InstallRunAndArtifact.yml

name: Install and Run

on:
  push:
    branches: [ "master" ]
  pull_request:
    branches: [ "master" ]

env:
  DOTNET_VERSION: 8.0.204
  DOTNET_FRAMEWORK: net8.0

jobs:
  install:
    name: Create Installer Artifact
    runs-on: windows-latest

    steps:
      - uses: actions/checkout@v4

      - name: Setup .NET
        uses: actions/setup-dotnet@v4
        with:
          dotnet-version: ${{ env.DOTNET_VERSION }}

      - name: Setup MSBuild
        uses: microsoft/setup-msbuild@v2

      - name: Restore dependencies
        run: dotnet restore ./MetaMorpheus/MetaMorpheus.sln

      - name: Build solution
        run: dotnet msbuild -v:minimal -p:Configuration=Release -p:UseSharedCompilation=false ./MetaMorpheus/

      - name: Build installer
        run: |
          msbuild ./MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj /p:Configuration=Release /verbosity=minimal /p:UseSharedCompilation=false
          msbuild ./MetaMorpheus/Bootstrapper/Bootstrapper.wixproj /p:Configuration=Release /p:UseSharedCompilation=false

      - name: Verify installer exists
        run: |
          if (!(Test-Path "./MetaMorpheus/MetaMorpheusSetup/bin/Release/MetaMorpheusInstaller.msi")) {
            Write-Host "❌ Installer build failed: MetaMorpheusInstaller.msi not found." -ForegroundColor Red
            exit 1
          }

      - name: Zip command-line version
        run: |
          7z a MetaMorpheus_CommandLine.zip .\MetaMorpheus\CMD\bin\Release\$env:DOTNET_FRAMEWORK\* "-x!*.xml"

      # check that installer is greater than 1 kb to avoid pushing an empty artifact
      - name: Validate command-line zip artifact
        run: |
          if ((Get-Item MetaMorpheus_CommandLine.zip).length -lt 1kb) {
            Write-Host "❌ The build failed because the command-line .zip did not build properly; it is empty." -ForegroundColor Red
            exit 1
          }

      - name: Upload installer artifact
        uses: actions/upload-artifact@v4
        with:
          name: MetaMorpheusInstaller
          path: ./MetaMorpheus/MetaMorpheusSetup/bin/Release/MetaMorpheusInstaller.msi

      - name: Upload command-line zip artifact
        uses: actions/upload-artifact@v4
        with:
          name: MetaMorpheus_CommandLine
          path: MetaMorpheus_CommandLine.zip


  test_installer:
    name: Search with Installed
    runs-on: windows-latest
    needs: install

    steps:
      - uses: actions/checkout@v4

      - name: Setup .NET
        uses: actions/setup-dotnet@v4
        with:
          dotnet-version: ${{ env.DOTNET_VERSION }}

      - name: Download installer artifact
        uses: actions/download-artifact@v4
        with:
          name: MetaMorpheusInstaller

      - name: Install MetaMorpheus MSI
        run: |
          Start-Process -FilePath msiexec.exe -ArgumentList "/i `"$(Get-Location)\MetaMorpheusInstaller.msi`" /qn /l*v install.log" -Wait


      - name: Display workspace directory tree
        run: |
          function Show-Tree ($path, $indent = "") {
              Get-ChildItem -LiteralPath $path | ForEach-Object {
                  Write-Host "$indent|- $($_.Name)"
                  if ($_.PSIsContainer) {
                      Show-Tree -path $_.FullName -indent ("$indent   ")
                  }
              }
          }
          $workspace = Get-Location
          Write-Host "Workspace directory tree for: $workspace"
          Show-Tree $workspace

      - name: Microvinette with installed CMD.exe
        run: |
          $dataDir = "$(Get-Location)\MetaMorpheus\MetaMorpheus\Test\TestData"
          & "C:\Program Files\MetaMorpheus\CMD.exe" --test -o "$dataDir\exe_output" -v minimal
          if ($LASTEXITCODE -ne 0) {
            Write-Host "❌ CMD.exe search failed with exit code $LASTEXITCODE" -ForegroundColor Red
            exit $LASTEXITCODE
          }

      - name: Generate Default TOMLs with installed CMD.dll
        run: |
          dotnet "C:\Program Files\MetaMorpheus\CMD.dll" -g -o "$(Get-Location)\MetaMorpheus\EngineLayer\Data"

      - name: Run search with installed CMD.dll
        run: |
          $dataDir = "$(Get-Location)\MetaMorpheus\EngineLayer\Data"
          dotnet "C:\Program Files\MetaMorpheus\CMD.dll" -s "$dataDir\SmallCalibratible_Yeast.mzML" -d "$dataDir\SmallYeast.fasta" -t "$dataDir\SearchTask.toml" -o "$dataDir\dll_output" -v minimal
          if ($LASTEXITCODE -ne 0) {
            Write-Host "❌ CMD.dll search failed with exit code $LASTEXITCODE" -ForegroundColor Red
            exit $LASTEXITCODE
          }

  test_build:
    name: Search with Built
    runs-on: windows-latest

    steps:
      - uses: actions/checkout@v4

      - name: Setup .NET
        uses: actions/setup-dotnet@v4
        with:
          dotnet-version: ${{ env.DOTNET_VERSION }}

      - name: Restore dependencies
        run: dotnet restore ./MetaMorpheus/MetaMorpheus.sln

      - name: Build solution
        run: dotnet msbuild -v:minimal -p:Configuration=Release -p:UseSharedCompilation=false ./MetaMorpheus/

      - name: Generate Default TOMLs
        run: |
          dotnet "$(Get-Location)\MetaMorpheus\CMD\bin\Release\$env:DOTNET_FRAMEWORK\CMD.dll" -g -o "$(Get-Location)\MetaMorpheus\CMD\bin\Release\$env:DOTNET_FRAMEWORK\Data"

