions: - contents: read - packages: write - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - - name: Log in to the Container registry - uses: docker/login-action@v1 - with: - registry: ${{ env.REGISTRY }} - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - - - name: Extract metadata (tags, labels) for Docker - id: meta - uses: docker/metadata-action@v3 - with: - images: ${{ env.REGISTRY }}/${{ env.REPOSITORY }}-${{ matrix.name }} - tags: | - type=ref,event=branch - type=ref,event=pr - type=semver,pattern={{version}} - type=semver,pattern={{major}}.{{minor - - - name: Build and push ${{ env.REGISTRY }}/${{ env.REPOSITORY }}-${{ matrix.name }} image - uses: docker/build-push-action@v2 - with: - context: ${{ matrix.path }} - file: ${{ matrix.file }} - tags: ${{ steps.meta.outputs.tags }} - labels: ${{ steps.meta.outputs.labels }} - push: true diff --git a/.github/workflows/graphdb-migrate.yml b/.github/workflows/graphdb-migrate.yml deleted file mode 100644 index de9d842f48..0000000000 --- a/.github/workflows/graphdb-migrate.yml +++ /dev/null @@ -1,84 +0,0 @@ -name: Grpah DB Migrate - -on: - workflow_dispatch: - inputs: - neo4j_host: - description: Neo4j target host - type: string - required: true - neo4j_username: - description: Neo4j username - type: string - required: true - default: neo4j - neo4j_password: - description: Neo4j password - type: string - required: true - log_level: - description: Log level - type: choice - required: true - default: info - options: - - debug - - info - - warn - - error - release_lock: - description: Release any present lock before executing - type: boolean - required: true - default: true - datafiles_prefix: - description: Prefix of the datafiles in remote storage (stage/prod) - type: choice - required: true - default: stage - options: - - stage - - prod - chunk_size: - description: Liquibase transaction chunk size - type: string - required: true - default: '2000' - changelog: - description: Path to the changelog file - type: string - required: true - default: 'lifelike-graph/changelog-master.xml' - migrator_image_tag: - description: Tag of the graphdb-migrator image to use - type: string - required: true - default: latest - -jobs: - migrate: - name: Migrate Neo4j DB - runs-on: self-hosted - timeout-minutes: 360 - container: - image: ghcr.io/sbrg/lifelike-graphdb-migrator:${{ github.event.inputs.migrator_image_tag }} - options: --user root - env: - NEO4J_HOST: ${{ github.event.inputs.neo4j_host }} - NEO4J_USERNAME: ${{ github.event.inputs.neo4j_username }} - NEO4J_PASSWORD: ${{ github.event.inputs.neo4j_password }} - LOG_LEVEL: ${{ github.event.inputs.log_level }} - CHANGELOG_FILE: ${{ github.event.inputs.changelog }} - DATAFILES_PREFIX: ${{ github.event.inputs.datafiles_prefix }} - AZURE_ACCOUNT_STORAGE_KEY: ${{ secrets.AZURE_ACCOUNT_STORAGE_KEY }} - AZURE_ACCOUNT_STORAGE_NAME: ${{ secrets.AZURE_ACCOUNT_STORAGE_NAME }} - CHUNK_SIZE: ${{ github.event.inputs.chunk_size }} - steps: - - uses: actions/checkout@v2 - - name: Copy changelog files - run: cp -rp graph-db/changelog/* /liquibase/changelog/ - - name: Release previous lock - if: ${{ github.event.inputs.release_lock }} - run: /docker-entrypoint.sh releaseLocks - - name: Run Liquibase migrations - run: /docker-entrypoint.sh update diff --git a/.github/workflows/integration-tests.yml b/.github/workflows/integration-tests.yml index b100f06f55..05d76760b0 100644 --- a/.github/workflows/integration-tests.yml +++ b/.github/workflows/integration-tests.yml @@ -21,17 +21,6 @@ jobs: - uses: actions/checkout@v3 - - name: Build appserver image - uses: whoan/docker-build-with-cache-action@v5 - with: - username: ${{ secrets.AZURE_CR_USERNAME }} - password: ${{ secrets.AZURE_CR_PASSWORD }} - registry: lifelike.azurecr.io - image_name: kg-appserver - image_tag: ${{ github.sha }} - context: ./appserver - dockerfile: ./Dockerfile - - name: Create environment variable to pass in GitHub hash for Docker Compose run: echo "GITHUB_HASH=${{ github.sha }}" >> .env diff --git a/.github/workflows/traefik-az.yml b/.github/workflows/traefik-az.yml deleted file mode 100644 index 2eca1579eb..0000000000 --- a/.github/workflows/traefik-az.yml +++ /dev/null @@ -1,18 +0,0 @@ -name: Azure Traefik deployment - -on: - workflow_dispatch: - push: - tags: [traefik-az] - branches: [traefik-az/**] - -jobs: - call-deployment-gcp: - uses: ./.github/workflows/traefik.yml - with: - playbook_path: playbooks/proxy-azure.yml - inventory_path: inventories/hosts-az.yml - secrets: - VAULT_PASSWORD: ${{ secrets.ANSIBLE_VAULT }} - SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} - INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/traefik.yml b/.github/workflows/traefik.yml deleted file mode 100644 index e5c6367820..0000000000 --- a/.github/workflows/traefik.yml +++ /dev/null @@ -1,46 +0,0 @@ -name: Lifelike Traefik deployment - -on: - workflow_call: - inputs: - playbook_path: - description: File path to Ansible playbook - required: true - type: string - inventory_path: - description: File path to Ansible inventory - required: true - type: string - secrets: - VAULT_PASSWORD: - required: true - SSH_KEY: - required: true - INFRA_PAT: - required: true - -jobs: - deploy: - name: Deploy - needs: - - build - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v3 - with: - token: ${{ secrets.INFRA_PAT }} - submodules: recursive - - - name: Run Ansible deployment action - uses: ./.github/actions/ansible - with: - workspace_dir: deployment/ansible - playbook_file_path: ${{ inputs.playbook_path }} - inventory_file_path: ${{ inputs.inventory_path }} - vault_password: ${{ secrets.VAULT_PASSWORD }} - ssh_key: ${{ secrets.SSH_KEY }} - options: | - --user ansible - --verbose diff --git a/.gitignore b/.gitignore index 62a9d48bb5..1147a0ce50 100755 --- a/.gitignore +++ b/.gitignore @@ -88,4 +88,4 @@ arangodb/data/* arangodb/apps/* # Arango seed data -arangodb/bin/seed_data \ No newline at end of file +arangodb/bin/seed_data diff --git a/.gitmodules b/.gitmodules index 98bab4898e..e69de29bb2 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,13 +0,0 @@ -[submodule "lifelike-oss"] - path = lifelike-oss - url = https://github.com/SBRG/lifelike -[submodule "keycloak"] - path = keycloak - url = https://github.com/SBRG/lifelike-keycloak -[submodule "website"] - path = website - url = https://github.com/SBRG/lifelike-website -[submodule "deployment"] - path = deployment - url = git@github.com:SBRG/lifelike-infra.git - branch = ansible diff --git a/README.md b/README.md index f5abb35137..29cbaf7fff 100644 --- a/README.md +++ b/README.md @@ -120,7 +120,7 @@ Lifelike is a distributed system comprised of the following components: ### Backing services - **PostgreSQL** as a RDBMS. -- **Neo4j** as a graph database. +- **ArangoDB** as a graph database. - **Elasticsearch** as a full-text search engine. - **Redis** as a key-value cache store. - **PDFParser** as a document parsing library. diff --git a/appserver/Dockerfile b/appserver/Dockerfile index 66b2431483..7b1380edd7 100644 --- a/appserver/Dockerfile +++ b/appserver/Dockerfile @@ -1,7 +1,7 @@ # ======================================== # Base image # ======================================== -FROM python:3.10-slim as base +FROM python:3.9-slim as base ENV LANG C.UTF-8 ENV LC_ALL C.UTF-8 @@ -82,12 +82,12 @@ ENV POSTGRES_USER=postgres ENV POSTGRES_PASSWORD=postgres ENV POSTGRES_DB=postgres -# Neo4j configuration -ENV NEO4J_HOST=neo4j -ENV NEO4J_PORT=7687 -ENV NEO4J_AUTH=neo4j/password -ENV NEO4J_DATABASE=neo4j -ENV NEO4J_SCHEME=bolt +# ArangoDB configuration +ENV ARANGODB_HOST=arangodb +ENV ARANGODB_PORT=7687 +ENV ARANGODB_AUTH=arangodb/password +ENV ARANGODB_DATABASE=arangodb +ENV ARANGODB_SCHEME=bolt # Elasticsearch configuration ENV ELASTICSEARCH_URL=http://elasticsearch:9200 @@ -129,5 +129,5 @@ EXPOSE $PORT HEALTHCHECK --start-period=30s \ CMD curl -f localhost:$PORT/meta || exit 1 -RUN chmod +x bin/docker-entrypoint.sh -ENTRYPOINT ["bin/docker-entrypoint.sh"] +RUN chmod +x bin/startup.sh +ENTRYPOINT ["bin/startup.sh"] diff --git a/appserver/Pipfile b/appserver/Pipfile index b1286c1a99..6b16e584b0 100644 --- a/appserver/Pipfile +++ b/appserver/Pipfile @@ -53,7 +53,6 @@ paramiko = "==2.7.2" google-cloud-storage = "==1.36.1" fastjsonschema = "==2.15.0" marshmallow-dataclass = "==8.3.1" -marshmallow-enum = "==1.5.1" deepdiff = "==5.2.3" timeflake = "==0.3.3" scipy = "==1.6.1" @@ -61,7 +60,6 @@ statsmodels = "==0.12.2" sqlalchemy = "==1.3.23" azure-storage-file = "==2.1.0" azure-storage-blob = "==12.8.0" -neo4j = "==4.2.1" python-magic = "==0.4.22" httpretty = "==1.0.5" sendgrid = "==6.7.0" @@ -79,6 +77,7 @@ openai = "*" types-cachetools = "*" mypy = "==0.981" pyyaml = "==6.0.1" +marshmallow-enum = "*" [requires] python_version = "3.9" diff --git a/appserver/Pipfile.lock b/appserver/Pipfile.lock index 7647f4ee56..0280160e85 100644 --- a/appserver/Pipfile.lock +++ b/appserver/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "e8e18968eada4f4eba2a7ea35293b9f680b6e0a10413292556849adaa5ea1a61" + "sha256": "723e0fba23007871efc048ff1ab5a6333defdd4688df64ab94c5cca1c6e8bb34" }, "pipfile-spec": 6, "requires": { @@ -16,138 +16,45 @@ ] }, "default": { - "aiohttp": { - "hashes": [ - "sha256:03543dcf98a6619254b409be2d22b51f21ec66272be4ebda7b04e6412e4b2e14", - "sha256:03baa76b730e4e15a45f81dfe29a8d910314143414e528737f8589ec60cf7391", - "sha256:0a63f03189a6fa7c900226e3ef5ba4d3bd047e18f445e69adbd65af433add5a2", - "sha256:10c8cefcff98fd9168cdd86c4da8b84baaa90bf2da2269c6161984e6737bf23e", - "sha256:147ae376f14b55f4f3c2b118b95be50a369b89b38a971e80a17c3fd623f280c9", - "sha256:176a64b24c0935869d5bbc4c96e82f89f643bcdf08ec947701b9dbb3c956b7dd", - "sha256:17b79c2963db82086229012cff93ea55196ed31f6493bb1ccd2c62f1724324e4", - "sha256:1a45865451439eb320784918617ba54b7a377e3501fb70402ab84d38c2cd891b", - "sha256:1b3ea7edd2d24538959c1c1abf97c744d879d4e541d38305f9bd7d9b10c9ec41", - "sha256:22f6eab15b6db242499a16de87939a342f5a950ad0abaf1532038e2ce7d31567", - 