buildkite/pipeline.yml

steps:
  - label: ":microscope: Sequence plugin and scientific platform (Linux)"
    key: "sequence-viewer:scientific-platform-linux"
    agents:
      queue: applied-bk-agent-openai
    timeout_in_minutes: 40
    commands:
      - 'export TMPDIR="$$PWD/.viewer-ci/sequence-$${BUILDKITE_JOB_ID:-local}"'
      - 'mkdir -p "$${TMPDIR}"'
      - 'export NVM_DIR="$${TMPDIR}/nvm"'
      - . ./chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform/scripts/install-nvm.sh
      - corepack enable pnpm
      - cd chatgpt/oai-maintained-plugins/plugins/sequence-viewer
      - pnpm install --frozen-lockfile --config.confirmModulesPurge=false
      - 'ln -s "$$PWD/node_modules" ../scientific-viewer-platform/node_modules'
      - pnpm exec tsc --noEmit
      - >-
        pnpm exec vitest run
        src/compressed-file-name.test.ts
        src/file-kind.test.ts
        src/plugin-manifest.test.ts
        src/server.test.ts
        src/sequence/file-kind.test.ts
        src/msa/file-kind.test.ts
        src/views/app.test.tsx
        src/views/app-native.test.tsx
        src/views/app-resource-loading.test.tsx
        src/viewer-operations.test.ts
        src/export-actions-workspace.test.tsx
        src/incremental-export-validator.test.ts
        src/workbench-exports.test.ts
        src/workspace-browser-protocol.test.ts
        src/workspace-track-browser.test.ts
        src/workspace-atomic-publisher.test.ts
        src/workspace-export-publisher.test.ts
        src/server-workbench-store.test.ts
        src/server-workbench-upload.test.ts
        src/chat-file-resource.test.ts
        src/indexed-sequence-parser.test.ts
        src/bam-decoder.test.ts
        src/cram-decoder.test.ts
        src/persistent/durable-viewer-state.test.ts
        src/persistent/native-workspace-publisher.test.ts
        src/persistent/recovery-adapter.test.ts
        src/persistent/scientific-data-client.test.ts
        src/persistent/streaming-source-replacement.test.ts
        src/persistent/session-adapter.test.ts
        src/scientific-platform.test.ts
        --maxWorkers=1 --no-file-parallelism
        --testTimeout=600000 --hookTimeout=600000
      - >-
        pnpm exec vitest run
        --root ../scientific-viewer-platform
        tests/sequence
        --maxWorkers=1 --no-file-parallelism
        --testTimeout=600000 --hookTimeout=600000

  - label: ":windows: Sequence plugin and scientific platform (Windows)"
    key: "sequence-viewer:scientific-platform-windows"
    depends_on: "scientific-viewer-platform:prepare-merge-checkout"
    agents:
      queue: applied-bk-agent-windows
    timeout_in_minutes: 40
    env:
      BUILDKITE_CLEAN_CHECKOUT: "true"
      BUILDKITE_SKIP_CHECKOUT: "true"
    commands:
      - '$$ErrorActionPreference = "Stop"'
      - "$$PSNativeCommandUseErrorActionPreference = $$true"
      - &sequence_viewer_merge_checkout |
        if (-not $$env:BUILDKITE_BUILD_PATH) {
          throw "The Sequence viewer checkout requires Buildkite's writable build path."
        }
        $$scientificViewerBootstrapRoot = Join-Path $$env:BUILDKITE_BUILD_PATH (
          "svt-" + [System.Guid]::NewGuid().ToString("N").Substring(0, 8)
        )
        New-Item -ItemType Directory -Force -Path $$scientificViewerBootstrapRoot | Out-Null
        $$env:TEMP = $$scientificViewerBootstrapRoot
        $$env:TMP = $$scientificViewerBootstrapRoot
        try {
          $$scientificViewerCheckoutRoot = Join-Path $$env:TEMP "scientific-viewer-checkout-$$env:BUILDKITE_JOB_ID"
          New-Item -ItemType Directory -Force -Path $$scientificViewerCheckoutRoot | Out-Null
          buildkite-agent artifact download --step "scientific-viewer-platform:prepare-merge-checkout" "chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform/scripts/checkout-merge-bundle.ps1" $$scientificViewerCheckoutRoot
          if ($$LASTEXITCODE -ne 0) {
            throw "Could not download the scientific viewer merge checkout helper."
          }
          $$scientificViewerCheckout = Join-Path $$scientificViewerCheckoutRoot "chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform/scripts/checkout-merge-bundle.ps1"
          . $$scientificViewerCheckout -SparsePath @(
            "chatgpt/oai-maintained-plugins/plugins/sequence-viewer",
            "chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform"
          )
          $$sequenceViewerTempRoot = Join-Path (Get-Location).Path ".scientific-sequence/$$env:BUILDKITE_JOB_ID"
          New-Item -ItemType Directory -Force -Path $$sequenceViewerTempRoot | Out-Null
          $$env:TEMP = $$sequenceViewerTempRoot
          $$env:TMP = $$sequenceViewerTempRoot
        } finally {
          if (Test-Path -LiteralPath $$scientificViewerBootstrapRoot) {
            Remove-Item -LiteralPath $$scientificViewerBootstrapRoot -Recurse -Force
          }
        }
        Get-PSDrive -Name (Get-Item "$$env:TEMP").PSDrive.Name | Select-Object Name, Free, Used
      - ./chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform/scripts/install-node.ps1
      - corepack enable
      - cd chatgpt/oai-maintained-plugins/plugins/sequence-viewer
      - pnpm install --frozen-lockfile --config.confirmModulesPurge=false
      - 'New-Item -ItemType Junction -Path "../scientific-viewer-platform/node_modules" -Target (Resolve-Path "node_modules") | Out-Null'
      - pnpm exec tsc --noEmit
      - >-
        pnpm exec vitest run
        src/compressed-file-name.test.ts
        src/file-kind.test.ts
        src/plugin-manifest.test.ts
        src/server.test.ts
        src/sequence/file-kind.test.ts
        src/msa/file-kind.test.ts
        src/views/app.test.tsx
        src/views/app-native.test.tsx
        src/views/app-resource-loading.test.tsx
        src/viewer-operations.test.ts
        src/export-actions-workspace.test.tsx
        src/incremental-export-validator.test.ts
        src/workbench-exports.test.ts
        src/workspace-browser-protocol.test.ts
        src/workspace-track-browser.test.ts
        src/workspace-atomic-publisher.test.ts
        src/workspace-export-publisher.test.ts
        src/server-workbench-store.test.ts
        src/server-workbench-upload.test.ts
        src/chat-file-resource.test.ts
        src/indexed-sequence-parser.test.ts
        src/bam-decoder.test.ts
        src/cram-decoder.test.ts
        src/persistent/durable-viewer-state.test.ts
        src/persistent/native-workspace-publisher.test.ts
        src/persistent/recovery-adapter.test.ts
        src/persistent/scientific-data-client.test.ts
        src/persistent/streaming-source-replacement.test.ts
        src/persistent/session-adapter.test.ts
        src/scientific-platform.test.ts
        --maxWorkers=1 --no-file-parallelism
        --testTimeout=600000 --hookTimeout=600000
      - >-
        pnpm exec vitest run
        --root ../scientific-viewer-platform
        tests/sequence
        --maxWorkers=1 --no-file-parallelism
        --testTimeout=600000 --hookTimeout=600000

