Merge remote-tracking branch 'origin/main' into hotfix/ifpartpattern #1148
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| name: .NET Core | |
| on: [push] | |
| env: | |
| DOTNET_NOLOGO: true | |
| MSSQL_SA_PASSWORD: "YourStrong!Passw0rd" | |
| ACCEPT_EULA: "Y" | |
| MSSQL_PID: "developer" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| services: | |
| postgres: | |
| image: postgres:latest | |
| env: | |
| POSTGRES_PASSWORD: pgpass4291 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - name: Disable disk flushing on CI and add libarchive-tools | |
| run: sudo apt-get install -y libeatmydata1 libarchive-tools | |
| - uses: actions/checkout@v3 | |
| - name: Setup .NET Core | |
| uses: actions/setup-dotnet@v3 | |
| with: | |
| dotnet-version: "6.0.x" | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "adopt" | |
| java-version: "11" | |
| cache: "maven" | |
| - name: Start MySQL | |
| run: | | |
| mv Tests/IsIdentifiableTests/TestDatabases-github.xml Tests/IsIdentifiableTests/TestDatabases.xml | |
| sudo systemctl start mysql.service | |
| - name: Start MongoDb | |
| uses: supercharge/[email protected] | |
| with: | |
| mongodb-version: "6.0" | |
| - name: Install MS SQL Server | |
| run: | | |
| sudo wget -qO/etc/apt/trusted.gpg.d/microsoft.asc https://packages.microsoft.com/keys/microsoft.asc | |
| sudo add-apt-repository "$(wget -qO- https://packages.microsoft.com/config/ubuntu/20.04/mssql-server-2022.list)" | |
| sudo apt-get install -y --no-install-recommends postgresql mssql-tools mssql-server | |
| sudo -E /opt/mssql/bin/mssql-conf -n setup accept-eula | |
| - name: Fetch tessdata | |
| run: | | |
| bash data/tessdata/download.sh | |
| mv eng.traineddata ./data/tessdata/eng.traineddata | |
| - name: Build | |
| run: dotnet build --configuration Release --nologo | |
| - name: Test | |
| run: dotnet test --blame -l:"console;verbosity=normal" --no-restore --nologo -p:CollectCoverage=true -p:CoverletOutput="$(pwd)/coverage/" -p:CoverletOutputFormat="cobertura" | |
| - name: upload coverage | |
| uses: codecov/[email protected] | |
| with: | |
| files: ./coverage/coverage.cobertura.xml | |
| fail_ci_if_error: true | |
| token: 42f74c8f-0e77-40db-8497-fa05f20837f6 | |
| - name: Build Java NERD | |
| run: | | |
| set -exuo pipefail | |
| cd nlp/uk.ac.dundee.hic.nerd | |
| mkdir -p target/stanford-ner-2018-10-16 | |
| curl -sL https://nlp.stanford.edu/software/stanford-ner-2018-10-16.zip | bsdtar -xf- -C target/stanford-ner-2018-10-16 | |
| mvn -B -q compile assembly:single | |
| java -jar target/nerd-0.0.1-SNAPSHOT.jar & | |
| timeout 30 sh -c 'until nc -z 127.0.0.1 1881; do sleep 1; done' | |
| printf "University of Dundee\0Fred Bloggs\0Ninewells Hospital\0person\0woman\0man\0camera\0tv\0" | nc -N 127.0.0.1 1881 | |
| kill $! | |
| mkdir -p ../../release | |
| dotnet publish --self-contained --nologo -r linux-x64 -o smi-nerd-linux-$(fgrep AssemblyVersion ../../SharedAssemblyInfo.cs | cut -d'"' -f2) | |
| dotnet publish --self-contained --nologo -r win-x64 -o smi-nerd-win-$(fgrep AssemblyVersion ../../SharedAssemblyInfo.cs | cut -d'"' -f2) | |