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"sha256:794f385653e2b749387a42afb1e14c2135e18daeb027e0d97162e4b7031210f8", - "sha256:8ad21d4c9d3673726cf986ea1d0c9fb66905258709550ddf7944c8f885f208be", - "sha256:8e8e49aa9cc23aa4c926dc200ce32959d3501c4905147a66ce032f05cb5ecb92", - "sha256:9f362470a3480165c4c6151786b5379351b790d56952005be18bdbdd4c7ce0ae", - "sha256:a16a0145d6d7d00fbede2da3a3096dcc9ecea091adfa8da48fa6a7b75d35562d", - "sha256:ad77c13037d3402fbeffda07d51e3f228ba078d1c7096a73759c9419ea031bf4", - "sha256:b6ede64e52257931315826fdbfc6ea878d89a965580d1a65638ef77cb551f56d", - "sha256:c9e0efb95ed6ca1654951bd5ec2f3fa91b295d78bf6527e026529d4aaa1e0c30", - "sha256:ce65f70b14a21fdac84c294cde75e6dbdabbcff22975335e20827b3b94bdbf49", - "sha256:d1debb09043e1f5ee845fa1e96d180e89115b30e47c5d3ce53bc967bab53f62d", - "sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", - "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", - "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", - "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", - "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", - "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" - ], - "index": "pypi", - "version": "==0.981" - }, - "mypy-extensions": { - "hashes": [ - "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d", - "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8" + "sha256:686b06abe565edfab151cb8fd385a05651e1fdf8f0a14191e4439283421f8684", + "sha256:8fccb480c43d3e99a00087634c06dd02b0d50fbf088b380de5a41a015ec239e1" ], - "version": "==0.4.3" + "markers": "python_version >= '3.8'", + "version": "==10.2.0" }, "packaging": { "hashes": [ - "sha256:714ac14496c3e68c99c29b00845f7a2b85f3bb6f1078fd9f72fd20f0570002b2", - "sha256:b6ad297f8907de0fa2fe1ccbd26fdaf387f5f47c7275fedf8cce89f99446cf97" + "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5", + "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9" ], "markers": "python_version >= '3.7'", - "version": "==23.0" + "version": "==24.0" }, "pluggy": { "hashes": [ @@ -2453,6 +2231,7 @@ "sha256:c389c1d06bf7904078ca03399a4816f974a1d590090fecea0c63ec26ebaf1cef" ], "index": "pypi", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.7.0" }, "pyflakes": { @@ -2469,6 +2248,7 @@ "sha256:ff615c761e25eb25df19edddc0b970302d2a9091fbce0e7213298d85fb61fef6" ], "index": "pypi", + "markers": "python_version >= '3.5'", "version": "==5.3.5" }, "redis": { @@ -2477,14 +2257,19 @@ "sha256:6d65e84bc58091140081ee9d9c187aab0480097750fac44239307a3bdf0b1251" ], "index": "pypi", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", "version": "==3.5.2" }, "requests": { + "extras": [ + "socks" + ], "hashes": [ "sha256:27973dd4a904a4f13b263a19c866c13b92a39ed1c964655f025f3f8d3d75b804", "sha256:c210084e36a42ae6b9219e00e48287def368a26d03a048ddad7bfee44f75871e" ], "index": "pypi", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", "version": "==2.25.1" }, "responses": { @@ -2493,15 +2278,16 @@ "sha256:b82502eb5f09a0289d8e209e7bad71ef3978334f56d09b444253d5ad67bf5253" ], "index": "pypi", + "markers": "python_version >= '3.7'", "version": "==0.21.0" }, "setuptools": { "hashes": [ - "sha256:a78d01d1e2c175c474884671dde039962c9d74c7223db7369771fcf6e29ceeab", - "sha256:bd6eb2d6722568de6d14b87c44a96fac54b2a45ff5e940e639979a3d1792adb6" + "sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e", + "sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c" ], - "markers": "python_version >= '3.7'", - "version": "==66.0.0" + "markers": "python_version >= '3.8'", + "version": "==69.2.0" }, "six": { "hashes": [ @@ -2518,14 +2304,6 @@ ], "version": "==2.4.0" }, - "toml": { - "hashes": [ - "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b", - "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f" - ], - "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'", - "version": "==0.10.2" - }, "types-cryptography": { "hashes": [ "sha256:09cc53f273dd4d8c29fa7ad11fefd9b734126d467960162397bc5e3e604dea75", @@ -2565,28 +2343,20 @@ "index": "pypi", "version": "==2.25.8" }, - "typing-extensions": { - "hashes": [ - "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa", - "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e" - ], - "markers": "python_version >= '3.7'", - "version": "==4.4.0" - }, "urllib3": { "hashes": [ - "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72", - "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1" + "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07", + "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0" ], "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", - "version": "==1.26.14" + "version": "==1.26.18" }, "wcwidth": { "hashes": [ - "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e", - "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0" + "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859", + "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5" ], - "version": "==0.2.6" + "version": "==0.2.13" } } } diff --git a/appserver/bin/docker-entrypoint.sh b/appserver/bin/docker-entrypoint.sh deleted file mode 100755 index feb2d11530..0000000000 --- a/appserver/bin/docker-entrypoint.sh +++ /dev/null @@ -1,43 +0,0 @@ -#!/bin/bash -## This scripts serves as the Docker entrypoint. -## If any command is specified, it runs it as is, -## else, it runs the appserver Flask application. - -set -e - -if [ "$1" ]; then - ## A command is specified, then run it. - exec "$@" -else - if [ "$MIGRATE_DB" ]; then - ## If $MIGRATE_DB is set, wait for PostgreSQL and run any required migrations. - while ! curl $POSTGRES_HOST:$POSTGRES_PORT 2>&1 | grep '52'; do - echo "Waiting for PostgreSQL to be available in $POSTGRES_HOST:$POSTGRES_PORT" - sleep 5; - done - echo "PostreSQL is ready. Executing DB migrations now" - flask db upgrade --x-arg data_migrate="True" - echo "Finished executing DB migrations" - fi - - ## Create initial user if $INITIAL_ADMIN_EMAIL is set. - if [ "$INITIAL_ADMIN_EMAIL" ]; then - echo "Trying to create initial admin user: $INITIAL_ADMIN_EMAIL" - flask create-user "Admin" "$INITIAL_ADMIN_EMAIL" > /dev/null 2>&1 || true - flask set-role "$INITIAL_ADMIN_EMAIL" "admin" > /dev/null 2>&1 || true - fi - - ## Run the Flask appserver app, using the built-in development Flask server, - ## or gunicron WSGI server if the $FLASK_ENV is not set to development. - if [ "${FLASK_ENV}" = "development" ]; then - flask run -h 0.0.0.0 -p ${PORT:-5000} - else - gunicorn \ - -b 0.0.0.0:${PORT:-5000} \ - --workers=${GUNICORN_WORKERS:-9} \ - --threads=${GUNICORN_THREADS:-10} \ - --timeout=${GUNICORN_TIMEOUT:-300} \ - --max-requests=${GUNICORN_MAX_REQUESTS:-120} \ - app:app - fi -fi diff --git a/appserver/bin/startup.sh b/appserver/bin/startup.sh index 87179382d4..53c67775f1 100755 --- a/appserver/bin/startup.sh +++ b/appserver/bin/startup.sh @@ -8,7 +8,7 @@ if [ "${FLASK_ENV}" = "development" ] && [ "${FLASK_APP_CONFIG}" = "Development" __dir__="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" # wait for postgres timeout 300 ${__dir__}/wait-for-postgres - # wait for neo4j + # wait for arangodb timeout 300 ${__dir__}/wait-for-arango #wait for elastic timeout 300 ${__dir__}/wait-for-elastic diff --git a/appserver/bin/wait-for-neo4j b/appserver/bin/wait-for-neo4j deleted file mode 100755 index c85c5339b8..0000000000 --- a/appserver/bin/wait-for-neo4j +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -echo "Waiting for Neo4J" - -NEO4J_STATUS="000" - -until [ "$NEO4J_STATUS" = "200" ] -do - NEO4J_STATUS=`curl -s -o /dev/null -I -w "%{http_code}" http://${NEO4J_HOST}:7474` - echo "Status of Neo4J: $NEO4J_STATUS" - sleep 2 -done - -# Run command | https://docs.docker.com/compose/startup-order/ ->&2 echo "Neo4j started - executing command" -exec $@ diff --git a/appserver/config.py b/appserver/config.py index 3f01a758f0..c094e85bb1 100644 --- a/appserver/config.py +++ b/appserver/config.py @@ -29,12 +29,6 @@ class Base: POSTGRES_PASSWORD = os.environ.get('POSTGRES_PASSWORD') POSTGRES_DB = os.environ.get('POSTGRES_DB') - NEO4J_HOST = os.environ.get('NEO4J_HOST', '0.0.0.0') - NEO4J_SCHEME = os.environ.get('NEO4J_SCHEME', 'bolt') - NEO4J_AUTH = os.environ.get('NEO4J_AUTH', 'neo4j/password') - NEO4J_PORT = os.environ.get('NEO4J_PORT', '7687') - NEO4J_DATABASE = os.environ.get('NEO4J_DATABASE') - ARANGO_HOST = os.environ.get('ARANGO_HOST', 'http://localhost:8529') ARANGO_USERNAME = os.environ.get('ARANGO_USERNAME', 'root') ARANGO_PASSWORD = os.environ.get('ARANGO_PASSWORD', 'password') diff --git a/appserver/neo4japp/data_transfer_objects/search.py b/appserver/neo4japp/data_transfer_objects/search.py index f5ee549bdc..018b767158 100644 --- a/appserver/neo4japp/data_transfer_objects/search.py +++ b/appserver/neo4japp/data_transfer_objects/search.py @@ -8,7 +8,7 @@ @attr.s(frozen=True) class FTSQueryRecord(CamelDictMixin): - """Single record from a full text query in Neo4j""" + """Single record from a full text query in ArangoDB""" node: GraphNode = attr.ib() @@ -36,7 +36,7 @@ class FTSReferenceRecord(FTSQueryRecord): @attr.s(frozen=True) class FTSResult(CamelDictMixin): - """Paginated results for a full text search query in Neo4j""" + """Paginated results for a full text search query in ArangoDB""" query: str = attr.ib() nodes: List[FTSQueryRecord] = attr.ib() diff --git a/appserver/neo4japp/services/annotations/README.md b/appserver/neo4japp/services/annotations/README.md index 71ab2d16d1..be769a411b 100644 --- a/appserver/neo4japp/services/annotations/README.md +++ b/appserver/neo4japp/services/annotations/README.md @@ -146,9 +146,9 @@ A global inclusion/exclusion is **both** a local and a global. Local inclusions/exclusions are stored in