8.1.0 Release

.github/workflows/build.yml

@@ -22,30 +22,26 @@ jobs:
         shell: bash
         run: touch package-lock.json
       - name: Install Node for coverage reporting
-        uses: actions/setup-node@v3.5.1
+        uses: actions/setup-node@v3.8.1
         with:
           node-version: '16.x'
           cache: 'npm'
       - name: LCov merger tool
         run: npm install -g lcov-result-merger
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Determine RDMP build version
         id: version
-        shell: cmd
-        run: perl -ne "print \"::set-output name=rdmpversion::$1\" if /AssemblyVersion\(\"([0-9.]+)\"\)/;" SharedAssemblyInfo.cs
-      - uses: actions/cache@v3
-        with:
-          path: ~/.nuget/packages
-          key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
-          restore-keys: |
-            ${{ runner.os }}-nuget-
+        shell: bash
+        run: perl -ne "print \"rdmpversion=\$1\n\" if /AssemblyInformationalVersion\(\"([0-9a-z.-]+)\"\)/;" SharedAssemblyInfo.cs >> $GITHUB_OUTPUT
+      - name: Check output
+        run: echo ${{ steps.version.outputs.rdmpversion }}
       - name: Setup .NET Core
-        uses: actions/setup-dotnet@v3.0.3
+        uses: actions/setup-dotnet@v3.2.0
         with:
           dotnet-version: 6.0.x
       - name: Install MS SQL 2019 Express LocalDB
-        uses: crazy-max/ghaction-chocolatey@v2
+        uses: crazy-max/ghaction-chocolatey@v3
         with:
           args: install -r sqllocaldb --no-progress
       - name: Initialise LocalDB
@@ -59,17 +55,20 @@ jobs:
           mysql-version: '8.0'
           root-password: 'YourStrong!Passw0rd'
           auto-start: true
-      - name: Create MySql Logging Db
-        run: dotnet run -c Release --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/
-      - name: Create MySql DQE Db
-        run: dotnet run -c Release --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/
-      - name: Create MySql Cohort Building Query Caching Db
-        run: dotnet run -c Release --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: Populate Databases.yaml 
+        shell: bash
+        run: |
+            find ./Tools/rdmp/Databases.yaml -type f -exec sed -i 's/RDMP_/TEST_/g' {} \;
       - name: Build
         run: dotnet build --configuration Release --verbosity minimal
+      - 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: Initialise RDMP
-        run: dotnet run -c Release --project Tools/rdmp/rdmp.csproj -- install --createdatabasetimeout 180 "(localdb)\MSSQLLocalDB" TEST_ -e
-      - name: Populate Databases.yaml 
+        run: dotnet run -c Release --no-build --project Tools/rdmp/rdmp.csproj -- install --createdatabasetimeout 180 "(localdb)\MSSQLLocalDB" TEST_ -e
+      - name: Populate Databases.yaml
         shell: bash
         run: |
           cat > ./Tools/rdmp/Databases.yaml << EOF
@@ -78,61 +77,40 @@ jobs:
           EOF
       - name: Run integration test scripts
         run: |
-            dotnet run -c Release --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 Reusable code
+            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
-          dotnet test "Reusable/Tests/ReusableCodeTests/ReusableCodeTests.csproj" --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -r coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
-          mv `find coverage -type f` recode.lcov
-      - name: Test Core code
-        shell: bash
-        run: |
-          dotnet test "./Rdmp.Core.Tests/Rdmp.Core.Tests.csproj" --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -r coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
-          mv `find coverage -type f` core.lcov
-      - name: Test UI code
-        shell: bash
-        run: |
-          dotnet test "./Rdmp.UI.Tests/Rdmp.UI.Tests.csproj" --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -r coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
-          mv `find coverage -type f` ui.lcov
+          dotnet test Rdmp.UI.Tests/Rdmp.UI.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release --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 --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
+          mv `find coverage -type f` db-core.lcov
       - name: Test with local file system
         shell: bash
         run:  |
