update markdown #6060
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| name: Build | |
| # Run this workflow every time a new commit pushed to your repository | |
| on: | |
| push | |
| env: | |
| DOTNET_NOLOGO: 1 | |
| DOTNET_SKIP_FIRST_TIME_EXPERIENCE: true | |
| jobs: | |
| # Set the job key. The key is displayed as the job name | |
| # when a job name is not provided | |
| tests_db: | |
| name: Run Database Tests | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Populate Databases.yaml | |
| shell: bash | |
| run: | | |
| cat > ./Tools/rdmp/Databases.yaml << EOF | |
| CatalogueConnectionString: Server=(localdb)\MSSQLLocalDB;Database=TEST_Catalogue;Trusted_Connection=True;TrustServerCertificate=true; | |
| DataExportConnectionString: Server=(localdb)\MSSQLLocalDB;Database=TEST_DataExport;Trusted_Connection=True;TrustServerCertificate=true; | |
| EOF | |
| - name: Build | |
| run: | | |
| dotnet build --configuration Release --verbosity minimal | |
| - name: Install MS SQL 2019 Express LocalDB | |
| uses: crazy-max/ghaction-chocolatey@v3 | |
| with: | |
| args: install -r sqllocaldb --no-progress | |
| - name: Initialise LocalDB | |
| shell: bash | |
| run: | | |
| SqlLocalDB.exe create MSSQLLocalDB -s | |
| sqlcmd -l 180 -S '(localdb)\MSSQLLocalDB' -Q "SELECT @@VERSION;" | |
| sed -i'' -e 's/localhost/\(localdb\)\\MSSQLLocalDB/' Tests.Common/TestDatabases.txt | |
| - uses: shogo82148/actions-setup-mysql@v1 | |
| with: | |
| mysql-version: '8.0' | |
| root-password: 'YourStrong!Passw0rd' | |
| auto-start: true | |
| - name: Build | |
| run: dotnet build --configuration Release --verbosity minimal | |
| - name: Initialise RDMP | |
| run: | | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- install --createdatabasetimeout 180 "(localdb)\MSSQLLocalDB" TEST_ -e | |
| - name: Create MySql Logging, DQE and Cohort Building Cache Db | |
| run: | | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- createnewexternaldatabaseserver LiveLoggingServer_ID "DatabaseType:MySQL:Server=127.0.0.1;Uid=root;Pwd=YourStrong!Passw0rd;Database=rdmp_logging2" --dir ~/rdmp/rdmp-yaml/ | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- createnewexternaldatabaseserver DQE "DatabaseType:MySQL:Server=127.0.0.1;Uid=root;Pwd=YourStrong!Passw0rd;Database=rdmp_dqe" --dir ~/rdmp/rdmp-yaml/ | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- createnewexternaldatabaseserver CohortIdentificationQueryCachingServer_ID "DatabaseType:MySQL:Server=127.0.0.1;Uid=root;Pwd=YourStrong!Passw0rd;Database=rdmp_cache" --dir ~/rdmp/rdmp-yaml/ | |
| - name: Run integration test scripts | |
| run: | | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/create_list_destroy_catalogue.yaml | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/create_cohort.yaml | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/create_dataload.yaml | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/orphan_extractable_column.yaml | |
| - name: Test (DB) | |
| shell: bash | |
| run: | | |
| rm -rf coverage | |
| curl -L "https://dl.min.io/server/minio/release/windows-amd64/minio.exe" > minio.exe | |
| ./minio.exe server ./minio --console-address :9001 & | |
| mkdir ~/.aws | |
| echo -e "[minio]\naws_access_key_id=minioadmin\naws_secret_access_key=minioadmin\naws_endpoint_url=http://127.0.0.1:9001" > ~/.aws/credentials | |
| dotnet test Rdmp.UI.Tests/Rdmp.UI.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -e AWS_ENDPOINT_URL="http://127.0.0.1:9000" --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov | |
| mv `find coverage -type f` db-ui.lcov | |
| dotnet test Rdmp.Core.Tests/Rdmp.Core.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -e AWS_ENDPOINT_URL="http://127.0.0.1:9000" --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov | |
| mv `find coverage -type f` db-core.lcov | |
| - uses: coverallsapp/[email protected] | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| files: ./db-ui.lcov ./db-core.lcov | |