Postgres, as well as global exclusions. The locals are saved in the `files` table, while the globals are in `global_list`. -The global inclusions are stored in Neo4j under the label `:GlobalInclusion` if they do not map to any existing nodes, otherwise use that existing node and create a new synonym relationship with it. +The global inclusions are stored in ArangoDB under the label `:GlobalInclusion` if they do not map to any existing nodes, otherwise use that existing node and create a new synonym relationship with it. -Because we do not curate before they're added to Neo4j, a user can potentially create a bad global inclusion. To correctly delete, we need the property `original_entity_types` so we don't accidentally delete the wrong thing. See https://sbrgsoftware.atlassian.net/browse/LL-3625 for more information. +Because we do not curate before they're added to ArangoDB, a user can potentially create a bad global inclusion. To correctly delete, we need the property `original_entity_types` so we don't accidentally delete the wrong thing. See https://sbrgsoftware.atlassian.net/browse/LL-3625 for more information. ## NLP Service diff --git a/cache-invalidator/Dockerfile b/cache-invalidator/Dockerfile index 33f146b5ba..1c52bb3e62 100644 --- a/cache-invalidator/Dockerfile +++ b/cache-invalidator/Dockerfile @@ -1,7 +1,7 @@ # ======================================== # Base image # ======================================== -FROM python:3.10-slim as base +FROM python:3.11-slim as base ENV LANG C.UTF-8 ENV LC_ALL C.UTF-8 @@ -42,12 +42,12 @@ USER app # Copy application code COPY --chown=app main.py ./ -# Neo4j configuration -ENV NEO4J_HOST=neo4j -ENV NEO4J_PORT=7687 -ENV NEO4J_AUTH=neo4j/password -ENV NEO4J_SCHEME=bolt -ENV NEO4J_DATABASE=neo4j +# ArangoDB configuration +ENV ARANGODB_HOST=arangodb +ENV ARANGODB_PORT=7687 +ENV ARANGODB_AUTH=arangodb/password +ENV ARANGODB_SCHEME=bolt +ENV ARANGODB_DATABASE=arangodb # Redis cache configuration ENV REDIS_HOST=redis diff --git a/cache-invalidator/Pipfile.lock b/cache-invalidator/Pipfile.lock index e95b37a95e..12972e9c28 100644 --- a/cache-invalidator/Pipfile.lock +++ b/cache-invalidator/Pipfile.lock @@ -18,42 +18,123 @@ "default": { "certifi": { "hashes": [ - "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3", - "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18" + "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f", + "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1" ], "markers": "python_version >= '3.6'", - "version": "==2022.12.7" + "version": "==2024.2.2" }, "charset-normalizer": { "hashes": [ - "sha256:5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845", - "sha256:83e9a75d1911279afd89352c68b45348559d1fc0506b054b346651b5e7fee29f" - ], - "markers": "python_version >= '3.6'", - "version": "==2.1.1" + "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027", + 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"sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c" ], - "markers": "python_version >= '3.7'", - "version": "==65.6.3" + "markers": "python_version >= '3.8'", + "version": "==69.2.0" }, "urllib3": { "hashes": [ - "sha256:47cc05d99aaa09c9e72ed5809b60e7ba354e64b59c9c173ac3018642d8bb41fc", - "sha256:c083dd0dce68dbfbe1129d5271cb90f9447dea7d52097c6e0126120c521ddea8" + "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d", + "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", - "version": "==1.26.13" + "markers": "python_version >= '3.8'", + "version": "==2.2.1" } }, "develop": { @@ -139,14 +215,16 @@ "sha256:edf7237137a1a9330046dbb14796963d734dd740a98d5e144a3eb1d267f5f9ee" ], "index": "pypi", + "markers": "python_version >= '3.6'", "version": "==0.942" }, "mypy-extensions": { "hashes": [ - "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d", - "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8" + "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d", + "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782" ], - "version": "==0.4.3" + "markers": "python_version >= '3.5'", + "version": "==1.0.0" }, "pycodestyle": { "hashes": [ @@ -154,6 +232,7 @@ "sha256:c389c1d06bf7904078ca03399a4816f974a1d590090fecea0c63ec26ebaf1cef" ], "index": "pypi", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.7.0" }, "tomli": { @@ -166,11 +245,11 @@ }, "typing-extensions": { "hashes": [ - "sha256:1a9462dcc3347a79b1f1c0271fbe79e844580bb598bafa1ed208b94da3cdcd42", - "sha256:21c85e0fe4b9a155d0799430b0ad741cdce7e359660ccbd8b530613e8df88ce2" + "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475", + "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb" ], - "markers": "python_version >= '3.6'", - "version": "==4.1.1" + "markers": "python_version >= '3.8'", + "version": "==4.10.0" } } } diff --git a/client/Dockerfile b/client/Dockerfile index 268192f7ce..b15603ee86 100644 --- a/client/Dockerfile +++ b/client/Dockerfile @@ -1,5 +1,20 @@ ARG NODE_IMAGE_TAG=node:14 +# ======================================== +# Landing page +# ======================================== +FROM $NODE_IMAGE_TAG as landing-build +WORKDIR /app + +# Install dependencies +COPY landing/package.json landing/yarn.lock ./ +RUN yarn install + +# Build landing page +COPY landing ./ +RUN yarn build + + # ================================================================== # Angular app dependencies by default used for local development # ================================================================== @@ -11,23 +26,28 @@ COPY package.json yarn.lock ./ ARG YARN_INSTALL_OPTS RUN yarn install ${YARN_INSTALL_OPTS} -ENV ENVIRONMENT_CONFIG development - +# build time arguments for Angular environment +ARG ANGULAR_CONFIG=development +ARG CLIENT_VERSION=undefined +# default enviroment presets +ENV ENVIRONMENT_CONFIG $ANGULAR_CONFIG # ======================================== # Angular app bundle build # ======================================== FROM angular-deps as angular-build +# build time arguments for Angular environment +ARG ANGULAR_CONFIG=production +ARG CLIENT_VERSION=undefined + # Copy the code and build the app bundle COPY src ./src COPY tslint ./tslint COPY e2e ./e2e COPY *.json browserslist ./ - -ARG ANGULAR_CONFIG=production -ENV NODE_OPTIONS=--max-old-space-size=4096 -RUN yarn build --configuration=$ANGULAR_CONFIG --output-path=dist +RUN sed -i "s/__VERSION__/${CLIENT_VERSION}/" src/environments/environment.ts +RUN yarn build --configuration=$ANGULAR_CONFIG --aot --output-path=dist # When targeting this image stage, run angulat dev server EXPOSE 4200 @@ -39,27 +59,43 @@ CMD yarn dev-start # ======================================== # Runtime stage - NGINX # ======================================== -FROM nginx:1.21 -LABEL org.opencontainers.image.source https://github.com/SBRG/lifelike - +FROM nginx:1.25.1 +LABEL app=kg-prototypes WORKDIR /usr/share/nginx/html -# Copy built assets -COPY --from=angular-build /app/dist ./ +# URL to proxy requests to /api +ENV APPSERVER_UPSTREAM http://appserver:5000 -# Copy nginx configuraiton template -COPY nginx.conf /etc/nginx/templates/default.conf.template +# Whether to run the app in prod mode +ENV PRODUCTION_MODE true + +# Whether we are running with valid KEGG license +ENV KEGG_ENABLED false -# appserver URL to proxy /api requests -ENV APPSERVER_URL http://appserver:5000 +# Whether to run the app with oauth login +ENV OAUTH_ENABLED false + +# OAuth issuer discovert URL +ENV OAUTH_ISSUER "" + +# Client ID of the OAuth application +ENV OAUTH_CLIENT_ID "" # List of space delimited list of non-stantdard MIME types # which are known to benefit from gzip compression (text based content) ENV GZIP_EXTRA_TYPES text/tsv vnd.lifelike.document/bioc vnd.lifelike.document/enrichment-table vnd.lifelike.document/graph vnd.lifelike.document/map -# Runtime environment configuration preset -ENV ENVIRONMENT_CONFIG production +# build time argument for Angular environment +ARG ANGULAR_CONFIG=production + +# default enviroment presets +ENV ENVIRONMENT_CONFIG $ANGULAR_CONFIG + +# Copy nginx configuraiton template +COPY nginx.conf /etc/nginx/templates/default.conf.template + +# Copy built assets +COPY --from=landing-build /app/dist ./ +COPY --from=angular-build /app/dist ./ -# Listen port -ENV PORT 80 -EXPOSE $PORT +EXPOSE 80 diff --git a/client/src/app/sankey/components/entity-details/node-details.component.html b/client/src/app/sankey/components/entity-details/node-details.component.html index bd2780277c..20a49aafbc 100644 --- a/client/src/app/sankey/components/entity-details/node-details.component.html +++ b/client/src/app/sankey/components/entity-details/node-details.component.html @@ -69,7 +69,7 @@ - +
  • {{ label }}
    • diff --git a/client/src/app/search/components/graph-search.component.ts b/client/src/app/search/components/graph-search.component.ts index a710d77e8e..67900606ce 100644 --- a/client/src/app/search/components/graph-search.component.ts +++ b/client/src/app/search/components/graph-search.component.ts @@ -79,7 +79,7 @@ export class GraphSearchComponent implements OnInit, OnDestroy, ModuleAwareCompo map( (legend) => // Keys of the result dict are all lowercase, need to change the first character - // to uppercase to match Neo4j labels + // to uppercase to match ArangoDB labels new Map(Object.entries(legend).map(([label, { color }]) => [label, color])) ), startWith(new Map()) diff --git a/client/src/app/shortest-path/components/route-builder.component.html b/client/src/app/shortest-path/components/route-builder.component.html deleted file mode 100644 index ab0280681e..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.html +++ /dev/null @@ -1,47 +0,0 @@ -
    - -
    -
    -
    - -
    -
    - -
    -
    -
    -
    -
    - -
    -

    Loading pre-defined queries...

    -
    -
    -
    - - -
    -

    Could not load pre-defined shortest path queries!