  - label: ":microscope: Sequence actual 6 GiB BGZF qualification (Linux)"
    key: "sequence-viewer:physical-bgzf-linux"
    agents:
      queue: applied-bk-agent-openai
    timeout_in_minutes: 90
    env:
      SCIENTIFIC_SEQUENCE_HUGE_FILE_E2E: "1"
    commands:
      - 'export TMPDIR="$$PWD/.viewer-ci/sequence-$${BUILDKITE_JOB_ID:-local}"'
      - 'mkdir -p "$${TMPDIR}"'
      - 'export NVM_DIR="$${TMPDIR}/nvm"'
      - . ./chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform/scripts/install-nvm.sh
      - corepack enable pnpm
      - cd chatgpt/oai-maintained-plugins/plugins/sequence-viewer
      - pnpm install --frozen-lockfile --config.confirmModulesPurge=false
      - 'ln -s "$$PWD/node_modules" ../scientific-viewer-platform/node_modules'
      - >-
        pnpm exec vitest run
        --root ../scientific-viewer-platform
        tests/sequence/scientific-sequence-huge-physical.test.ts
        --maxWorkers=1 --no-file-parallelism --maxConcurrency=1
        --testTimeout=600000 --hookTimeout=600000

  - label: ":windows: Sequence actual 6 GiB BGZF qualification (Windows)"
    key: "sequence-viewer:physical-bgzf-windows"
    depends_on: "scientific-viewer-platform:prepare-merge-checkout"
    agents:
      queue: applied-bk-agent-windows
    timeout_in_minutes: 90
    env:
      BUILDKITE_CLEAN_CHECKOUT: "true"
      BUILDKITE_SKIP_CHECKOUT: "true"
      SCIENTIFIC_SEQUENCE_HUGE_FILE_E2E: "1"
    commands:
      - '$$ErrorActionPreference = "Stop"'
      - "$$PSNativeCommandUseErrorActionPreference = $$true"
      - *sequence_viewer_merge_checkout
      - ./chatgpt/oai-maintained-plugins/plugins/scientific-viewer-platform/scripts/install-node.ps1
      - corepack enable
      - cd chatgpt/oai-maintained-plugins/plugins/sequence-viewer
      - pnpm install --frozen-lockfile --config.confirmModulesPurge=false
      - 'New-Item -ItemType Junction -Path "../scientific-viewer-platform/node_modules" -Target (Resolve-Path "node_modules") | Out-Null'
      - >-
        pnpm exec vitest run
        --root ../scientific-viewer-platform
        tests/sequence/scientific-sequence-huge-physical.test.ts
        --maxWorkers=1 --no-file-parallelism --maxConcurrency=1
        --testTimeout=600000 --hookTimeout=600000