initial commit

.dockerignore

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+**/node_modules
+**/.env
+**/spec
+**/target
+build
+config
+docs
+jenkinsfile
+node_modules
+tests
+
+#Exclude specific files/folders
+!build/hana

.github/ISSUE_TEMPLATE.md

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+[//]: # (When creating a new issue, please read our wiki first:)
+[//]: # (https://alp.atlassian.net/wiki/spaces/CS/pages/3554870121/How+to+report+bugs)
+[//]: # (Then, provide the following information:)
+
+**1. Summary**:
+**2. Steps to Reproduce**:
+**3. Your Expected Result**:
+**4. Actual Result**:
+**5. System Version**:
+**6. BCP/Customer Info**:
+
+
+[//]: # (Finally, add the *bug* label to the issue.)
+[//]: # (If you have further information about this bug being a candidate for the)
+[//]: # (current patch, please add the *patch candidate* label to it too.)

.github/PULL_REQUEST_TEMPLATE.md

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+### Merge Checklist
+
+Please cross check this list if additions / modifications needs to be done on top of your core changes and tick them off. Reviewer can as well glance through and help the developer if something is missed out.
+
+- [ ] Automated Tests (Jasmine integration tests, Unit tests, and/or Performance tests)
+- [ ] Updated Manual tests / Demo Config
+- [ ] Documentation (Application guide, Admin guide, Markdown, Readme and/or Wiki)
+- [ ] Verified that local development environment is working with latest changes (integrated with latest `develop` branch)
+- [ ] following best practices in [code review doc](../code_review.md)

.github/workflows/alp-dataflow-gen-test.yml

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+name: ALP dataflow-gen unit tests
+
+on:
+  pull_request:
+    types: [opened, ready_for_review, reopened, synchronize]
+  push:
+    branches:
+      - develop
+
+jobs:
+  test-alp-dataflow-gen:
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Install dependencies
+      # protobuf-compiler required for python build dask-sql
+      run: sudo apt-get install protobuf-compiler
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - uses: dorny/paths-filter@v2
+      id: check_file_changed
+      with:
+        filters: |
+          alp_dataflow_gen_changed:
+            - 'services/alp-dataflow-gen/**'
+            
+    - name: Setup python if files have changed
+      uses: actions/setup-python@v2
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.alp_dataflow_gen_changed == 'True'
+      with:
+        python-version: 3.11.7
+        cache: 'pip'
+
+    - name: Install pip packages if files have changed
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.alp_dataflow_gen_changed == 'True'
+      working-directory: ./services/alp-dataflow-gen
+      run: pip install -r requirements-dev.txt
+
+    - name: Run unit tests if files have changed
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.alp_dataflow_gen_changed == 'True'
+      working-directory: ./services/alp-dataflow-gen/pysrc
+      run: python3 -m pytest -v --disable-pytest-warnings

.github/workflows/alp-dataflow-test.yml

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+name: ALP Dataflow unit tests
+
+on:
+  pull_request:
+    types: [opened, ready_for_review, reopened, synchronize]
+  push:
+    branches:
+      - develop
+jobs:
+  test-alp-dataflow:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - uses: dorny/paths-filter@v2
+      id: check_file_changed
+      with:
+        filters: |
+          dataflow_changed:
+            - 'services/alp-dataflow/**'
+    - name: Setup node if files have changed
+      uses: actions/setup-node@v3
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.dataflow_changed == 'True'
+      with:
+        node-version: '18.14.0'
+    # Run the step only with "dataflow_changed" equals "True"
+    - name: Run unit tests if files have changed
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.dataflow_changed == 'True'
+      run: |
+        cd services/alp-dataflow
+        yarn --prefer-offline
+        yarn build:lint
+        yarn test

.github/workflows/alp-db-credentials-test.yml

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+name: ALP DB Credentials unit tests
+
+on:
+  pull_request:
+    types: [opened, ready_for_review, reopened, synchronize]
+  push:
+    branches:
+      - develop
+jobs:
+  test-alp-db-credentials:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - uses: dorny/paths-filter@v2
+      id: check_file_changed
+      with:
+        filters: |
+          db_credentials_changed:
+            - 'services/alp-db-credentials/**'
+    - name: Setup node if files have changed
+      uses: actions/setup-node@v3
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.db_credentials_changed == 'True'
+      with:
+        node-version: '18.14.0'
+    # Run the step only with "db_credentials_changed" equals "True"
+    - name: Run unit tests if files have changed
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.db_credentials_changed == 'True'
+      run: |
+        cd services/alp-db-credentials
+        yarn --prefer-offline
+        yarn build:lint
+        yarn test