| flag-name: unit tests | |
| tests_file_system: | |
| name: Run File System Tests | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Populate Databases.yaml | |
| shell: bash | |
| run: | | |
| cat > ./Tools/rdmp/Databases.yaml << EOF | |
| CatalogueConnectionString: Server=(localdb)\MSSQLLocalDB;Database=TEST_Catalogue;Trusted_Connection=True;TrustServerCertificate=true; | |
| DataExportConnectionString: Server=(localdb)\MSSQLLocalDB;Database=TEST_DataExport;Trusted_Connection=True;TrustServerCertificate=true; | |
| EOF | |
| - name: Build | |
| run: | | |
| dotnet build --configuration Release --verbosity minimal | |
| - name: Install MS SQL 2019 Express LocalDB | |
| uses: crazy-max/ghaction-chocolatey@v3 | |
| with: | |
| args: install -r sqllocaldb --no-progress | |
| - name: Initialise LocalDB | |
| shell: bash | |
| run: | | |
| SqlLocalDB.exe create MSSQLLocalDB -s | |
| sqlcmd -l 180 -S '(localdb)\MSSQLLocalDB' -Q "SELECT @@VERSION;" | |
| sed -i'' -e 's/localhost/\(localdb\)\\MSSQLLocalDB/' Tests.Common/TestDatabases.txt | |
| - uses: shogo82148/actions-setup-mysql@v1 | |
| with: | |
| mysql-version: '8.0' | |
| root-password: 'YourStrong!Passw0rd' | |
| auto-start: true | |
| - name: Build | |
| run: dotnet build --configuration Release --verbosity minimal | |
| - name: Initialise RDMP | |
| run: | | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- install --createdatabasetimeout 180 "(localdb)\MSSQLLocalDB" TEST_ -e | |
| - name: Create MySql Logging, DQE and Cohort Building Cache Db | |
| run: | | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- createnewexternaldatabaseserver LiveLoggingServer_ID "DatabaseType:MySQL:Server=127.0.0.1;Uid=root;Pwd=YourStrong!Passw0rd;Database=rdmp_logging2" --dir ~/rdmp/rdmp-yaml/ | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- createnewexternaldatabaseserver DQE "DatabaseType:MySQL:Server=127.0.0.1;Uid=root;Pwd=YourStrong!Passw0rd;Database=rdmp_dqe" --dir ~/rdmp/rdmp-yaml/ | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- createnewexternaldatabaseserver CohortIdentificationQueryCachingServer_ID "DatabaseType:MySQL:Server=127.0.0.1;Uid=root;Pwd=YourStrong!Passw0rd;Database=rdmp_cache" --dir ~/rdmp/rdmp-yaml/ | |
| - name: Run integration test scripts | |
| run: | | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/create_list_destroy_catalogue.yaml | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/create_cohort.yaml | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/create_dataload.yaml | |
| dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- -f ./scripts/orphan_extractable_column.yaml | |
| - name: Test with local file system | |
| shell: bash | |
| run: | | |
| echo "UseFileSystemRepo: true" >> Tests.Common/TestDatabases.txt | |
| curl -L "https://dl.min.io/server/minio/release/windows-amd64/minio.exe" > minio.exe | |
| ./minio.exe server ./minio --console-address :9001 & | |
| mkdir ~/.aws | |
| echo -e "[minio]\naws_access_key_id=minioadmin\naws_secret_access_key=minioadmin\naws_endpoint_url=http:127.0.0.1:9001" > ~/.aws/credentials | |
| dotnet test Rdmp.UI.Tests/Rdmp.UI.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -e AWS_ENDPOINT_URL="http://127.0.0.1:9000" --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov | |
| mv `find coverage -type f` fs-ui.lcov | |
| dotnet test Rdmp.Core.Tests/Rdmp.Core.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -e AWS_ENDPOINT_URL="http://127.0.0.1:9000" --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov | |
| mv `find coverage -type f` fs-core.lcov | |
| - uses: coverallsapp/[email protected] | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| files: ./fs-ui.lcov ./fs-core.lcov | |
| flag-name: unit tests | |
| bundle: | |
| name: Bundle Build | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Determine RDMP build version | |
| id: version | |
| shell: bash | |
| run: perl -ne "print \"rdmpversion=\$1\n\" if /AssemblyInformationalVersion\(\"([0-9a-z.-]+)\"\)/;" SharedAssemblyInfo.cs >> $GITHUB_OUTPUT | |