    -
    -
    - - -
    -
    -
    -
    diff --git a/client/src/app/shortest-path/components/route-builder.component.scss b/client/src/app/shortest-path/components/route-builder.component.scss deleted file mode 100644 index 357cdccf59..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.scss +++ /dev/null @@ -1,27 +0,0 @@ -.graph-type-btn-container { - height: 40px; - width: 40px; -} - -.route-builder-container-open { - position: absolute; - width: 400px; - right: 0; - z-index: 2; - transition: right .25s; -} - -.route-builder-container-closed { - position: absolute; - width: 400px; - right: -400px; - z-index: 2; - transition: right .25s; -} - -.toggle-route-builder-button { - height: 60px; - top: 28px; - right: 100%; - position: absolute; -} diff --git a/client/src/app/shortest-path/components/route-builder.component.spec.ts b/client/src/app/shortest-path/components/route-builder.component.spec.ts deleted file mode 100644 index a7884c15cd..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.spec.ts +++ /dev/null @@ -1,33 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; - -import { RootStoreModule } from 'app/root-store'; -import { SharedModule } from 'app/shared/shared.module'; - -import { RouteBuilderComponent } from './route-builder.component'; - -describe('RouteBuilderComponent', () => { - let component: RouteBuilderComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - imports: [ - RootStoreModule, - SharedModule - ], - declarations: [ RouteBuilderComponent ] - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(RouteBuilderComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/components/route-builder.component.ts b/client/src/app/shortest-path/components/route-builder.component.ts deleted file mode 100644 index 22c02806a9..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.ts +++ /dev/null @@ -1,74 +0,0 @@ -import { Component, EventEmitter, OnDestroy, OnInit, Output } from '@angular/core'; - -import { combineLatest, Subscription } from 'rxjs'; - -import { BackgroundTask } from 'app/shared/rxjs/background-task'; - -import { ShortestPathService } from '../services/shortest-path.service'; -import { DisplayType } from './route-display.component'; - -@Component({ - selector: 'app-route-builder', - templateUrl: './route-builder.component.html', - styleUrls: ['./route-builder.component.scss'] -}) -export class RouteBuilderComponent implements OnInit, OnDestroy { - @Output() loadNewQuery: EventEmitter; - @Output() changeDisplayType: EventEmitter; - - loadShortestPathQueries: BackgroundTask<[], any>; - queriesLoadedsub: Subscription; - - routeBuilderContainerClass: string; - - routeBuilderOpen: boolean; - - queries: string[][]; - - constructor( - public shortestPathService: ShortestPathService, - ) { - this.queries = []; - - this.routeBuilderContainerClass = 'route-builder-container-open'; - this.routeBuilderOpen = true; - - this.loadNewQuery = new EventEmitter(); - this.changeDisplayType = new EventEmitter(); - - this.loadShortestPathQueries = new BackgroundTask(() => { - return combineLatest( - this.shortestPathService.getShortestPathQueryList(), - ); - }); - this.queriesLoadedsub = this.loadShortestPathQueries.results$.subscribe(({ - result: [shortestPathQueries], - value: [], - }) => { - this.queries = Object.keys(shortestPathQueries).map(key => [key, shortestPathQueries[key]]); - }); - } - - ngOnInit() { - this.loadNewQuery.emit(0); - this.changeDisplayType.emit('NETWORK'); - this.loadShortestPathQueries.update([]); - } - - ngOnDestroy() { - this.queriesLoadedsub.unsubscribe(); - } - - toggleRouteBuilderOpen() { - this.routeBuilderOpen = !this.routeBuilderOpen; - this.routeBuilderContainerClass = this.routeBuilderOpen ? 'route-builder-container-open' : 'route-builder-container-closed'; - } - - requestQueryLoadFromParent(event: any) { - this.loadNewQuery.emit(Number.parseInt(event.target.value, 10)); - } - - requestChangeDisplayTypeFromParent(type: string) { - this.changeDisplayType.emit(type); - } -} diff --git a/client/src/app/shortest-path/components/route-display.component.html b/client/src/app/shortest-path/components/route-display.component.html deleted file mode 100644 index f0ba2043ec..0000000000 --- a/client/src/app/shortest-path/components/route-display.component.html +++ /dev/null @@ -1,18 +0,0 @@ -
    -
    -
    - -
    -
    - -
    -
    -
    diff --git a/client/src/app/shortest-path/components/route-display.component.scss b/client/src/app/shortest-path/components/route-display.component.scss deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/client/src/app/shortest-path/components/route-display.component.spec.ts b/client/src/app/shortest-path/components/route-display.component.spec.ts deleted file mode 100644 index e04e8f259d..0000000000 --- a/client/src/app/shortest-path/components/route-display.component.spec.ts +++ /dev/null @@ -1,36 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; -import { MockComponents } from 'ng-mocks'; - -import { PlotlySankeyDiagramComponent } from 'app/shared/components/plotly-sankey-diagram/plotly-sankey-diagram.component'; -import { VisJsNetworkComponent } from 'app/shared/components/vis-js-network/vis-js-network.component'; - -import { RouteDisplayComponent } from './route-display.component'; - -describe('RouteDisplayComponent', () => { - let component: RouteDisplayComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - declarations: [ - RouteDisplayComponent, - MockComponents( - PlotlySankeyDiagramComponent, - VisJsNetworkComponent - ) - ] - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(RouteDisplayComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/components/route-display.component.ts b/client/src/app/shortest-path/components/route-display.component.ts deleted file mode 100644 index 43a68748ee..0000000000 --- a/client/src/app/shortest-path/components/route-display.component.ts +++ /dev/null @@ -1,191 +0,0 @@ -import { Component, Input } from '@angular/core'; - -import { isNil } from 'lodash-es'; -import { Options } from 'vis-network'; - -import { GraphData } from 'app/interfaces/vis-js.interface'; - -export enum DisplayType { - NETWORK = 'network', - SANKEY = 'sankey' -} - -@Component({ - selector: 'app-route-display', - templateUrl: './route-display.component.html', - styleUrls: ['./route-display.component.scss'] -}) -export class RouteDisplayComponent { - @Input() set displayType(displayType: DisplayType) { - this.currentDisplay = DisplayType[displayType]; - } - @Input() set graphData(graphData: GraphData) { - // Update vis js data - this.networkData = graphData; - - // Update sankey data - this.generateSankeyData(graphData.nodes, graphData.edges); - - // Update legend - this.setupLegend(graphData.nodes); - } - - currentDisplay: string; - - networkConfig: Options; - networkData: GraphData; - - sankeyConfig: any; - sankeyData: any; - - legend: Map; - - constructor() { - this.initVisJsSettings(); - this.initPlotlySankeySettings(); - this.legend = new Map(); - } - - initVisJsSettings() { - // Init vis js network settings - this.networkConfig = { - interaction: { - hover: true, - multiselect: true, - selectConnectedEdges: false, - }, - physics: { - enabled: true, - solver: 'barnesHut', - }, - edges: { - font: { - size: 12, - }, - length: 250, - widthConstraint: { - maximum: 90, - }, - }, - nodes: { - scaling: { - min: 25, - max: 50, - label: { - enabled: true, - min: 12, - max: 72, - maxVisible: 72, - drawThreshold: 5, - }, - }, - shape: 'box', - widthConstraint: { - maximum: 180, - }, - }, - }; - - this.networkData = { - nodes: [], - edges: [], - }; - } - - generateSankeyData(nodes: any[], edges: any[]) { - const source = []; - const target = []; - const value = []; - const label = []; - const color = []; - - const nodeIdentityMap = new Map(); - nodes.forEach((node, i) => { - nodeIdentityMap.set(node.id, i); - label.push(node.label); - color.push(node.color.border); - }); - - const seenEdges = new Map(); - edges.forEach(edge => { - const sankeyEdge = [nodeIdentityMap.get(edge.from), nodeIdentityMap.get(edge.to)]; - if (seenEdges.has(sankeyEdge.toString())) { - value[seenEdges.get(sankeyEdge.toString())] += 1; - } else { - source.push(sankeyEdge[0]); - target.push(sankeyEdge[1]); - value.push(1); - seenEdges.set(sankeyEdge.toString(), value.length - 1); - } - }); - - this.sankeyData = { - type: 'sankey', - orientation: 'h', - node: { - arrangement: 'snap', - pad: 15, - thickness: 20, - line: { - color: 'black', - width: 0.5 - }, - label, - color, - }, - - link: { - source, - target, - value - } - }; - } - - initPlotlySankeySettings() { - // Init plotly sankey settings - this.sankeyData = { - type: 'sankey', - orientation: 'h', - node: { - arrangement: 'snap', - pad: 15, - thickness: 20, - line: { - color: 'black', - width: 0.5 - }, - label: [], - color: [], - }, - - link: { - source: [], - target: [], - value: [] - } - }; - - this.sankeyConfig = { - font: { - size: 10 - } - }; - } - - /** - * Given a list of input nodes, generates a Map object representing a node legend. Keys are the label of the nodes, and values are a list - * of colors representing the border and background of the node. - * @param nodes list of node objects - */ - setupLegend(nodes: any) { - nodes.forEach((node) => { - if (!isNil(node.databaseLabel)) { - if (!this.legend.has(node.databaseLabel)) { - this.legend.set(node.databaseLabel, [node.color.border, node.color.background]); - } - } - }); - } - -} diff --git a/client/src/app/shortest-path/containers/route-search.component.html b/client/src/app/shortest-path/containers/route-search.component.html deleted file mode 100644 index 542f90ab00..0000000000 --- a/client/src/app/shortest-path/containers/route-search.component.html +++ /dev/null @@ -1 +0,0 @@ -

    route-search works!