-              echo "UseFileSystemRepo: true" >> Tests.Common/TestDatabases.txt
-              cat Tests.Common/TestDatabases.txt
-      - name: Test Reusable (with file system repo)
-        shell: bash
-        run: |
-          dotnet test "Reusable/Tests/ReusableCodeTests/ReusableCodeTests.csproj" --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -r coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
-          mv `find coverage -type f` recodefs.lcov
-      - name: Test Core (with file system repo)
-        shell: bash
-        run: |
-          dotnet test "./Rdmp.Core.Tests/Rdmp.Core.Tests.csproj" --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -r coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
-          mv `find coverage -type f` corefs.lcov
-      - name: Test UI (with file system repo)
-        shell: bash
-        run: |
-          dotnet test "./Rdmp.UI.Tests/Rdmp.UI.Tests.csproj" --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -r coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
-          mv `find coverage -type f` uifs.lcov
-
+          echo "UseFileSystemRepo: true" >> Tests.Common/TestDatabases.txt
+          dotnet test Rdmp.UI.Tests/Rdmp.UI.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release --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 --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
+          mv `find coverage -type f` fs-core.lcov
       - name: Merge LCovs
-        run: lcov-result-merger "{ui,core,recode}{,fs}.lcov" all.lcov
+        run: lcov-result-merger "{db,fs}-{ui,core}.lcov" all.lcov
       - name: Coveralls
         uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.github_token }}
           path-to-lcov: all.lcov
           flag-name: unit tests
-      
+
       - name: Package
         run: |
-          dotnet publish Application/ResearchDataManagementPlatform/ResearchDataManagementPlatform.csproj -r win-x64 --self-contained -c Release -o PublishWinForms -p:GenerateDocumentationFile=false -p:PublishSingleFile=false --verbosity minimal --nologo
-          dotnet publish Tools/rdmp/rdmp.csproj -r win-x64 --self-contained -c Release -o PublishWindows -p:GenerateDocumentationFile=false -p:PublishSingleFile=false --verbosity minimal --nologo
-          dotnet publish Tools/rdmp/rdmp.csproj -r linux-x64 --self-contained -c Release -o PublishLinux -p:GenerateDocumentationFile=false -p:PublishSingleFile=false --verbosity minimal --nologo
+          dotnet publish Application/ResearchDataManagementPlatform/ResearchDataManagementPlatform.csproj -r win-x64 --self-contained -c Release -o PublishWinForms -p:GenerateDocumentationFile=false -p:PublishSingleFile=true -p:PublishReadyToRun=true --verbosity minimal --nologo
+          dotnet publish Tools/rdmp/rdmp.csproj -r win-x64 --self-contained -c Release -o PublishWindows -p:GenerateDocumentationFile=false -p:PublishSingleFile=true -p:PublishReadyToRun=true --verbosity minimal --nologo
+          dotnet publish Tools/rdmp/rdmp.csproj -r linux-x64 --self-contained -c Release -o PublishLinux -p:GenerateDocumentationFile=false -p:PublishSingleFile=true -p:PublishReadyToRun=true --verbosity minimal --nologo
       - name: BundleSource
         shell: bash
         run: |
@@ -148,7 +126,7 @@ jobs:
           signtool=${signtool[${#signtool[@]}-1]}
           signtool=`echo $signtool | sed -e 's#^/c#c:#' | tr / \\\\`
           echo ${{ secrets.DIGICERT_PFX }} | base64 --decode > GitHubActionsWorkflow.pfx
-          echo '"'$signtool'"' 'Sign  /f GitHubActionsWorkflow.pfx /fd sha256 /tr http://timestamp.digicert.com /td sha256 /p ${{ secrets.DIGICERT_PASSWORD }} PublishWindows/*.exe PublishWinForms/*.exe PublishWinForms/Hunspell*.dll' | cmd
+          echo '"'$signtool'"' 'Sign  /f GitHubActionsWorkflow.pfx /fd sha256 /tr http://timestamp.digicert.com /td sha256 /p ${{ secrets.DIGICERT_PASSWORD }} PublishWindows/*.exe PublishWinForms/*.exe' | cmd
           mkdir -p dist
           cmd /c wix\\build.cmd ${{ steps.version.outputs.rdmpversion }}
           echo '"'$signtool'"' 'Sign  /f GitHubActionsWorkflow.pfx /fd sha256 /tr http://timestamp.digicert.com /td sha256 /p ${{ secrets.DIGICERT_PASSWORD }} dist/rdmp.msi' | cmd
@@ -159,7 +137,7 @@ jobs:
           (cd PublishWinForms ; echo 7z a -mx=9 ../dist/rdmp-${{ steps.version.outputs.rdmpversion }}-client.zip . | cmd)
 