| tar czf smi-nerd-linux-$(fgrep AssemblyVersion ../../SharedAssemblyInfo.cs | cut -d'"' -f2).tar.gz smi-nerd-linux-$(fgrep AssemblyVersion ../../SharedAssemblyInfo.cs | cut -d'"' -f2) | |
| cd smi-nerd-win-$(fgrep AssemblyVersion ../../SharedAssemblyInfo.cs | cut -d'"' -f2) | |
| zip -9r ../smi-nerd-win-$(fgrep AssemblyVersion ../../../SharedAssemblyInfo.cs | cut -d'"' -f2).zip . | |
| cd - | |
| mv smi-nerd-*.tar.gz smi-nerd-*.zip ../../release/ | |
| mv target/nerd-0.0.1-SNAPSHOT.jar ../../release/smi-nerd-$(fgrep AssemblyVersion ../../SharedAssemblyInfo.cs | cut -d'"' -f2).jar | |
| - name: Package ii binary | |
| run: | | |
| tag="$(fgrep AssemblyVersion SharedAssemblyInfo.cs | cut -d'"' -f2)" | |
| cd ii | |
| dotnet publish --runtime win-x64 -c Release --self-contained true -o ../ii-win-x64 | |
| dotnet publish --runtime linux-x64 -c Release --self-contained true -o ../ii-"$tag"-cli-linux-x64 | |
| cd ../ii-win-x64 | |
| zip -q9r ../release/ii-"$tag"-cli-win-x64.zip . | |
| cd .. | |
| tar -zcvf ./release/ii-"$tag"-cli-linux-x64.tar.gz ii-"$tag"-cli-linux-x64 | |
| git_tag="$(git rev-parse --short HEAD)" | |
| cp ./release/ii-"$tag"-cli-linux-x64.tar.gz ./ii-"$git_tag"-cli-linux-x64.tar.gz | |
| - name: Store created ii binary | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ii | |
| path: "*.tar.gz" | |
| retention-days: 1 | |
| - name: Test ii binary | |
| run: | | |
| set -e | |
| mkdir ./testii | |
| cd ./testii | |
| tar -xzf ../release/ii-*-cli-linux-x64.tar.gz | |
| ./ii-*-cli-linux-x64/ii --help | |
| cd .. | |
| wget -qO- https://github.com/HicServices/BadMedicine.Dicom/releases/download/v0.0.14/baddicom-linux-x64-v0.0.14.tar.gz | tar -xzf - | |
| ./linux-x64/BadDicom -s 100 ./testdicoms/ 10 10 CT | |
| ./testii/ii-*-cli-linux-x64/ii dir -d ./testdicoms --tessdirectory ./data/tessdata/ --storereport | |
| - name: Pack | |
| run: dotnet pack IsIdentifiable/IsIdentifiable.csproj -c Release -p:PackageVersion=$(fgrep AssemblyVersion SharedAssemblyInfo.cs|cut -d'"' -f2) --nologo --include-source -o . | |
| - name: Package RDMP Plugin | |
| run: | | |
| cd IsIdentifiablePlugin | |
| dotnet publish --self-contained false | |
| nuget pack ./IsIdentifiablePlugin.nuspec -Properties Configuration=Debug -IncludeReferencedProjects -Symbols -Version $(grep AssemblyInformationalVersion ../SharedAssemblyInfo.cs | cut -d'"' -f2) | |
| mv ./IsIdentifiablePlugin.*.nupkg ../release/ | |
| cd .. | |
| - name: Nuget push | |
| if: contains(github.ref,'refs/tags/') | |
| run: dotnet nuget push IsIdentifiable.*.nupkg -s https://api.nuget.org/v3/index.json -k ${{ secrets.NUGET_KEY }} --skip-duplicate | |
| - name: Store created nupkg files | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: IsIdentifiablePlugin | |
| path: release/IsIdentifiablePlugin.*.nupkg | |
| retention-days: 1 | |
| - name: Upload binaries to release | |
| uses: svenstaro/[email protected] | |
| if: contains(github.ref, 'refs/tags/v') | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: release/* | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| file_glob: true |