    diff --git a/client/src/app/shortest-path/containers/route-search.component.scss b/client/src/app/shortest-path/containers/route-search.component.scss deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/client/src/app/shortest-path/containers/route-search.component.spec.ts b/client/src/app/shortest-path/containers/route-search.component.spec.ts deleted file mode 100644 index 7a5354fab2..0000000000 --- a/client/src/app/shortest-path/containers/route-search.component.spec.ts +++ /dev/null @@ -1,31 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; - -import { RootStoreModule } from 'app/root-store'; - -import { RouteSearchComponent } from './route-search.component'; - -describe('RouteSearchComponent', () => { - let component: RouteSearchComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - imports: [ - RootStoreModule - ], - declarations: [ RouteSearchComponent ] - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(RouteSearchComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/containers/route-search.component.ts b/client/src/app/shortest-path/containers/route-search.component.ts deleted file mode 100644 index 10d8fa3313..0000000000 --- a/client/src/app/shortest-path/containers/route-search.component.ts +++ /dev/null @@ -1,15 +0,0 @@ -import { Component, OnInit } from '@angular/core'; - -@Component({ - selector: 'app-route-search', - templateUrl: './route-search.component.html', - styleUrls: ['./route-search.component.scss'] -}) -export class RouteSearchComponent implements OnInit { - - constructor() { } - - ngOnInit() { - } - -} diff --git a/client/src/app/shortest-path/containers/shortest-path.component.html b/client/src/app/shortest-path/containers/shortest-path.component.html deleted file mode 100644 index 58514a26c1..0000000000 --- a/client/src/app/shortest-path/containers/shortest-path.component.html +++ /dev/null @@ -1,20 +0,0 @@ -
    - -
    - -
    - - - -
    - -
    -     -
    diff --git a/client/src/app/shortest-path/containers/shortest-path.component.scss b/client/src/app/shortest-path/containers/shortest-path.component.scss deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/client/src/app/shortest-path/containers/shortest-path.component.spec.ts b/client/src/app/shortest-path/containers/shortest-path.component.spec.ts deleted file mode 100644 index 01988d548c..0000000000 --- a/client/src/app/shortest-path/containers/shortest-path.component.spec.ts +++ /dev/null @@ -1,42 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; -import { MockComponents } from 'ng-mocks'; - -import { RootStoreModule } from 'app/root-store'; -import { SharedModule } from 'app/shared/shared.module'; - -import { RouteBuilderComponent } from '../components/route-builder.component'; -import { RouteDisplayComponent } from '../components/route-display.component'; -import { ShortestPathComponent } from './shortest-path.component'; - -describe('ShortestPathComponent', () => { - let component: ShortestPathComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - imports: [ - RootStoreModule, - SharedModule, - ], - declarations: [ - ShortestPathComponent, - MockComponents( - RouteBuilderComponent, - RouteDisplayComponent, - ), - ] - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(ShortestPathComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/containers/shortest-path.component.ts b/client/src/app/shortest-path/containers/shortest-path.component.ts deleted file mode 100644 index 9fa38e6a88..0000000000 --- a/client/src/app/shortest-path/containers/shortest-path.component.ts +++ /dev/null @@ -1,57 +0,0 @@ -import { Component, OnDestroy } from '@angular/core'; - -import { combineLatest, Subscription } from 'rxjs'; - -import { GraphData } from 'app/interfaces/vis-js.interface'; -import { BackgroundTask } from 'app/shared/rxjs/background-task'; - -import { ShortestPathService } from '../services/shortest-path.service'; - - -@Component({ - selector: 'app-shortest-path', - templateUrl: './shortest-path.component.html', - styleUrls: ['./shortest-path.component.scss'] -}) -export class ShortestPathComponent implements OnDestroy { - - loadTask: BackgroundTask<[], any>; - shortestPathLoadedSub: Subscription; - - loadedQuery: number; - displayType: string; - graphData: GraphData; - - constructor( - public shortestPathService: ShortestPathService, - ) { - this.loadTask = new BackgroundTask(() => { - return combineLatest( - this.shortestPathService.getShortestPathQueryResult(this.loadedQuery), - ); - }); - this.shortestPathLoadedSub = this.loadTask.results$.subscribe(({ - result: [shortestPathResult], - value: [], - }) => { - this.graphData = { - nodes: shortestPathResult.nodes, - edges: shortestPathResult.edges, - }; - }); - } - - ngOnDestroy() { - this.shortestPathLoadedSub.unsubscribe(); - } - - changeDisplayType(type: string) { - this.displayType = type; - } - - loadNewQuery(query: number) { - this.graphData = null; - this.loadedQuery = query; - this.loadTask.update([]); - } -} diff --git a/client/src/app/shortest-path/services/shortest-path.service.ts b/client/src/app/shortest-path/services/shortest-path.service.ts deleted file mode 100644 index 84a4ba0337..0000000000 --- a/client/src/app/shortest-path/services/shortest-path.service.ts +++ /dev/null @@ -1,39 +0,0 @@ -import { HttpClient } from '@angular/common/http'; -import { Injectable } from '@angular/core'; - -import { Observable } from 'rxjs'; -import { map } from 'rxjs/operators'; - -import { AuthenticationService } from 'app/auth/services/authentication.service'; -import { AbstractService } from 'app/shared/services/abstract-service'; - -@Injectable({ - providedIn: 'root' -}) -export class ShortestPathService extends AbstractService { - readonly kgAPI = '/api/knowledge-graph'; - - constructor(auth: AuthenticationService, http: HttpClient) { - super(auth, http); - } - - getShortestPathQueryResult(queryId: number): Observable { - return this.http.get<{result: any}>( - `${this.kgAPI}/shortest-path-query/${queryId}`, { - ...this.getHttpOptions(true), - } - ).pipe( - map((resp: any) => resp.result), - ); - } - - getShortestPathQueryList(): Observable { - return this.http.get<{result: Map}>( - `${this.kgAPI}/shortest-path-query-list`, { - ...this.getHttpOptions(true), - } - ).pipe( - map((resp: any) => resp.result), - ); - } -} diff --git a/client/src/app/shortest-path/shortest-path.module.ts b/client/src/app/shortest-path/shortest-path.module.ts deleted file mode 100644 index 13801d1634..0000000000 --- a/client/src/app/shortest-path/shortest-path.module.ts +++ /dev/null @@ -1,25 +0,0 @@ -import { NgModule } from '@angular/core'; -import { CommonModule } from '@angular/common'; - -import { SharedModule } from 'app/shared/shared.module'; - -import { ShortestPathComponent } from './containers/shortest-path.component'; -import { RouteSearchComponent } from './containers/route-search.component'; -import { RouteBuilderComponent } from './components/route-builder.component'; -import { RouteDisplayComponent } from './components/route-display.component'; - -const components = [ - ShortestPathComponent, - RouteSearchComponent, - RouteBuilderComponent, - RouteDisplayComponent, -]; - -@NgModule({ - declarations: [...components], - imports: [ - CommonModule, - SharedModule, - ] -}) -export class ShortestPathModule { } diff --git a/deployment b/deployment deleted file mode 160000 index 0f1943080f..0000000000 --- a/deployment +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 0f1943080f4dd462a64535248e2f63ede809faa2 diff --git a/docker-compose.ci-test.yml b/docker-compose.ci-test.yml index dec5adbd8c..2a85d2aae5 100644 --- a/docker-compose.ci-test.yml +++ b/docker-compose.ci-test.yml @@ -2,11 +2,11 @@ version: "3.8" x-appserver: &appserver + build: + context: appserver + dockerfile: Dockerfile image: lifelike.azurecr.io/kg-appserver:${GITHUB_HASH} environment: - - NEO4J_HOST=neo4j - - NEO4J_AUTH=neo4j/password - - NEO4J_PORT=7687 - FLASK_DEBUG=1 - FLASK_ENV=development - FLASK_APP=app @@ -33,7 +33,6 @@ x-appserver: &appserver depends_on: - postgres - elasticsearch - - neo4j - redis - arangodb @@ -52,13 +51,6 @@ services: environment: - POSTGRES_PASSWORD=postgres - neo4j: - image: neo4j:4.4-community - restart: on-failure - environment: - - NEO4J_AUTH=neo4j/password - - NEO4JLABS_PLUGINS=["apoc", "n10s"] - elasticsearch: image: ghcr.io/sbrg/lifelike-elasticsearch:latest restart: on-failure diff --git a/docker-compose.override.yml b/docker-compose.override.yml index ca4ec289d8..2df05883fb 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -2,8 +2,6 @@ version: "3.8" x-appserver: &appserver build: ./appserver - env_file: - - azure-secrets.env environment: # Log Services - FORMAT_AS_JSON=false diff --git a/docker/Makefile b/docker/Makefile index 1ca4de303e..44cc20abe2 100644 --- a/docker/Makefile +++ b/docker/Makefile @@ -3,7 +3,7 @@ DOCKER_REGISTRY:=us.gcr.io/able-goods-221820 # Base Docker Compose command -------------------------------------------------- # docker-compose.yml -> Base services containers -# docker-compose.services.yml -> Third party services (PostgreSQL, Neo4j, Elasticsearch, Redis) +# docker-compose.services.yml -> Third party services (PostgreSQL, ArangoDB, Elasticsearch, Redis) # docker-compose.dev.yml -> Override base services for local development COMPOSE_COMMAND=docker-compose -p lifelike \ -f ${DOCKER_DIR}/docker-compose.yml \ diff --git a/docker/README.md b/docker/README.md index 0296ad16ba..bc35a8cf69 100644 --- a/docker/README.md +++ b/docker/README.md @@ -1,3 +1,5 @@ + + # Getting Started with Lifelike using Docker Docker is an easy way to get started with Lifelike. @@ -50,7 +52,7 @@ The stack definition is divided into three Docker Compose files: ```tree ├── docker-compose.yml --> Base core services ├── docker-compose.dev.yml --> Overrides base core services for local development and debugging. -└── docker-compose.services.yml --> Adds third party services (PostgreSQL, Neo4j, Elasticsearch, Redis) +└── docker-compose.services.yml --> Adds third party services (PostgreSQL, ArangoDB, Elasticsearch, Redis) ``` You may combine them as you need and/or add your own `docker-compose.override.yml` to override any configuration. (this file will be ignored by Git) diff --git a/docker/diagram.svg b/docker/diagram.svg index e9b292e909..e3ddfdb2bf 100644 --- a/docker/diagram.svg +++ b/docker/diagram.svg @@ -3,7 +3,7 @@ entity appserver-->cache-invalidatorelasticsearchfrontendneo4jarangodbpdfparserpostgresredisdepends ondepends ondepends ondepends ondepends ondepends ondepends ondepends ondepends ondepends on \ No newline at end of file +--> diff --git a/docker/docker-compose.services.yml b/docker/docker-compose.services.yml index 1b18dcbfbf..ceae580e7c 100644 --- a/docker/docker-compose.services.yml +++ b/docker/docker-compose.services.yml @@ -5,7 +5,7 @@ version: "3.8" services: # PostgreSQL database postgres: - image: postgres:13 + image: postgres:11 restart: unless-stopped container_name: postgres environment: @@ -18,45 +18,52 @@ services: test: ["CMD", "pg_isready", "-U", "postgres", "-q"] start_period: 10s - ## Neo4j graph database - neo4j: - image: neo4j:4.4-community - restart: unless-stopped - container_name: neo4j + ## ArangoDB graph database + arangodb: + build: + # Note that this Dockerfile simply adds a user directory and installs the helper scripts into it, and then executes the default arango + # entrypoint as normal. + context: ../arangodb + dockerfile: Dockerfile + container_name: arangodb environment: - - NEO4J_AUTH=neo4j/password - - NEO4JLABS_PLUGINS=["apoc"] + ARANGO_ROOT_PASSWORD: password + LIFELIKE_DB_NAME: lifelike ports: - - 7687:7687 - - 7474:7474 + - 8529:8529 volumes: - - neo4j:/var/lib/neo4j/data - healthcheck: - test: ["CMD", "wget", "localhost:7474", "-O", "-"] - start_period: 1m + - ../arangodb/bin:/home/dbuser/bin # the /home/dbuser directory is setup in the Dockerfile + - ../arangodb/data:/var/lib/arangodb3 + - ../arangodb/apps:/var/lib/arangodb3-apps ## Ekasticsearch search engine elasticsearch: - image: ghcr.io/sbrg/lifelike-elasticsearch:7.16.3 - restart: unless-stopped container_name: elasticsearch + build: + dockerfile: Dockerfile + context: ../elasticsearch environment: - discovery.type=single-node + - http.max_content_length=200mb #allow 200mb of content to be sent for indexing - bootstrap.memory_lock=true - ports: - - 9200 + - xpack.graph.enabled=false + - xpack.watcher.enabled=false + - xpack.license.self_generated.type=basic volumes: - - elasticsearch:/usr/share/elasticsearch/data + - ../elasticsearch:/usr/share/elasticsearch/data ulimits: memlock: soft: -1 hard: -1 + ports: + - "9200:9200" + - "9300:9300" healthcheck: test: ["CMD", "curl", "-f", "localhost:9200/_cluster/health"] start_period: 1m redis: - image: redis:alpine + image: redis:6-alpine restart: unless-stopped container_name: redis ports: @@ -68,34 +75,43 @@ services: environment: - POSTGRES_HOST=postgres - POSTGRES_PASSWORD=postgres - - NEO4J_HOST=neo4j - - NEO4J_AUTH=neo4j/password + # Arango + - ARANGO_HOST=http://arangodb:8529 + - ARANGO_USERNAME=root + - ARANGO_PASSWORD=password + - ARANGO_DB_NAME=lifelike - ELASTICSEARCH_URL=http://elasticsearch:9200 - REDIS_HOST=redis depends_on: - postgres - - neo4j + - arangodb - elasticsearch statistical-enrichment: environment: - - NEO4J_HOST=neo4j - - NEO4J_AUTH=neo4j/password + # Arango + - ARANGO_HOST=http://arangodb:8529 + - ARANGO_USERNAME=root + - ARANGO_PASSWORD=password + - ARANGO_DB_NAME=lifelike - REDIS_HOST=redis depends_on: - - neo4j + - arangodb - redis cache-invalidator: environment: - - NEO4J_HOST=neo4j - - NEO4J_AUTH=neo4j/password + # Arango + - ARANGO_HOST=http://arangodb:8529 + - ARANGO_USERNAME=root + - ARANGO_PASSWORD=password + - ARANGO_DB_NAME=lifelike - REDIS_HOST=redis depends_on: - - neo4j + - arangodb - redis volumes: postgres: - neo4j: + arangodb: elasticsearch: diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml index 556013ab1b..48dd0de11d 100644 --- a/docker/docker-compose.yml +++ b/docker/docker-compose.yml @@ -3,7 +3,9 @@ version: "3.8" services: ## Frontend web server frontend: - image: ghcr.io/sbrg/lifelike-frontend:${FRONTEND_IMAGE_TAG:-latest} + build: + context: ../client + dockerfile: Dockerfile restart: unless-stopped container_name: frontend environment: @@ -15,7 +17,9 @@ services: ## Backend application server appserver: - image: ghcr.io/sbrg/lifelike-appserver:${APPSERVER_IMAGE_TAG:-latest} + build: + context: ../appserver + dockerfile: Dockerfile restart: unless-stopped container_name: appserver ports: @@ -43,7 +47,9 @@ services: ## Statistical enrichment service statistical-enrichment: - image: ghcr.io/sbrg/lifelike-statistical-enrichment:${STATISTICAL_ENRICHMENT_IMAGE_TAG:-latest} + build: + context: ../statistical-enrichment + dockerfile: Dockerfile restart: unless-stopped container_name: statistical-enrichment ports: @@ -51,7 +57,9 @@ services: # Cache invalidator service cache-invalidator: - image: ghcr.io/sbrg/lifelike-cache-invalidator:${CACHE_INVALIDATOR_IMAGE_TAG:-latest} + build: + context: ../cache-invalidator + dockerfile: Dockerfile restart: unless-stopped container_name: cache-invalidator diff --git a/docs/wiki/development/general-introduction.md b/docs/wiki/development/general-introduction.md index 919c4609ec..d64d279805 100644 --- a/docs/wiki/development/general-introduction.md +++ b/docs/wiki/development/general-introduction.md @@ -101,7 +101,7 @@ For `$container_name`, you have a choice of: docker compose exec pgdatabase psql -U postgres -h pgdatabase -d postgres ``` -### Neo4j +### ArangoDB ```sh docker compose exec database cypher-shell -u neo4j diff --git a/docs/wiki/elk/introduction.md b/docs/wiki/elk/introduction.md index 05f64707f0..901a30c5c2 100644 --- a/docs/wiki/elk/introduction.md +++ b/docs/wiki/elk/introduction.md @@ -7,8 +7,6 @@ - To seed LMDB data to Kibana: ```bash -./deployment/kibana.sh -a None -# or docker compose exec appserver python neo4japp/services/annotations/index_annotations.py -a ``` diff --git a/graph-db/docker-compose.yml b/graph-db/docker-compose.yml index 04adee3783..ca11a7fb66 100644 --- a/graph-db/docker-compose.yml +++ b/graph-db/docker-compose.yml @@ -1,25 +1,27 @@ version: "3.8" +# Hasn't been migrated to Arango - not working + services: - neo4j: - image: neo4j:4.4-community + arangodb: + image: arangodb:4.4-community restart: on-failure environment: - - NEO4J_AUTH=neo4j/password - - NEO4JLABS_PLUGINS=["apoc"] - - NEO4J_dbms.unmanaged_extension_classes=n10s.endpoint=/rdf # for the neosemantics-4.3.0.0.jar + - ARANGODB_AUTH=arangodb/password + - ARANGODBLABS_PLUGINS=["apoc"] + - ARANGODB_dbms.unmanaged_extension_classes=n10s.endpoint=/rdf # for the neosemantics-4.3.0.0.jar ports: - 7687:7687 - 7474:7474 volumes: - - neo4j:/var/lib/neo4j/data + - arangodb:/var/lib/arangodb/data migrator: build: context: migrator environment: - - NEO4J_HOST=neo4j - - NEO4J_PASSWORD=password + - ARANGODB_HOST=arangodb + - ARANGODB_PASSWORD=password - CHANGELOG_FILE=lifelike-graph/changelog-master.xml - DATAFILES_PREFIX=stage - LOG_LEVEL=debug @@ -29,9 +31,9 @@ services: - ./changelog:/liquibase/changelog - ./tmp:/tmp depends_on: - - neo4j + - arangodb links: - - neo4j + - arangodb volumes: - neo4j: {} + arangodb: {} diff --git a/graph-db/docs/reactome/Reactome GDS.ipynb b/graph-db/docs/reactome/Reactome GDS.ipynb index 71a35cdb79..e0ced77a15 100644 --- a/graph-db/docs/reactome/Reactome GDS.ipynb +++ b/graph-db/docs/reactome/Reactome GDS.ipynb @@ -92,9 +92,9 @@ "source": [ "load_dotenv() # These params are set in .env file\n", "\n", - "URI = os.getenv(\"NEO4J_URI\")\n", - "AUTH = (os.getenv(\"NEO4J_USER\"), os.getenv(\"NEO4J_PASSWORD\"))\n", - "DATABASE = os.getenv(\"NEO4J_DATABASE\")\n", + "URI = os.getenv(\"ARANGODB_URI\")\n", + "AUTH = (os.getenv(\"ARANGODB_USER\"), os.getenv(\"ARANGODB_PASSWORD\"))\n", + "DATABASE = os.getenv(\"ARANGODB_DATABASE\")\n", "\n", "driver = GraphDatabase.driver(URI, auth=AUTH)\n", "with driver as session:\n", diff --git a/graph-db/migrator/Dockerfile b/graph-db/migrator/Dockerfile index 2f15ee818e..0348bc17b9 100644 --- a/graph-db/migrator/Dockerfile +++ b/graph-db/migrator/Dockerfile @@ -20,23 +20,23 @@ RUN mvn -B clean package -DskipTests FROM liquibase/liquibase:$LIQUIBASE_IMAGE_TAG LABEL org.opencontainers.image.source https://github.com/SBRG/lifelike -ARG LIQUIBASE_NEO4J_VERSION=4.7.1.3 -ARG NEO4J_JDBC_VERSION=4.0.5 +ARG LIQUIBASE_ARANGODB_VERSION=4.7.1.3 +ARG ARANGODB_JDBC_VERSION=4.0.5 -# Install liquibase-neo4j extension -RUN lpm update && lpm add --global liquibase-neo4j@$LIQUIBASE_NEO4J_VERSION +# Install liquibase-arangodb extension +RUN lpm update && lpm add --global liquibase-arangodb@$LIQUIBASE_ARANGODB_VERSION -# Download Neo4j JDBC driver -ADD --chown=liquibase:liquibase https://github.com/neo4j-contrib/neo4j-jdbc/releases/download/${NEO4J_JDBC_VERSION}/neo4j-jdbc-driver-${NEO4J_JDBC_VERSION}.jar lib/ +# Download ArangoDB JDBC driver +ADD --chown=liquibase:liquibase https://github.com/arangodb-contrib/arangodb-jdbc/releases/download/${ARANGODB_JDBC_VERSION}/arangodb-jdbc-driver-${ARANGODB_JDBC_VERSION}.jar lib/ # Copy JAR from build stage COPY --from=build --chown=liquibase:liquibase /target/graphdb-migrator-*.jar ./lib -# Neo4j database configuration -ENV NEO4J_HOST= -ENV NEO4J_USERNAME=neo4j -ENV NEO4J_PASSWORD=neo4j -ENV NEO4J_DATABASE=neo4j +# ArangoDB database configuration +ENV ARANGODB_HOST= +ENV ARANGODB_USERNAME=arangodb +ENV ARANGODB_PASSWORD=arangodb +ENV ARANGODB_DATABASE=arangodb # Master changelog file. e.g. lifelike-graph/changelog-master.xml ENV CHANGELOG_FILE= diff --git a/graph-db/migrator/README.md b/graph-db/migrator/README.md index 2e019af219..edcdb210c6 100644 --- a/graph-db/migrator/README.md +++ b/graph-db/migrator/README.md @@ -1,6 +1,8 @@ +# Legacy - not used anymore + # Lifelike Graph DB migrator -Liquibase based migrator for Neo4j +Liquibase based migrator for ArangoDB ## Run with Docker @@ -9,8 +11,8 @@ To run migrations from Lifelike Docker registry latest image, you can run the fo ```bash # Update using bundled changelog files docker run --rm \ - --env NEO4J_HOST=neo4j:7687 \ - --env NEO4J_PASSWORD=password \ + --env ARANGODB_HOST=neo4j:7687 \ + --env ARANGODB_PASSWORD=password \ --env AZURE_ACCOUNT_STORAGE_NAME=lifelike \ --env AZURE_ACCOUNT_STORAGE_KEY= \ --env CHANGELOG_DIR=lifelike-graph \ @@ -28,10 +30,10 @@ docket run --rm \ | Variable | Default | Comment | | -------------------------- | -------------- | ----------------------------------- | | CHANGELOG_DIR | lifelike-graph | Master changelog directory path | -| NEO4J_HOST | | Host and port of Neo4j instance | -| NEO4J_USERNAME | neo4j | Neo4j authentication username | -| NEO4J_PASSWORD | password | Neo4j