       - name: Install Perl dependencies
-        uses: shogo82148/actions-setup-perl@v1
+        uses: shogo82148/actions-setup-perl@v1.23.1
         with:
           install-modules-with: cpanm
           install-modules: Archive::Zip Archive::Tar
@@ -200,18 +178,16 @@ jobs:
           rm dist/rdmp-${{ steps.version.outputs.rdmpversion }}-cli-linux-x64.tar
 
       - name: Build Nuget packages
+        shell: bash
         run: |
-          nuget pack Plugins/Plugin/Plugin.nuspec -Properties Configuration=Release -IncludeReferencedProjects -Symbols -Version ${{ steps.version.outputs.rdmpversion }}
-          nuget pack Plugins/Plugin.UI/Plugin.UI.nuspec -Properties Configuration=Release -IncludeReferencedProjects -Symbols -Version ${{ steps.version.outputs.rdmpversion }}
-          nuget pack Plugins/Plugin.Test/Plugin.Test.nuspec -Properties Configuration=Release -IncludeReferencedProjects -Symbols -Version ${{ steps.version.outputs.rdmpversion }}
-          nuget pack Application/ResearchDataManagementPlatform/RDMP.nuspec -Properties Configuration=Release -Version ${{ steps.version.outputs.rdmpversion }}
+          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: Push Nuget packages
+      - name: Upload Nuget packages
         if: contains(github.ref, 'refs/tags/v')
-        run: |
-          nuget push HIC.RDMP.Plugin.${{ steps.version.outputs.rdmpversion }}.nupkg -skipDuplicate -Source https://api.nuget.org/v3/index.json -ApiKey ${{ secrets.NUGET_KEY }}
-          nuget push HIC.RDMP.Plugin.UI.${{ steps.version.outputs.rdmpversion }}.nupkg -skipDuplicate -Source https://api.nuget.org/v3/index.json -ApiKey ${{ secrets.NUGET_KEY }}
-          nuget push HIC.RDMP.Plugin.Test.${{ steps.version.outputs.rdmpversion }}.nupkg -skipDuplicate -Source https://api.nuget.org/v3/index.json -ApiKey ${{ secrets.NUGET_KEY }}
+        run: dotnet nuget push HIC.RDMP.Plugin*${{ steps.version.outputs.rdmpversion }}.nupkg -s https://api.nuget.org/v3/index.json --skip-duplicate -k ${{ secrets.NUGET_KEY }}
 
       - name: Calculate SHA256SUMS
         run: '&{foreach ($i in Get-ChildItem dist -Exclude *SUMS|Get-FileHash) { echo "$($i.Hash) $(echo $i | Split-Path -Leaf)" }} > dist/SHA256SUMS'
@@ -223,7 +199,7 @@ jobs:
           path: |
             dist
       - name: Upload binaries to release
-        uses: svenstaro/upload-release-action@2.3.0
+        uses: svenstaro/upload-release-action@2.7.0
         if: contains(github.ref, 'refs/tags/v')
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
+  schedule:
+    - cron: "16 21 * * 6"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ csharp ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Build
+        run: dotnet build
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

.github/workflows/docker.yml

@@ -13,11 +13,11 @@ jobs:
       packages: write
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: Setup .NET Core
-        uses: actions/setup-dotnet@v3.0.3
+        uses: actions/setup-dotnet@v3.2.0
         with:
           dotnet-version: 6.0.x
       - name: Cache Nuget

.github/workflows/links.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Run link check

.nuget/packages.config

@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
+
 <packages>
   <package id="NUnit.Console" version="3.9.0" />
   <package id="NUnit.ConsoleRunner" version="3.9.0" />