MetaMorpheusDIA #481
Workflow file for this run
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| 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: Debug secrets (PowerShell) | |
| shell: pwsh | |
| run: | | |
| if (-not $env:KEY_SECRET) { | |
| Write-Host "KEY_SECRET is not set!" | |
| } else { | |
| Write-Host "KEY_SECRET is set." | |
| } | |
| - 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: Decrypt security certificate | |
| shell: pwsh | |
| run: | | |
| if (-not $env:KEY_SECRET) { | |
| Write-Host "⚠️ KEY_SECRET is not set. Skipping certificate decryption." | |
| exit 0 | |
| } | |
| nuget install secure-file -ExcludeVersion | |
| secure-file/tools/secure-file -decrypt MetaMorpheus/smith_MM_certificate.pfx.enc -secret "$env:KEY_SECRET" | |
| # This currently has issues and leads to Microsoft waringing the user that MetaMorpheus is untrusted. | |
| - name: Sign installer | |
| shell: pwsh | |
| run: | | |
| if (-not $env:KEY_SECRET -or -not $env:KEY_CERT) { | |
| Write-Host "⚠️ Certificate secrets not available. Skipping signing." | |
| exit 0 | |
| } | |
| $cert = New-Object System.Security.Cryptography.X509Certificates.X509Certificate2("MetaMorpheus/smith_MM_certificate.pfx", "$env:KEY_CERT", "DefaultKeySet") | |
| Set-AuthenticodeSignature -FilePath "./MetaMorpheus/MetaMorpheusSetup/bin/Release/MetaMorpheusInstaller.msi" -Certificate $cert | |
| - 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 | |
| } |