      - name: Run search with built CMD.dll
        run: |
          $dataDir = "$(Get-Location)\MetaMorpheus\CMD\bin\Release\$env:DOTNET_FRAMEWORK\Data"
          dotnet "$(Get-Location)\MetaMorpheus\CMD\bin\Release\$env:DOTNET_FRAMEWORK\CMD.dll" -s "$dataDir\SmallCalibratible_Yeast.mzML" -d "$dataDir\SmallYeast.fasta" -t "$dataDir\SearchTask.toml" -o "$dataDir\built_dll_output" -v minimal
          if ($LASTEXITCODE -ne 0) {
            Write-Host "❌ Built CMD.dll search failed with exit code $LASTEXITCODE" -ForegroundColor Red
            exit $LASTEXITCODE
          }

  ## Installs and builds. Verifies that the same dlls exist
  validate_installer_contents:
    name: Validate Installer Contents
    runs-on: windows-latest
    needs: install

    steps:
      - uses: actions/checkout@v4

      - name: Setup .NET
        uses: actions/setup-dotnet@v4
        with:
          dotnet-version: ${{ env.DOTNET_VERSION }}

      - name: Download installer artifact
        uses: actions/download-artifact@v4
        with:
          name: MetaMorpheusInstaller

      - name: Install MetaMorpheus MSI
        run: |
          Start-Process -FilePath msiexec.exe -ArgumentList "/i `"$(Get-Location)\MetaMorpheusInstaller.msi`" /qn /l*v install.log" -Wait

      - name: Restore dependencies
        run: dotnet restore ./MetaMorpheus/MetaMorpheus.sln

      - name: Build solution
        run: dotnet msbuild -v:minimal -p:Configuration=Release -p:UseSharedCompilation=false ./MetaMorpheus/

      - name: Compare built DLLs to installed DLLs
        run: |
          $buildDir = $repoDir = Get-Location
          $installDir = "C:\Program Files\MetaMorpheus"

          # Get DLL names
          $buildDlls = Get-ChildItem -Path $buildDir -Filter *.dll | Select-Object -ExpandProperty Name
          $installedDlls = Get-ChildItem -Path $installDir -Filter *.dll | Select-Object -ExpandProperty Name

          # Define whitelist for missing DLLs (build-only) - Okay to not be installed
          $whitelistedMissingDlls = @(
            "System.Configuration.ConfigurationManager.dll",
            "System.Security.Cryptography.ProtectedData.dll",
            "System.Security.Permissions.dll",
            "System.Windows.Extensions.dll",
            "Microsoft.Win32.SystemEvents.dll",
            "Microsoft.Extensions.DependencyInjection.Abstractions.dll",
            "Microsoft.Extensions.DependencyInjection.dll",
            "Microsoft.Extensions.Logging.Abstractions.dll",
            "Microsoft.Extensions.Logging.dll",
            "Microsoft.Extensions.Options.dll",
            "Microsoft.Extensions.Primitives.dll"
          )

          # Define whitelist for extra DLLs (install-only)
          $whitelistedExtraDlls = @(

          )

          # Get all unique DLLs in the entire build repository
          # Define which folders to check in the repo
          $foldersToCheck = @(
              "$(Get-Location)\MetaMorpheus\EngineLayer\bin\Release\$env:DOTNET_FRAMEWORK",
              "$(Get-Location)\MetaMorpheus\CMD\bin\Release\$env:DOTNET_FRAMEWORK",
              "$(Get-Location)\MetaMorpheus\TaskLayer\bin\Release\$env:DOTNET_FRAMEWORK",
              "$(Get-Location)\MetaMorpheus\GUI\bin\Release\$env:DOTNET_FRAMEWORK-windows",
              "$(Get-Location)\MetaMorpheus\GuiFunctions\bin\Release\$env:DOTNET_FRAMEWORK"
          )

          # Collect DLLs and their source folders
          $buildDlls = @()
          $buildDllLocations = @{}

          foreach ($folder in $foldersToCheck) {
              if (Test-Path $folder) {
                  Get-ChildItem -Path $folder -Filter *.dll | ForEach-Object {
                      $dllName = $_.Name
                      $buildDlls += $dllName
                      $buildDllLocations[$dllName] = $folder
                  }
              }
          }
          $buildDlls = $buildDlls | Sort-Object -Unique

          # Get installed DLLs
          $installedDlls = Get-ChildItem -Path $installDir -Filter *.dll | Select-Object -ExpandProperty Name -Unique

          # Find missing DLLs (in build, not in install), ignoring whitelist
          $missingDlls = $buildDlls | Where-Object { $_ -notin $installedDlls -and $_ -notin $whitelistedMissingDlls }

          # Find extra DLLs (in install, not in build), ignoring whitelist
          $extraDlls = $installedDlls | Where-Object { $_ -notin $buildDlls -and $_ -notin $whitelistedExtraDlls }

          $hasError = $false

          if ($missingDlls.Count -gt 0) {
              Write-Host "❌ Missing DLLs from installer (not whitelisted):" -ForegroundColor Red
              $missingDlls | ForEach-Object {
                  $sourceFolder = $buildDllLocations[$_]
                  Write-Host "- $_ (from $sourceFolder)"
              }
              $hasError = $true
          }

          if ($extraDlls.Count -gt 0) {
              Write-Host "❌ Extra/unexpected DLLs in installer:" -ForegroundColor Red
              $extraDlls | ForEach-Object { Write-Host "- $_" }
              $hasError = $true
          }

          if ($hasError) {
              exit 1
          } else {
              Write-Host "✅ Installer DLLs match build output exactly." -ForegroundColor Green
          }