fix(drop_diseasystore): Fix logic testing #28
Workflow file for this run
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| on: push | |
| jobs: | |
| code-coverage-sqlite: | |
| name: "🧪 Tests: SCDB v0.3, ${{ matrix.config.backend }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - backend: SQLite | |
| id: sqlite | |
| args: 'list(dbname = file.path(tempdir(), "SQLite.SQLite"))' | |
| schemas: '' | |
| - backend: SQLite - w. schemas | |
| id: sqlite-schemas | |
| args: 'list(dbname = file.path(tempdir(), "SQLite_schemas.SQLite"))' | |
| schemas: 'test_ds,not_test_ds' | |
| env: | |
| BACKEND: ${{ matrix.config.backend }} | |
| BACKEND_DRV: RSQLite::SQLite | |
| BACKEND_ARGS: ${{ matrix.config.args }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: '1' | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Setup BACKEND_POST_CONNECT | |
| if: ${{ matrix.config.schemas != '' }} | |
| run: | | |
| set -o xtrace | |
| IFS=',' read -ra schemas <<< "${{ matrix.config.schemas }}" | |
| CONN_POST_CONNECT="list(" | |
| for schema in "${schemas[@]}"; do | |
| CONN_POST_CONNECT+="paste0(\"ATTACH '\", file.path(tempdir(), \"SQLite_schemas_${schema}.SQLite\"), \"' AS '${schema}'\"), " | |
| done | |
| # Trim trailing ", " from CONN_POST_CONNECT | |
| CONN_POST_CONNECT=${CONN_POST_CONNECT%??} | |
| CONN_POST_CONNECT+=")" | |
| echo "BACKEND_POST_CONNECT=$CONN_POST_CONNECT" >> $GITHUB_ENV | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| TESTTHAT_OUT=$(find ${{ runner.temp }}/package -name 'testthat.Rout*') | |
| cat $TESTTHAT_OUT | |
| # Throw errors on failures or warnings | |
| grep -q "FAIL 0" $TESTTHAT_OUT || { echo "Test failures found"; exit 1; } | |
| grep -q "WARN 0" $TESTTHAT_OUT || { echo "Test warnings found"; exit 1; } | |
| # Throw error if error: are found | |
| if grep -q "Error:" $TESTTHAT_OUT; then | |
| echo "Error: found" | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures-${{ matrix.config.id }} | |
| path: ${{ runner.temp }}/package | |
| code-coverage-postgres: | |
| name: "🧪 Tests: SCDB v0.3, PostgreSQL" | |
| runs-on: ubuntu-latest | |
| services: | |
| postgres: | |
| image: postgres:latest | |
| env: | |
| POSTGRES_DB: test | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| ports: | |
| - 5432:5432 | |
| options: --health-cmd "pg_isready -U postgres" --health-interval 10s --health-timeout 5s --health-retries 5 | |
| env: | |
| BACKEND: PostgreSQL | |
| BACKEND_DRV: RPostgres::Postgres | |
| BACKEND_ARGS: '' | |
| PGHOST: localhost | |
| PGPORT: 5432 | |
| PGDATABASE: test | |
| PGUSER: postgres | |
| PGPASSWORD: postgres | |
| steps: | |
| - name: Setup testing schemata in PostgreSQL | |
| if: ${{ inputs.schemas != 'none' }} | |
| run: | | |
| set -o xtrace | |
| IFS=',' read -ra schemas <<< "${{ inputs.schemas }}" | |
| for schema in "${schemas[@]}"; do | |
| psql test -c "CREATE SCHEMA \"$schema\";" | |
| done | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: '1' | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| TESTTHAT_OUT=$(find ${{ runner.temp }}/package -name 'testthat.Rout*') | |
| cat $TESTTHAT_OUT | |
| # Throw errors on failures or warnings | |
| grep -q "FAIL 0" $TESTTHAT_OUT || { echo "Test failures found"; exit 1; } | |
| grep -q "WARN 0" $TESTTHAT_OUT || { echo "Test warnings found"; exit 1; } | |