authentication password | -| NEO4J_DATABASE | neo4j | Neo4j target database | +| ARANGODB_HOST | | Host and port of ArangoDB instance | +| ARANGODB_USERNAME | neo4j | ArangoDB authentication username | +| ARANGODB_PASSWORD | password | ArangoDB authentication password | +| ARANGODB_DATABASE | neo4j | ArangoDB target database | | STORAGE_TYPE | azure | Remote storage type to get TSV data | | AZURE_ACCOUNT_STORAGE_NAME | | Azure Storage Account Name | | AZURE_ACCOUNT_STORAGE_KEY | | Azure Storage Key | @@ -42,5 +44,5 @@ docket run --rm \ | Argument | Default value | Comment | | ----------------------- | ------------- | ------- | | LIQUIBASE_IMAGE_TAG | 4.6 | Tag of the [Liquibase Docker image](https://hub.docker.com/r/liquibase/liquibase/tags) to use | -| LIQUIBASE_NEO4J_VERSION | 4.6.2 | [Liquibase-Neo4j plugin](https://github.com/liquibase/liquibase-neo4j) version to install | -| NEO4J_JDBC_VERSION | 4.0.5 | Neo4j JDBC driver version | +| LIQUIBASE_ARANGODB_VERSION | 4.6.2 | [Liquibase-ArangoDB plugin](https://github.com/liquibase/liquibase-neo4j) version to install | +| ARANGODB_JDBC_VERSION | 4.0.5 | ArangoDB JDBC driver version | diff --git a/graph-db/migrator/docker-entrypoint.sh b/graph-db/migrator/docker-entrypoint.sh index 01c4e0149c..1b7b5095ab 100755 --- a/graph-db/migrator/docker-entrypoint.sh +++ b/graph-db/migrator/docker-entrypoint.sh @@ -13,12 +13,12 @@ else liquibase "$@" else ## Validate envrioment variables - if [ -z "$NEO4J_HOST" ]; then - echo "NEO4J_HOST environment variable is not set. Please set it to the hostname or IP address of the Neo4j server." + if [ -z "$ARANGODB_HOST" ]; then + echo "ARANGODB_HOST environment variable is not set. Please set it to the hostname or IP address of the ArangoDB server." exit 1 - elif [[ "$NEO4J_HOST" != *":"* ]]; then + elif [[ "$ARANGODB_HOST" != *":"* ]]; then ## If no port is specified, use the default one - NEO4J_HOST="$NEO4J_HOST:7687" + ARANGODB_HOST="$ARANGODB_HOST:7687" fi if [ "$STORAGE_TYPE" != "azure" ]; then echo "STORAGE_TYPE environment is set to an invalid valie. `azure` is currently only supported." @@ -33,21 +33,21 @@ else exit 1 fi - ## Wait until Neo4j is available - /wait-for-it.sh "$NEO4J_HOST" --timeout=600 -- echo "Neo4j is up" + ## Wait until ArangoDB is available + /wait-for-it.sh "$ARANGODB_HOST" --timeout=600 -- echo "ArangoDB is up" ## Include standard defaultsFile liquibase \ - --url="jdbc:neo4j:bolt://$NEO4J_HOST?database=${NEO4J_DATABASE:-neo4j}" \ - --username="$NEO4J_USERNAME" \ - --password="$NEO4J_PASSWORD" \ + --url="jdbc:neo4j:bolt://$ARANGODB_HOST?database=${ARANGODB_DATABASE:-neo4j}" \ + --username="$ARANGODB_USERNAME" \ + --password="$ARANGODB_PASSWORD" \ --changelog-file="$CHANGELOG_FILE" \ --log-level="$LOG_LEVEL" \ --defaults-file=/liquibase/liquibase.docker.properties \ "$@" \ - -Dneo4jHost="bolt://$NEO4J_HOST" \ - -Dneo4jCredentials="$NEO4J_USERNAME,$NEO4J_PASSWORD" \ - -Dneo4jDatabase="${NEO4J_DATABASE:-neo4j}" \ + -Dneo4jHost="bolt://$ARANGODB_HOST" \ + -Dneo4jCredentials="$ARANGODB_USERNAME,$ARANGODB_PASSWORD" \ + -Dneo4jDatabase="${ARANGODB_DATABASE:-neo4j}" \ -DazureStorageName="$AZURE_ACCOUNT_STORAGE_NAME" \ -DazureStorageKey="$AZURE_ACCOUNT_STORAGE_KEY" \ -DlocalSaveFileDir=/tmp \ diff --git a/helm/lifelike/Chart.lock b/helm/lifelike/Chart.lock index d89a3eebfc..b93530d606 100644 --- a/helm/lifelike/Chart.lock +++ b/helm/lifelike/Chart.lock @@ -2,9 +2,9 @@ dependencies: - name: postgresql repository: https://charts.bitnami.com/bitnami version: 11.0.4 -- name: neo4j - repository: https://neo4j-contrib.github.io/neo4j-helm - version: 4.4.3 +- name: kube-arangodb + repository: https://github.com/arangodb/kube-arangodb + version: 1.2.39 - name: elasticsearch repository: https://helm.elastic.co version: 7.16.3 diff --git a/helm/lifelike/Chart.yaml b/helm/lifelike/Chart.yaml index ee409bf66f..e69ad794cc 100644 --- a/helm/lifelike/Chart.yaml +++ b/helm/lifelike/Chart.yaml @@ -25,10 +25,10 @@ dependencies: repository: https://charts.bitnami.com/bitnami version: 11.0.4 condition: postgresql.enabled - - name: neo4j + - name: kube-arangodb version: 4.4.3 - repository: https://neo4j-contrib.github.io/neo4j-helm - condition: neo4j.enabled + repository: https://github.com/arangodb/kube-arangodb + condition: 1.2.39 - name: elasticsearch version: 7.16.3 repository: https://helm.elastic.co diff --git a/helm/lifelike/README.md b/helm/lifelike/README.md index 25051e94bc..6fa2107749 100644 --- a/helm/lifelike/README.md +++ b/helm/lifelike/README.md @@ -22,7 +22,7 @@ Kubernetes: `>=1.20.0-0` | https://charts.bitnami.com/bitnami | postgresql | 11.0.4 | | https://charts.bitnami.com/bitnami | redis | 16.2.0 | | https://helm.elastic.co | elasticsearch | 7.16.3 | -| https://neo4j-contrib.github.io/neo4j-helm | neo4j | 4.4.3 | +| https://github.com/arangodb/kube-arangodb | kube-arangodb | 1.2.39 | ## Values @@ -40,11 +40,11 @@ Kubernetes: `>=1.20.0-0` | statisticalEnrichment | object | `{"image":{"repository":"ghcr.io/sbrg/lifelike-statistical-enrichment","tag":""},"livenessProbe":{"enabled":true,"failureThreshold":20,"initialDelaySeconds":20,"path":"/healthz","periodSeconds":10,"successThreshold":1,"timeoutSeconds":10},"readinessProbe":{"enabled":true,"failureThreshold":20,"initialDelaySeconds":20,"path":"/healthz","periodSeconds":10,"successThreshold":1,"timeoutSeconds":10},"replicaCount":1,"resources":{},"service":{"port":5000,"type":"ClusterIP"}}` | ---------------------------------------------------------------------------- | | pdfparser | object | `{"autoScaling":{"enabled":false,"maxReplicas":4,"minReplicas":2,"targetCPUUtilizationPercentage":80,"targetMemoryUtilizationPercentage":80},"image":{"repository":"ghcr.io/sbrg/lifelike-pdfparser","tag":"latest"},"livenessProbe":{"enabled":true,"failureThreshold":20,"initialDelaySeconds":20,"path":"/","periodSeconds":10,"successThreshold":1,"timeoutSeconds":10},"readinessProbe":{"enabled":true,"failureThreshold":20,"initialDelaySeconds":20,"path":"/","periodSeconds":10,"successThreshold":1,"timeoutSeconds":10},"replicaCount":1,"resources":{},"service":{"port":7600,"type":"ClusterIP"}}` | ---------------------------------------------------------------------------- | | postgresqlExternal | object | `{"database":"postgres","existingSecret":"","host":"postgres.local","password":"password","port":5432,"user":"postgres"}` | ---------------------------------------------------------------------------- | -| neo4jExternal.host | string | `"neo4j.local"` | | -| neo4jExternal.port | int | `7687` | | -| neo4jExternal.user | string | `"neo4j"` | | -| neo4jExternal.password | string | `"password"` | | -| neo4jExternal.database | string | `"neo4j"` | | +| arangodbExternal.host | string | `"arangodb.local"` | | +| arangodbExternal.port | int | `7687` | | +| arangodbExternal.user | string | `"arangodb"` | | +| arangodbExternal.password | string | `"password"` | | +| arangodbExternal.database | string | `"arangodb"` | | | redisExternal.host | string | `"redis.local"` | | | redisExternal.port | int | `6379` | | | redisExternal.password | string | `""` | | @@ -55,7 +55,7 @@ Kubernetes: `>=1.20.0-0` | elasticsearchExternal.ssl | bool | `false` | | | postgresql | object | `{"auth":{"database":"database","postgresPassword":"password"},"enabled":true}` | ---------------------------------------------------------------------------- | | postgresql.enabled | bool | `true` | Set to false to disable automatic deployment of PostgreSQL | -| neo4j | object | `{"core":{"numberOfServers":1,"persistentVolume":{"size":"100Gi"},"standalone":true},"enabled":true,"imageTag":"4.4.3-community","neo4jPassword":"password"}` | ---------------------------------------------------------------------------- | +| arangodb | object | `{"core":{"numberOfServers":1,"persistentVolume":{"size":"100Gi"},"standalone":true},"enabled":true,"imageTag":"4.4.3-community","arangodbPassword":"password"}` | ---------------------------------------------------------------------------- | | elasticsearch | object | `{"enabled":true,"esConfig":{"elasticsearch.yml":"node.store.allow_mmap: false\n"},"fullnameOverride":"elasticsearch","image":"ghcr.io/sbrg/lifelike-elasticsearch","imageTag":"7.16.3","volumeClaimTemplate":{"resources":{"requests":{"storage":"30Gi"}}}}` | ---------------------------------------------------------------------------- | | redis | object | `{"auth":{"password":"password"},"commonConfiguration":"# Disable persistence to disk\nsave \"\"\n# Disable AOF https://redis.io/topics/persistence#append-only-file\nappendonly no","enabled":true,"master":{"extraFlags":["--maxmemory-policy allkeys-lru"],"persistence":{"enabled":false}},"replica":{"extraFlags":["--maxmemory-policy allkeys-lru"],"persistence":{"enabled":false}}}` | ---------------------------------------------------------------------------- | diff --git a/helm/lifelike/examples/external-db.yaml b/helm/lifelike/examples/external-db.yaml index 69fbebdb47..edeb47c4fc 100644 --- a/helm/lifelike/examples/external-db.yaml +++ b/helm/lifelike/examples/external-db.yaml @@ -1,6 +1,6 @@ ## This is an example values files for installing Lifelike Helm chart ## connecting to external existing database services -## instead of installing the embedded subcharts (postgres, neo4j and elasticsearch) +## instead of installing the embedded subcharts (postgres, arangodb and elasticsearch) # Disable the embedded PostgreSQL subchart @@ -14,14 +14,14 @@ postgresqlExternal: database: postgres password: password -# Disable embedded Neo4j subchart -neo4j: +# Disable embedded ArangoDB subchart +arangodb: enabled: false -# Configure external Neo4j database -neo4jExternal: - host: neo4j.local +# Configure external ArangoDB database +arangodbExternal: + host: arangodb.local port: 7687 - user: neo4j + user: arangodb password: password # Disable embedded Elasticsearch subchart diff --git a/helm/lifelike/templates/_helpers.tpl b/helm/lifelike/templates/_helpers.tpl index 7823c85cb0..09defdf5ea 100644 --- a/helm/lifelike/templates/_helpers.tpl +++ b/helm/lifelike/templates/_helpers.tpl @@ -163,18 +163,18 @@ Set postgres secretKey {{/* ---------------------------------------------------------------------- */}} -{{/* Neo4J */}} +{{/* ArangoDB */}} {{/* ---------------------------------------------------------------------- */}} {{/* Create a default fully qualified app