| - name: Setup .NET Core | |
| uses: actions/[email protected] | |
| with: | |
| dotnet-version: 7.0.x | |
| - name: BundleSource | |
| shell: bash | |
| run: | | |
| mkdir -p Tools/BundleUpSourceIntoZip/output | |
| rm -f Tools/BundleUpSourceIntoZip/output/SourceCodeForSelfAwareness.zip | |
| echo "dir /s/b *.cs *.xml > srcbitsa.txt" | cmd | |
| perl -pe '$_=reverse' < srcbitsa.txt | sort -t'\' -k1,1 -u | perl -pe '$_=reverse' > srcbits.txt | |
| echo 7z a -mx=9 Tools/BundleUpSourceIntoZip/output/SourceCodeForSelfAwareness.zip @srcbits.txt | cmd | |
| - name: Package | |
| run: | | |
| dotnet publish Application/ResearchDataManagementPlatform/ResearchDataManagementPlatform.csproj -r win-x64 --self-contained -c Release -o PublishWinForms -p:GenerateDocumentationFile=false -p:PublishSingleFile=true -p:PublishReadyToRun=true -p:IncludeNativeLibrariesForSelfExtract=true --verbosity minimal --nologo | |
| dotnet publish Tools/rdmp/rdmp.csproj -r win-x64 --self-contained -c Release -o PublishWindows -p:GenerateDocumentationFile=false -p:PublishSingleFile=true -p:PublishReadyToRun=true --verbosity minimal -p:IncludeNativeLibrariesForSelfExtract=true --nologo | |
| dotnet publish Tools/rdmp/rdmp.csproj -r linux-x64 --self-contained -c Release -o PublishLinux -p:GenerateDocumentationFile=false -p:PublishSingleFile=true -p:PublishReadyToRun=true --verbosity minimal --nologo | |
| - name: Temporary Bundle of ddls for auto-updater | |
| shell: bash | |
| run: | | |
| cp -r Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/runtimes ./PublishWinForms | |
| cp -r Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/x64 ./PublishWinForms | |
| cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/D3DCompiler_47_cor3.dll ./PublishWinForms | |
| cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/PenImc_cor3.dll ./PublishWinForms | |
| cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/PresentationNative_cor3.dll ./PublishWinForms | |
| cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/vcruntime140_cor3.dll ./PublishWinForms | |
| cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/WebView2Loader.dll ./PublishWinForms | |
| cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/wpfgfx_cor3.dll ./PublishWinForms | |
| - name: Install Plugins | |
| shell: bash | |
| run: | | |
| for plugin in https://api.github.com/repos/SMI/RdmpDicom/releases/latest https://api.github.com/repos/HICServices/HicPlugin/releases/latest https://api.github.com/repos/HICServices/RdmpExtensions/releases/latest | |
| do | |
| PluginName="$(cut -d/ -f6 <<< $plugin)" | |
| NAME="$(curl -s $plugin | grep "browser_download_url.*$PluginName.*rdmp" | cut -d : -f 2,3 | cut -d "\"" -f 2)" | |
| curl -OL $NAME | |
| done | |
| for platform in PublishWindows PublishLinux PublishWinForms | |
| do | |
| cp *.rdmp $platform | |
| done | |
| rm *.rdmp | |
| - name: Sign & zip | |
| shell: bash | |
| run: | | |
| dotnet tool install --global AzureSignTool | |
| AzureSignTool sign -kvu "${{ secrets.AZURE_KEY_VAULT_URI }}" -kvi "${{ secrets.AZURE_CLIENT_ID }}" -kvt "${{ secrets.AZURE_TENANT_ID }}" -kvs "${{ secrets.AZURE_CLIENT_SECRET }}" -kvc ${{ secrets.AZURE_CERT_NAME }} -tr http://timestamp.digicert.com -v PublishWindows/rdmp.exe | |
| AzureSignTool sign -kvu "${{ secrets.AZURE_KEY_VAULT_URI }}" -kvi "${{ secrets.AZURE_CLIENT_ID }}" -kvt "${{ secrets.AZURE_TENANT_ID }}" -kvs "${{ secrets.AZURE_CLIENT_SECRET }}" -kvc ${{ secrets.AZURE_CERT_NAME }} -tr http://timestamp.digicert.com -v PublishWinForms/ResearchDataManagementPlatform.exe | |
| mkdir -p dist | |
| (cd PublishWindows ; echo 7z a -mx=9 ../dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-win-x64.zip . | cmd) | |
| (cd PublishLinux ; echo 7z a -mx=0 ../dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.zip . | cmd) | |
| mv PublishLinux rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux | |
| echo 7z a dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.tar rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux | cmd | |
| (cd PublishWinForms ; echo 7z a -mx=9 ../dist/rdmp-${{ steps.version.outputs.rdmpversion }}-client.zip . | cmd) | |
| - name: Install Perl dependencies | |
| uses: shogo82148/[email protected] | |
| with: | |
| install-modules-with: cpanm | |
| install-modules: Archive::Zip Archive::Tar | |
| - name: Fix execute permissions | |
| if: contains(github.ref, 'refs/tags/v') || contains('refs/heads/main refs/heads/develop',github.ref) | |
| shell: perl {0} | |
| run: | | |
| use strict; | |
| use warnings; | |
| use Archive::Zip qw( :ERROR_CODES :CONSTANTS ); | |
| use Archive::Tar; | |
| my ($tarname,$zipname)=('dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.tar','dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.zip'); | |
| # Find rdmp in .tar, set permissions 0755 | |
| my $tar=Archive::Tar->new($tarname) || die "read $tarname:$!\n"; | |
| my @tarbits=$tar->get_files(); | |
| foreach my $bit (@tarbits) { | |
| $bit->chmod('0755') if $bit->name =~ /\/rdmp$/; | |
| } | |
| $tar->write( $tarname ); | |
| # Find rdmp in .zip, set permissions 0755 | |
| my $srczip = Archive::Zip->new($zipname); | |
| my $zip=Archive::Zip->new(); | |
| foreach my $bit ($srczip->members()) { | |
| print "Adding ",$bit->fileName(),"\n"; | |
| my $m=$zip->addString($bit->contents(),$bit->fileName()); | |
| $m->fileName($bit->fileName()); | |
| my $iszip=$bit->fileName() =~ /\.zip$/i; | |
| $m->desiredCompressionMethod($iszip ? COMPRESSION_STORED : COMPRESSION_DEFLATED); | |
| $m->desiredCompressionLevel($iszip ? 0 : 9 ); | |
| } | |
| $zip->memberNamed('rdmp')->unixFileAttributes( 0755 ); | |
| $zip->overwriteAs($zipname); | |
| - name: Compress tar | |
| if: contains(github.ref, 'refs/tags/v') || contains('refs/heads/main refs/heads/develop',github.ref) | |
| run: | | |
| 7z a -txz dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.tar.xz dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.tar | |
| rm dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.tar | |
| - name: Build Nuget packages | |
| if: contains(github.ref, 'refs/tags/v') | |
| shell: bash | |
| run: | | |
| for i in Rdmp.Core/Rdmp.Core.csproj Rdmp.UI/Rdmp.UI.csproj Tests.Common/Tests.Common.csproj | |
| do | |
| dotnet pack $i -c Release --include-symbols --nologo -o . -v:m -p:Version=${{ steps.version.outputs.rdmpversion }} | |
| done | |
| - name: Calculate SHA256SUMS | |
| if: contains(github.ref, 'refs/tags/v') | |
| run: '&{foreach ($i in Get-ChildItem dist -Exclude *SUMS|Get-FileHash) { echo "$($i.Hash) $(echo $i | Split-Path -Leaf)" }} > dist/SHA256SUMS' | |
| - name: Archive production artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: | | |
| dist | |
| - name: Cache Build | |
| id: cache-build | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{ github.workspace }}/ | |
| key: ${{ github.sha }}-your-cache-key-bundled | |
| production-upload: | |
| name: Production Upload | |
| runs-on: windows-latest | |
| needs: ['bundle','tests_db','tests_file_system'] | |
| if: contains(github.ref, 'refs/tags/v') | |
| steps: | |
| - uses: actions/cache/restore@v4 | |
| id: restore-build | |
| with: | |
| path: ${{ github.workspace }}/ | |
| key: ${{ github.sha }}-your-cache-key-bundled | |
| - name: Determine RDMP build version | |
| id: version | |
| shell: bash | |
| run: perl -ne "print \"rdmpversion=\$1\n\" if /AssemblyInformationalVersion\(\"([0-9a-z.-]+)\"\)/;" SharedAssemblyInfo.cs >> $GITHUB_OUTPUT | |
| - name: Upload Nuget packages | |
| run: dotnet nuget push HIC.RDMP.Plugin*${{ steps.version.outputs.rdmpversion }}.nupkg -s https://api.nuget.org/v3/index.json --skip-duplicate -k ${{ secrets.NUGET_KEY }} | |
| - name: Upload binaries to release | |
| uses: svenstaro/[email protected] | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: dist/* | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| file_glob: true |