.github/workflows/alp-db-svc-test.yml

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+name: ALP DB-Svc integration tests with Azure Hana database and local Postgres database
+
+on:
+  pull_request:
+    types: [opened, ready_for_review, reopened, synchronize]
+  workflow_dispatch:
+  push:
+    branches:
+      - develop
+
+# Run only one job per branch
+concurrency:
+  group: ${{ github.head_ref || github.ref_name }}-db-svc-tests # Run the latest push
+  cancel-in-progress: true # Cancel in progress jobs of the workflow of the branch
+
+
+jobs:
+  test-alp-db-svc:
+    if: (github.ref_name == 'develop' ||  contains('release', github.ref_name) || github.event_name == 'workflow_dispatch') || ( github.event_name == 'pull_request' && !github.event.pull_request.draft ) # Should run if branch is develop/release/workflow_dispatch and doesnt have a PR
+    runs-on: ubuntu-latest
+    env:
+      # DB-SVC ENV
+      LB__LOG_LEVEL: "info"
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+      DB_SVC__LOG_LEVEL: "error"
+      DB_SVC__DEBUG: "false"
+      DB_SVC__PORT: "3333"
+      DB_SVC__PATH: "/alpdb"
+      OMOP__VOCAB_SCHEMA: "CDMVOCAB"
+      HANA__READ_ROLE: "TENANT_READ_ROLE"
+      HANA__DRIVER_CLASS_PATH: "db/drivers/hana/ngdbc-latest.jar"
+      POSTGRES__DRIVER_CLASS_PATH: "db/drivers/postgres/postgresql-42.3.1.jar"
+      B2C__ALP_APP__CLIENT_ID: "30dccbb9-5705-483f-bbaf-1f7c8f0f4fce"
+      AD__IDENTITY_METADATA: "https://login.microsoftonline.com/f59c7915-9283-4fb5-b633-435b9145ca00/v2.0/.well-known/openid-configuration"
+      AD__AUDIENCE: "30dccbb9-5705-483f-bbaf-1f7c8f0f4fce, 3da7b194-8456-4ef1-a790-00ef6360decd"
+      SKIP_AUTH: "TRUE"
+      DISABLE_SSL: "TRUE"
+      ROLLBACK_SCHEMA_CREATION_FOR_LIQUIBASE_SCRIPT_FAILURE: "TRUE"
+      HANA__TENANT_CONFIGS: "{}"
+      INTEGRATION_TEST__HANA__TENANT_CONFIGS: ${{ secrets.ALP_DB_SVC_INTEGRATION_TEST_HANA_TENANT_CONFIGS_GERMANY }}
+      PG__TENANT_CONFIGS: '{"alp":{"host":"localhost","port":"5432","databaseName":"alp","postgresAdminUser":"postgres","postgresAdminPassword":"Toor1234","postgresReadUser":"postgres_tenant_read_user","postgresReadPassword":"Toor1234"}}'
+      PG__READ_ROLE: "POSTGRES_TENANT_READ_ROLE"
+
+    services:
+      postgres:
+        image: postgres:15-alpine
+        env:
+          POSTGRES_USER: "postgres"
+          POSTGRES_PASSWORD: "Toor1234"
+          POSTGRES_DB: "alp"
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - uses: actions/checkout@v4
+        name: sameBranch checkout (OverrideRepo)
+        id: sameBranch-checkout
+        continue-on-error: true
+        with:
+          repository:  ${{ vars.OVERRIDE_REPO }}
+          token: ${{ secrets.CI_PAT }}
+          path: 'tmp'
+          sparse-checkout: 'alp-data-node-override'
+          sparse-checkout-cone-mode: false
+          ref: ${{ env.BRANCH_NAME }}
+
+      - shell: bash
+        name: sameBranch checkout test
+        id: sameBranch-checkout-test
+        run: |
+          ls -lhtr tmp
+          [ -d tmp/alp-data-node-override ] || echo OVERRIDE_DEVELOP_BRANCH=true | tee -a "$GITHUB_OUTPUT"
+
+      - uses: actions/checkout@v4
+        name: develop branch checkout (sameBranch checkout fails)
+        if: steps.sameBranch-checkout-test.outputs.OVERRIDE_DEVELOP_BRANCH == 'True' 
+        with:
+          repository:  ${{ vars.OVERRIDE_REPO }}
+          token: ${{ secrets.CI_PAT }}
+          path: 'tmp'
+          sparse-checkout: 'alp-data-node-override'
+          sparse-checkout-cone-mode: false
+          ref: develop
+
+      - shell: bash
+        name: merge files from override
+        id: merge_files_from_override
+        run: |
+          ls -l tmp/alp-data-node-override
+          cp -prnl ./tmp/alp-data-node-override/* .
+          ls -l ./services/alp-db-svc/db/drivers
+          ln -s tmp/alp-data-node-override alp-data-node-override
+
+      - name: Install 1Password CLI
+        uses: 1password/install-cli-action@v1
+
+      - name: Get alp-dbcli from 1password
+        env:
+          OP_SERVICE_ACCOUNT_TOKEN: ${{ secrets.OP_SERVICE_ACCOUNT_TOKEN }}
+        run: |
+          pwd
+          mkdir -p internal/build
