From b66bed38b6727e2756083e092e588f399dd74aaf Mon Sep 17 00:00:00 2001 From: chgl Date: Fri, 23 Feb 2024 16:56:33 +0100 Subject: [PATCH] feat: initial first draft version --- .dockerignore | 3 + .editorconfig | 24 + .gitattributes | 4 + .github/workflows/ci.yaml | 54 +++ .github/workflows/schedule.yaml | 19 + .github/workflows/scorecards.yaml | 73 +++ .gitignore | 484 +++++++++++++++++++ .mega-linter.yml | 30 ++ .vscode/launch.json | 34 ++ .vscode/tasks.json | 41 ++ Dockerfile | 24 + PathlingS3Import.sln | 27 ++ compose.yaml | 11 + src/PathlingS3Import/PathlingS3Import.csproj | 17 + src/PathlingS3Import/Program.cs | 140 ++++++ src/PathlingS3Import/packages.lock.json | 134 +++++ 16 files changed, 1119 insertions(+) create mode 100644 .dockerignore create mode 100644 .editorconfig create mode 100644 .gitattributes create mode 100644 .github/workflows/ci.yaml create mode 100644 .github/workflows/schedule.yaml create mode 100644 .github/workflows/scorecards.yaml create mode 100644 .gitignore create mode 100644 .mega-linter.yml create mode 100644 .vscode/launch.json create mode 100644 .vscode/tasks.json create mode 100644 Dockerfile create mode 100644 PathlingS3Import.sln create mode 100644 compose.yaml create mode 100644 src/PathlingS3Import/PathlingS3Import.csproj create mode 100644 src/PathlingS3Import/Program.cs create mode 100644 src/PathlingS3Import/packages.lock.json diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..a1c6a60 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,3 @@ +* +!src/ +!.editorconfig diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..d9db946 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,24 @@ +############################### +# Core EditorConfig Options # +############################### + +root = true + +# All files +[*] +indent_style = space[*] +insert_final_newline = true +charset = utf-8 + +[packages.lock.json] +insert_final_newline = false + +[*.sh] +end_of_line = lf + +[*.{cs,csx,vb,vbx}] +indent_size = 4 + +# YAML files +[*.{yml, yaml}] +indent_size = 2 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..5d543fe --- /dev/null +++ b/.gitattributes @@ -0,0 +1,4 @@ +* text=auto +*.sh text eol=lf +*.shellcheckrc text eol=lf +*Dockerfile text eol=lf diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 0000000..8b50d4b --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,54 @@ +name: ci + +on: + push: + branches: [master] + release: + types: [created] + pull_request: + branches: [master] + +permissions: read-all + +jobs: + build: + uses: miracum/.github/.github/workflows/standard-build.yaml@d09a237ae62959d3cf89d526a035fbd9d9d816ee # v1.5.8 + permissions: + contents: read + id-token: write + packages: write + pull-requests: write + actions: read + security-events: write + with: + enable-build-test-layer: false + enable-upload-test-image: false + secrets: + github-token: ${{ secrets.GITHUB_TOKEN }} + + lint: + uses: miracum/.github/.github/workflows/standard-lint.yaml@d09a237ae62959d3cf89d526a035fbd9d9d816ee # v1.5.8 + permissions: + contents: read + pull-requests: write + issues: write + security-events: write + actions: read + with: + enable-validate-gradle-wrapper: false + codeql-languages: '["csharp"]' + enable-codeql: true + enable-verify-base-image-signature: false + secrets: + github-token: ${{ secrets.GITHUB_TOKEN }} + + release: + uses: miracum/.github/.github/workflows/standard-release.yaml@d09a237ae62959d3cf89d526a035fbd9d9d816ee # v1.5.8 + needs: + - build + permissions: + contents: write + pull-requests: write + issues: write + secrets: + semantic-release-token: ${{ secrets.MIRACUM_BOT_SEMANTIC_RELEASE_TOKEN }} diff --git a/.github/workflows/schedule.yaml b/.github/workflows/schedule.yaml new file mode 100644 index 0000000..a7ef31d --- /dev/null +++ b/.github/workflows/schedule.yaml @@ -0,0 +1,19 @@ +name: scheduled + +on: + repository_dispatch: {} + workflow_dispatch: {} + schedule: + - cron: "00 18 * * *" + +permissions: read-all + +jobs: + schedule: + uses: miracum/.github/.github/workflows/standard-schedule.yaml@d09a237ae62959d3cf89d526a035fbd9d9d816ee # v1.5.8 + permissions: + contents: read + issues: write + security-events: write + secrets: + github-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/scorecards.yaml b/.github/workflows/scorecards.yaml new file mode 100644 index 0000000..936dd1f --- /dev/null +++ b/.github/workflows/scorecards.yaml @@ -0,0 +1,73 @@ +# This workflow uses actions that are not certified by GitHub. They are provided +# by a third-party and are governed by separate terms of service, privacy +# policy, and support documentation. + +name: Scorecards supply-chain security +on: + workflow_dispatch: + # For Branch-Protection check. Only the default branch is supported. See + # https://github.com/ossf/scorecard/blob/main/docs/checks.md#branch-protection + branch_protection_rule: + # To guarantee Maintained check is occasionally updated. See + # https://github.com/ossf/scorecard/blob/main/docs/checks.md#maintained + schedule: + - cron: "37 19 * * 1" + push: + branches: ["master"] + +# Declare default permissions as read only. +permissions: read-all + +jobs: + analysis: + name: Scorecards analysis + runs-on: ubuntu-latest + permissions: + # Needed to upload the results to code-scanning dashboard. + security-events: write + # Needed to publish results and get a badge (see publish_results below). + id-token: write + # Uncomment the permissions below if installing in a private repository. + # contents: read + # actions: read + + steps: + - name: "Checkout code" + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1 + with: + persist-credentials: false + + - name: "Run analysis" + uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1 + with: + results_file: results.sarif + results_format: sarif + # (Optional) Read-only PAT token. Uncomment the `repo_token` line below if: + # - you want to enable the Branch-Protection check on a *public* repository, or + # - you are installing Scorecards on a *private* repository + # To create the PAT, follow the steps in https://github.com/ossf/scorecard-action#authentication-with-pat. + # repo_token: ${{ secrets.SCORECARD_READ_TOKEN }} + + # Public repositories: + # - Publish results to OpenSSF REST API for easy access by consumers + # - Allows the repository to include the Scorecard badge. + # - See https://github.com/ossf/scorecard-action#publishing-results. + # For private repositories: + # - `publish_results` will always be set to `false`, regardless + # of the value entered here. + publish_results: true + + # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF + # format to the repository Actions tab. + - name: "Upload artifact" + uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1 + with: + name: SARIF file + path: results.sarif + retention-days: 5 + + # Upload the results to GitHub's code scanning dashboard. + - name: "Upload to code-scanning" + uses: github/codeql-action/upload-sarif@379614612a29c9e28f31f39a59013eb8012a51f0 # v3.24.3 + with: + sarif_file: results.sarif diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..104b544 --- /dev/null +++ b/.gitignore @@ -0,0 +1,484 @@ +## Ignore Visual Studio temporary files, build results, and +## files generated by popular Visual Studio add-ons. +## +## Get latest from `dotnet new gitignore` + +# dotenv files +.env + +# User-specific files +*.rsuser +*.suo +*.user +*.userosscache +*.sln.docstates + +# User-specific files (MonoDevelop/Xamarin Studio) +*.userprefs + +# Mono auto generated files +mono_crash.* + +# Build results +[Dd]ebug/ +[Dd]ebugPublic/ +[Rr]elease/ +[Rr]eleases/ +x64/ +x86/ +[Ww][Ii][Nn]32/ +[Aa][Rr][Mm]/ +[Aa][Rr][Mm]64/ +bld/ +[Bb]in/ +[Oo]bj/ +[Ll]og/ +[Ll]ogs/ + +# Visual Studio 2015/2017 cache/options directory +.vs/ +# Uncomment if you have tasks that create the project's static files in wwwroot +#wwwroot/ + +# Visual Studio 2017 auto generated files +Generated\ Files/ + +# MSTest test Results +[Tt]est[Rr]esult*/ +[Bb]uild[Ll]og.