| # Throw error if error: are found | |
| if grep -q "Error:" $TESTTHAT_OUT; then | |
| echo "Error: found" | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures-postgres | |
| path: ${{ runner.temp }}/package | |
| - name: Collect docker logs | |
| if: always() | |
| uses: jwalton/gh-docker-logs@v2 | |
| with: | |
| dest: '${{ runner.workspace }}/logs-docker' | |
| - name: Check docker logs for PostgreSQL ERRORs | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| log=$(find ${{ runner.workspace }}/logs-docker/ -name '*postgres*.log') | |
| errors=$(awk '/(ERROR:|STATEMENT:)/{flag=1}/LOG:|^[A-Z]/{flag=0}flag {print $0}' $log) | |
| echo "$output" | |
| # Throw error if ERRORs are found | |
| if [[ -n "$errors" ]]; then | |
| echo "$errors" | |
| exit 1 | |
| fi | |
| code-coverage-mssql: | |
| name: "🧪 Tests: SCDB v0.3, SQL Server 2019" | |
| runs-on: ubuntu-latest | |
| env: | |
| BACKEND: MSSQL | |
| BACKEND_DRV: odbc::odbc | |
| BACKEND_ARGS: '' | |
| CONN_ARGS_JSON: > | |
| { | |
| "MSSQL": { | |
| "driver": "ODBC Driver 17 for SQL Server", | |
| "server": "localhost", | |
| "database": "master", | |
| "UID": "SA", | |
| "PWD": "dbatools.I0" | |
| } | |
| } | |
| steps: | |
| - name: Install a SQL Server suite of tools | |
| uses: potatoqualitee/[email protected] | |
| with: | |
| install: sqlengine, sqlpackage, sqlclient | |
| show-log: true | |
| - name: Setup testing schemata in SQL server | |
| if: ${{ inputs.schemas != 'none' }} | |
| run: | | |
| set -o xtrace | |
| sqlcmd -V 10 -S localhost -U SA -P dbatools.I0 -Q "ALTER LOGIN SA WITH DEFAULT_DATABASE = master;" | |
| IFS=',' read -ra schemas <<< "${{ inputs.schemas }}" | |
| for schema in "${schemas[@]}"; do | |
| sqlcmd -V 10 -S localhost -U SA -P dbatools.I0 -d master -Q "CREATE SCHEMA [$schema];" | |
| sqlcmd -V 10 -S localhost -U SA -P dbatools.I0 -d master -Q "GO" | |
| done | |
| sqlcmd -V 10 -S localhost -U SA -P dbatools.I0 -d master -Q "SELECT * FROM sys.schemas" | |
| sqlcmd -V 10 -S localhost -U SA -P dbatools.I0 -d master -Q "SELECT schema_name FROM INFORMATION_SCHEMA.SCHEMATA WHERE schema_name = 'test'" | |
| sqlcmd -V 10 -S localhost -U SA -P dbatools.I0 -d master -Q "SELECT schema_name FROM INFORMATION_SCHEMA.SCHEMATA WHERE schema_name = 'test.one'" | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: '1' | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| TESTTHAT_OUT=$(find ${{ runner.temp }}/package -name 'testthat.Rout*') | |
| cat $TESTTHAT_OUT | |
| # Throw errors on failures or warnings | |
| grep -q "FAIL 0" $TESTTHAT_OUT || { echo "Test failures found"; exit 1; } | |
| grep -q "WARN 0" $TESTTHAT_OUT || { echo "Test warnings found"; exit 1; } | |
| # Throw error if error: are found | |
| if grep -q "Error:" $TESTTHAT_OUT; then | |
| echo "Error: found" | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures-mssql | |
| path: ${{ runner.temp }}/package | |
| - name: Collect docker logs | |
| if: always() | |
| uses: jwalton/gh-docker-logs@v2 | |
| with: | |
| dest: '${{ runner.workspace }}/logs-docker' | |
| - name: Check docker logs for SQL Server ERRORs | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| log=$(find ${{ runner.workspace }}/logs-docker/ -name 'sql.log') | |
| cat "$log" |