+          op read --out-file internal/build/alp-dbcli-v1.0.0.tgz "op://${{ vars.OP_VAULT_NAME }}/alp-dbcli-v1.0.0.tgz/alp-dbcli-v1.0.0.tgz"
+          ls -l internal/build
+
+      - shell: bash
+        # Give an id to the step, so we can reference it later
+        name: check if files changed
+        id: check_file_changed
+        run: |
+          # Fetch develop & get file changes from feature branch
+          git fetch origin develop
+
+          # Diff HEAD with the last commit of develop & filter for 'services/alp-db-svc/**'
+          diff=$(git diff --name-only origin/develop HEAD | grep '^services/alp-db-svc/**' || :)
+
+          # Check if a file under services/alp-db-svc/** has changed (added, modified, deleted)
+          hasDiff=$(if [ ${#diff} -gt 0 ] ; then echo "True" ; else echo "False"; fi)
+
+          # Set the output named "has_dbsvc_changed"
+          echo "has_dbsvc_changed=$hasDiff" >> $GITHUB_OUTPUT
+          echo "Files changed: $diff"
+          echo "Does db-svc have changes: $hasDiff"
+
+      - uses: actions/setup-node@v3
+        if: github.ref_name == 'develop' || steps.check_file_changed.outputs.has_dbsvc_changed == 'True'
+        with:
+          node-version: "18.14.0"
+
+      - name: Build Project (DB-SVC)
+        if: github.ref_name == 'develop' || steps.check_file_changed.outputs.has_dbsvc_changed == 'True'
+        run: |
+          # Build alp-libs dependencies for alp-db-svc
+          yarn install --frozen-lockfile
+          yarn workspace @alp/alp-base-utils run compile
+
+          # Build alp-db-svc
+          cd services/alp-db-svc
+          yarn
+          yarn compile
+
+      - name: Setup Test DB (postgres)
+        if: github.ref_name == 'develop' || steps.check_file_changed.outputs.has_dbsvc_changed == 'True'
+        working-directory: ./services/alp-db-svc
+        run: |
+          # Create cdmvocab and cdmdefault schema for db-svc integration tests
+          yarn workspace alp-db-svc cdm-install-script post /alpdb/postgres/database/alp/data-model/omop5-4/schema/cdmvocab "{\"cleansedSchemaOption\": false, \"vocabSchema\": \"${OMOP__VOCAB_SCHEMA}\"}" && yarn workspace alp-db-svc cdm-install-script post /alpdb/postgres/database/alp/data-model/omop5-4/schema/cdmdefault "{\"cleansedSchemaOption\": false, \"vocabSchema\": \"${OMOP__VOCAB_SCHEMA}\"}"
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.CI_GITHUB_PKGS_NPM_TOKEN }}
+
+      - name: Run integration tests for DB-SVC POSTGRES
+        working-directory: ./services/alp-db-svc
+        # run only if files in 'has_dbsvc_changed' is set to 'True'
+        if: github.ref_name == 'develop' || steps.check_file_changed.outputs.has_dbsvc_changed == 'True'
+        run: |
+          npm run pgtest
+      - name: Run integration tests for DB-SVC HANA
+        working-directory: ./services/alp-db-svc
+        # run only if files in 'has_dbsvc_changed' is set to 'True'
+        if: github.ref_name == 'develop' || steps.check_file_changed.outputs.has_dbsvc_changed == 'True'
+        run: |
+          npm run test

.github/workflows/alp-portal-server-test.yml

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+name: ALP Portal Server unit tests
+
+on:
+  pull_request:
+    types: [opened, ready_for_review, reopened, synchronize]
+  push:
+    branches:
+      - develop
+jobs:
+  test-alp-portal-server:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - uses: dorny/paths-filter@v2
+      id: check_file_changed
+      with:
+        filters: |
+          portal_server_changed:
+            - 'services/alp-portal-server/**'
+    - name: Setup node if files have changed
+      uses: actions/setup-node@v3
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.portal_server_changed == 'True'
+      with:
+        node-version: '18.14.0'
+    # Run the step only with "portal_server_changed" equals "True"
+    - name: Run unit tests if files have changed
+      if: github.ref_name == 'develop' || steps.check_file_changed.outputs.portal_server_changed == 'True'
+      run: |
+        cd services/alp-portal-server
+        yarn --prefer-offline
+        yarn build:lint
+        yarn test