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[ENHC0010012B] Workflow executions: End to end integration test (#621)
* github actions sapporo * fix exclude keyword * remove coverage from sapporo test * Fix normal tests * Store ga4gh wes server endpoint in config to allow test servers * have main test runner skip sapporo integration * simplify wes api endpoint inti * add tmp/storage/ to clean_dev script
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| name: Sapporo CI | ||
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| on: | ||
| pull_request: | ||
| branches: [main] | ||
| push: | ||
| branches: [main] | ||
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| jobs: | ||
| test: | ||
| timeout-minutes: 10 | ||
| runs-on: ubuntu-latest | ||
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| services: | ||
| postgres: | ||
| image: postgres:14.6 | ||
| env: | ||
| POSTGRES_DB: irida_next_test | ||
| POSTGRES_PASSWORD: test | ||
| POSTGRES_USER: test | ||
| POSTGRES_HOST: postgres | ||
| ports: | ||
| - 5432:5432 | ||
| # Set health checks to wait until postgres has started | ||
| options: >- | ||
| --health-cmd pg_isready | ||
| --health-interval 10s | ||
| --health-timeout 5s | ||
| --health-retries 5 | ||
| steps: | ||
| - name: Check out code | ||
| uses: actions/checkout@v3 | ||
| - name: Set up Ruby | ||
| uses: ruby/setup-ruby@v1 | ||
| with: | ||
| bundler-cache: true # runs 'bundle install' and caches installed gems automatically | ||
| - name: Set up PNPM | ||
| uses: pnpm/action-setup@v2 | ||
| with: | ||
| version: 7 | ||
| - name: Use Node.js 19 | ||
| uses: actions/setup-node@v3 | ||
| with: | ||
| node-version: 19 | ||
| cache: "pnpm" | ||
| - name: Install dependencies | ||
| run: pnpm install | ||
| - name: Install Sapporo dependencies | ||
| uses: actions/setup-java@v4 | ||
| with: | ||
| distribution: adopt | ||
| java-version: 16 | ||
| - name: Download Sapporo | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: phac-nml/sapporo-service | ||
| ref: irida-next | ||
| path: ./sapporo | ||
| - name: Build Sapporo | ||
| run: | | ||
| cd sapporo | ||
| IRIDA_NEXT_PATH=${GITHUB_WORKSPACE}/tmp MYUID="$(id -u)" MYGID="$(id -g)" docker compose -f compose.irida-next.yml up -d --build | ||
| cd .. | ||
| - name: Run Sapporo | ||
| uses: JarvusInnovations/background-action@v1 | ||
| with: | ||
| run: | | ||
| IRIDA_NEXT_PATH=${GITHUB_WORKSPACE}/tmp MYUID="$(id -u)" MYGID="$(id -g)" docker compose -f compose.irida-next.yml exec app bash -c "sapporo" | ||
| wait-on: | ||
| http://localhost:1122/service-info | ||
| wait-for: 2m | ||
| working-directory: sapporo | ||
| - name: Update permissions | ||
| run: sudo chmod -R 777 ${GITHUB_WORKSPACE} | ||
| - name: Run tests | ||
| run: | | ||
| bin/rails test test/integration/sapporo.rb |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,47 @@ | ||
| # frozen_string_literal: true | ||
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| require 'test_helper' | ||
| require 'active_job_test_case' | ||
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| class IntegrationSapporoTest < ActiveJobTestCase | ||
| def setup | ||
| @workflow_execution = workflow_executions(:irida_next_example_end_to_end) | ||
| Rails.configuration.ga4gh_wes_server_endpoint = 'http://localhost:1122/' | ||
| end | ||
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| def teardown | ||
| Rails.configuration.ga4gh_wes_server_endpoint = nil | ||
| end | ||
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| test 'integration sapporo end to end' do | ||
| # Before starting test, check if Sapporo Integration is running. | ||
| begin | ||
| ga4gh_client = Integrations::Ga4ghWesApi::V1::Client.new | ||
| ga4gh_client.service_info | ||
| rescue Integrations::ApiExceptions::ConnectionError | ||
| skip 'Sapporo server is not running' | ||
| end | ||
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| assert_equal 'initial', @workflow_execution.state | ||
| assert_not @workflow_execution.cleaned? | ||
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| WorkflowExecutionPreparationJob.perform_later(@workflow_execution) | ||
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| perform_enqueued_jobs_sequentially(except: WorkflowExecutionSubmissionJob) | ||
| assert_equal 'prepared', @workflow_execution.reload.state | ||
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| perform_enqueued_jobs_sequentially(except: WorkflowExecutionStatusJob) | ||
| assert_equal 'submitted', @workflow_execution.reload.state | ||
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| perform_enqueued_jobs_sequentially(delay_seconds: 10, except: WorkflowExecutionCompletionJob) | ||
| assert_equal 'completing', @workflow_execution.reload.state | ||
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| perform_enqueued_jobs_sequentially(except: WorkflowExecutionCleanupJob) | ||
| assert_equal 'completed', @workflow_execution.reload.state | ||
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| perform_enqueued_jobs_sequentially | ||
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| assert_equal 'completed', @workflow_execution.reload.state | ||
| assert @workflow_execution.cleaned? | ||
| end | ||
| end |