name. We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec). */}} -{{- define "lifelike.neo4j.fullname" -}} -{{- if .Values.neo4j.fullnameOverride -}} -{{- .Values.neo4j.fullnameOverride | trunc 63 | trimSuffix "-" -}} +{{- define "lifelike.arangodb.fullname" -}} +{{- if .Values.arangodb.fullnameOverride -}} +{{- .Values.arangodb.fullnameOverride | trunc 63 | trimSuffix "-" -}} {{- else -}} -{{- $name := default "neo4j" .Values.neo4j.nameOverride -}} +{{- $name := default "arangodb" .Values.arangodb.nameOverride -}} {{- if contains $name .Release.Name -}} {{- .Release.Name | trunc 63 | trimSuffix "-" -}} {{- else -}} @@ -184,57 +184,57 @@ We truncate at 63 chars because some Kubernetes name fields are limited to this {{- end -}} {{/* -Return the Neo4j hostname +Return the ArangoDB hostname */}} -{{- define "lifelike.neo4jHost" -}} -{{- if .Values.neo4j.enabled }} - {{- printf "%s" (include "lifelike.neo4j.fullname" .) -}} +{{- define "lifelike.arangodbHost" -}} +{{- if .Values.arangodb.enabled }} + {{- printf "%s" (include "lifelike.arangodb.fullname" .) -}} {{- else -}} - {{- printf "%s" .Values.neo4jExternal.host -}} + {{- printf "%s" .Values.arangodbExternal.host -}} {{- end -}} {{- end -}} {{/* -Return the Neo4j port +Return the ArangoDB port */}} -{{- define "lifelike.neo4jPort" -}} -{{- if .Values.neo4j.enabled }} +{{- define "lifelike.arangodbPort" -}} +{{- if .Values.arangodb.enabled }} {{- printf "7687" -}} {{- else -}} - {{- .Values.neo4jExternal.port -}} + {{- .Values.arangodbExternal.port -}} {{- end -}} {{- end -}} {{/* -Return the Neo4j user +Return the ArangoDB user */}} -{{- define "lifelike.neo4jUser" -}} -{{- if .Values.neo4j.enabled }} - {{- printf "neo4j" -}} +{{- define "lifelike.arangodbUser" -}} +{{- if .Values.arangodb.enabled }} + {{- printf "arangodb" -}} {{- else -}} - {{- printf "%s" .Values.neo4jExternal.user -}} + {{- printf "%s" .Values.arangodbExternal.user -}} {{- end -}} {{- end -}} {{/* -Return the Neo4j password +Return the ArangoDB password */}} -{{- define "lifelike.neo4jPassword" -}} -{{- if .Values.neo4j.enabled }} - {{- printf "%s" .Values.neo4j.neo4jPassword -}} +{{- define "lifelike.arangodbPassword" -}} +{{- if .Values.arangodb.enabled }} + {{- printf "%s" .Values.arangodb.arangodbPassword -}} {{- else -}} - {{- printf "%s" .Values.neo4jExternal.password -}} + {{- printf "%s" .Values.arangodbExternal.password -}} {{- end -}} {{- end -}} {{/* -Return the Neo4j database name +Return the ArangoDB database name */}} -{{- define "lifelike.neo4jDatabase" -}} -{{- if .Values.neo4j.enabled }} - {{- default "neo4j" .Values.neo4j.defaultDatabase -}} +{{- define "lifelike.arangodbDatabase" -}} +{{- if .Values.arangodb.enabled }} + {{- default "arangodb" .Values.arangodb.defaultDatabase -}} {{- else -}} - {{- default "neo4j" .Values.neo4jExternal.database -}} + {{- default "arangodb" .Values.arangodbExternal.database -}} {{- end -}} {{- end -}} @@ -282,7 +282,7 @@ Return the Elasticsearch port {{- end -}} {{/* -Return the Neo4j user +Return the ArangoDB user */}} {{- define "lifelike.elasticsearchUser" -}} {{- if .Values.elasticsearch.enabled }} @@ -472,17 +472,17 @@ PostgreSQL environment variables helper {{/* -Neo4j environment variables helper +ArangoDB environment variables helper */}} -{{- define "lifelike.neo4jEnv" -}} -- name: NEO4J_HOST - value: {{ template "lifelike.neo4jHost" . }} -- name: NEO4J_PORT - value: {{ include "lifelike.neo4jPort" . | quote }} -- name: NEO4J_AUTH - value: {{ template "lifelike.neo4jUser" . }}/{{ template "lifelike.neo4jPassword" . }} -- name: NEO4J_DB - value: {{ template "lifelike.neo4jDatabase" . }} +{{- define "lifelike.arangodbEnv" -}} +- name: ARANGODB_HOST + value: {{ template "lifelike.arangodbHost" . }} +- name: ARANGODB_PORT + value: {{ include "lifelike.arangodbPort" . | quote }} +- name: ARANGODB_AUTH + value: {{ template "lifelike.arangodbUser" . }}/{{ template "lifelike.arangodbPassword" . }} +- name: ARANGODB_DB + value: {{ template "lifelike.arangodbDatabase" . }} {{- end -}} diff --git a/helm/lifelike/templates/api/deployment.yaml b/helm/lifelike/templates/api/deployment.yaml index 3b2f5dc0cd..38b09da121 100644 --- a/helm/lifelike/templates/api/deployment.yaml +++ b/helm/lifelike/templates/api/deployment.yaml @@ -47,14 +47,14 @@ spec: - --port={{ template "lifelike.postgresqlPort" . }} - --timeout={{ default 30 .Values.api.dbWaiter.timeoutSeconds }} {{- end }} - {{- if .Values.neo4j.enabled }} - - name: wait-for-neo4j + {{- if .Values.arangodb.enabled }} + - name: wait-for-arangodb image: {{ .Values.api.dbWaiter.image.repository }}:{{ .Values.api.dbWaiter.image.tag }} imagePullPolicy: {{ default "IfNotPresent" .Values.api.dbWaiter.image.imagePullPolicy }} command: - /wait-for-it.sh - - --host={{ template "lifelike.neo4jHost" . }} - - --port={{ template "lifelike.neo4jPort" . }} + - --host={{ template "lifelike.arangodbHost" . }} + - --port={{ template "lifelike.arangodbPort" . }} - --timeout={{ default 30 .Values.api.dbWaiter.timeoutSeconds }} {{- end }} - name: migrate-db diff --git a/helm/lifelike/values.schema.json b/helm/lifelike/values.schema.json index 9fc39fb453..84cd16eeca 100644 --- a/helm/lifelike/values.schema.json +++ b/helm/lifelike/values.schema.json @@ -363,7 +363,7 @@ } } }, - "neo4j": { + "arangodb": { "type": "object", "properties": { "core": { @@ -391,12 +391,12 @@ "imageTag": { "type": "string" }, - "neo4jPassword": { + "arangodbPassword": { "type": "string" } } }, - "neo4jExternal": { + "arangodbExternal": { "type": "object", "properties": { "database": { diff --git a/helm/lifelike/values.yaml b/helm/lifelike/values.yaml index 915f62b3f6..aed8f642e8 100644 --- a/helm/lifelike/values.yaml +++ b/helm/lifelike/values.yaml @@ -207,7 +207,7 @@ statisticalEnrichment: periodSeconds: 10 successThreshold: 1 timeoutSeconds: 10 - + service: type: ClusterIP port: 5000 @@ -282,13 +282,13 @@ postgresqlExternal: ## -- Read password from an existing secret, must contain key "postgres-password" existingSecret: "" -## -- External Neo4j connection details, ignored if neo4j.enabled is set to true -neo4jExternal: - host: neo4j.local +## -- External ArangoDB connection details, ignored if arangodb.enabled is set to true +arangodbExternal: + host: arangodb.local port: 7687 - user: neo4j + user: arangodb password: password - database: neo4j + database: arangodb ## -- External Redis connection details, ignored if redis.enabled is set to true @@ -328,19 +328,19 @@ postgresql: database: database # ------------------------------------------------------------------------------ -# Neo4j database +# ArangoDB database # ------------------------------------------------------------------------------ -## -- Embedded Neo4j subchart deployment -## -- See all available values: https://github.com/neo4j-contrib/neo4j-helm/blob/master/values.yaml -neo4j: - ## -- Set to false to disable automatic deployment of Neo4j +## -- Embedded ArangoDB subchart deployment +## -- See all available values: https://github.com/arangodb-contrib/arangodb-helm/blob/master/values.yaml +arangodb: + ## -- Set to false to disable automatic deployment of ArangoDB enabled: true imageTag: 4.4.3-community - ## -- Neo4j password - neo4jPassword: password + ## -- ArangoDB password + arangodbPassword: password core: ## -- Whether to deploy a standalone server or a replicated cluster diff --git a/keycloak b/keycloak deleted file mode 160000 index 738310c786..0000000000 --- a/keycloak +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 738310c786fafb5b1f2f15c3c313e8cb535fe287 diff --git a/lifelike-oss b/lifelike-oss deleted file mode 160000 index 034c727d7c..0000000000 --- a/lifelike-oss +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 034c727d7c5cafbfdcc022fb0ffdadc727b2fdca diff --git a/makefile b/makefile index d0adea1d44..a6d04e8ddf 100644 --- a/makefile +++ b/makefile @@ -1,19 +1,6 @@ APPSERVER_PATH=./appserver -ANSIBLE_PATH=./deployment/ansible LMDB_PATH = $(APPSERVER_PATH)/neo4japp/services/annotations/lmdb -# Fetches the password to unlock Ansible vault files -ansible-secrets: - az storage blob download --account-name lifelike --container-name lifelike-secrets --name .vault_secrets_pw --file $(ANSIBLE_PATH)/.vault_secrets_pw --auth-mode login - -# Fetches the credentials (env file) for Azure services -azure-secrets: - az storage blob download --account-name lifelike --container-name lifelike-secrets --name azure-secrets.env --file ./azure-secrets.env --auth-mode login - -# Log into azure container registry -container-login: - az acr login --name lifelike - # Fetches the LMDB files needed to run the application lmdb: docker compose up -d appserver @@ -22,7 +9,7 @@ lmdb: # Sets up everything you need to run the application # Mostly used for first time dev environment setup -init: ansible-secrets azure-secrets container-login githooks docker-build lmdb +init: githooks docker-build lmdb # Sets up commit hooks for linting githooks: @@ -32,11 +19,11 @@ docker-build: docker compose build # Runs enough containers for the application to function -docker-run: azure-secrets container-login lmdb +docker-run: lmdb docker compose up -d # Runs additional containers such as Kibana/Logstash/Filebeat -docker-run-all: azure-secrets container-login lmdb +docker-run-all: lmdb docker compose -f docker-compose.yml -f docker-compose.override.yml -f docker-compose.middleware.yml up -d docker-stop: diff --git a/statistical-enrichment/Dockerfile b/statistical-enrichment/Dockerfile index a9e34baaf2..0bbc5c830d 100644 --- a/statistical-enrichment/Dockerfile +++ b/statistical-enrichment/Dockerfile @@ -1,7 +1,7 @@ # ======================================== # Base image # ======================================== -FROM python:3.10-slim as base +FROM python:3.8-slim as base ENV LANG C.UTF-8 ENV LC_ALL C.UTF-8 @@ -45,11 +45,11 @@ USER app # Copy application code COPY --chown=app . . -# Neo4j configuration -ENV NEO4J_HOST=neo4j -ENV NEO4J_PORT=7687 -ENV NEO4J_AUTH=neo4j/password -ENV NEO4J_SCHEME=bolt +# ArangoDB configuration +ENV ARANGODB_HOST='' +ENV ARANGODB_PORT='' +ENV ARANGODB_AUTH='' +ENV ARANGODB_SCHEME='' # Redis cache configuration ENV REDIS_HOST=redis diff --git a/website b/website deleted file mode 160000 index 81ad65ebf3..0000000000 --- a/website +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 81ad65ebf32776cbcfff37f40fc10c540fc7074f