* + +# NUnit +*.VisualState.xml +TestResult.xml +nunit-*.xml + +# Build Results of an ATL Project +[Dd]ebugPS/ +[Rr]eleasePS/ +dlldata.c + +# Benchmark Results +BenchmarkDotNet.Artifacts/ + +# .NET +project.lock.json +project.fragment.lock.json +artifacts/ + +# Tye +.tye/ + +# ASP.NET Scaffolding +ScaffoldingReadMe.txt + +# StyleCop +StyleCopReport.xml + +# Files built by Visual Studio +*_i.c +*_p.c +*_h.h +*.ilk +*.meta +*.obj +*.iobj +*.pch +*.pdb +*.ipdb +*.pgc +*.pgd +*.rsp +*.sbr +*.tlb +*.tli +*.tlh +*.tmp +*.tmp_proj +*_wpftmp.csproj +*.log +*.tlog +*.vspscc +*.vssscc +.builds +*.pidb +*.svclog +*.scc + +# Chutzpah Test files +_Chutzpah* + +# Visual C++ cache files +ipch/ +*.aps +*.ncb +*.opendb +*.opensdf +*.sdf +*.cachefile +*.VC.db +*.VC.VC.opendb + +# Visual Studio profiler +*.psess +*.vsp +*.vspx +*.sap + +# Visual Studio Trace Files +*.e2e + +# TFS 2012 Local Workspace +$tf/ + +# Guidance Automation Toolkit +*.gpState + +# ReSharper is a .NET coding add-in +_ReSharper*/ +*.[Rr]e[Ss]harper +*.DotSettings.user + +# TeamCity is a build add-in +_TeamCity* + +# DotCover is a Code Coverage Tool +*.dotCover + +# AxoCover is a Code Coverage Tool +.axoCover/* +!.axoCover/settings.json + +# Coverlet is a free, cross platform Code Coverage Tool +coverage*.json +coverage*.xml +coverage*.info + +# Visual Studio code coverage results +*.coverage +*.coveragexml + +# NCrunch +_NCrunch_* +.*crunch*.local.xml +nCrunchTemp_* + +# MightyMoose +*.mm.* +AutoTest.Net/ + +# Web workbench (sass) +.sass-cache/ + +# Installshield output folder +[Ee]xpress/ + +# DocProject is a documentation generator add-in +DocProject/buildhelp/ +DocProject/Help/*.HxT +DocProject/Help/*.HxC +DocProject/Help/*.hhc +DocProject/Help/*.hhk +DocProject/Help/*.hhp +DocProject/Help/Html2 +DocProject/Help/html + +# Click-Once directory +publish/ + +# Publish Web Output +*.[Pp]ublish.xml +*.azurePubxml +# Note: Comment the next line if you want to checkin your web deploy settings, +# but database connection strings (with potential passwords) will be unencrypted +*.pubxml +*.publishproj + +# Microsoft Azure Web App publish settings. Comment the next line if you want to +# checkin your Azure Web App publish settings, but sensitive information contained +# in these scripts will be unencrypted +PublishScripts/ + +# NuGet Packages +*.nupkg +# NuGet Symbol Packages +*.snupkg +# The packages folder can be ignored because of Package Restore +**/[Pp]ackages/* +# except build/, which is used as an MSBuild target. +!**/[Pp]ackages/build/ +# Uncomment if necessary however generally it will be regenerated when needed +#!**/[Pp]ackages/repositories.config +# NuGet v3's project.json files produces more ignorable files +*.nuget.props +*.nuget.targets + +# Microsoft Azure Build Output +csx/ +*.build.csdef + +# Microsoft Azure Emulator +ecf/ +rcf/ + +# Windows Store app package directories and files +AppPackages/ +BundleArtifacts/ +Package.StoreAssociation.xml +_pkginfo.txt +*.appx +*.appxbundle +*.appxupload + +# Visual Studio cache files +# files ending in .cache can be ignored +*.[Cc]ache +# but keep track of directories ending in .cache +!?*.[Cc]ache/ + +# Others +ClientBin/ +~$* +*~ +*.dbmdl +*.dbproj.schemaview +*.jfm +*.pfx +*.publishsettings +orleans.codegen.cs + +# Including strong name files can present a security risk +# (https://github.com/github/gitignore/pull/2483#issue-259490424) +#*.snk + +# Since there are multiple workflows, uncomment next line to ignore bower_components +# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622) +#bower_components/ + +# RIA/Silverlight projects +Generated_Code/ + +# Backup & report files from converting an old project file +# to a newer Visual Studio version. Backup files are not needed, +# because we have git ;-) +_UpgradeReport_Files/ +Backup*/ +UpgradeLog*.XML +UpgradeLog*.htm +ServiceFabricBackup/ +*.rptproj.bak + +# SQL Server files +*.mdf +*.ldf +*.ndf + +# Business Intelligence projects +*.rdl.data +*.bim.layout +*.bim_*.settings +*.rptproj.rsuser +*- [Bb]ackup.rdl +*- [Bb]ackup ([0-9]).rdl +*- [Bb]ackup ([0-9][0-9]).rdl + +# Microsoft Fakes +FakesAssemblies/ + +# GhostDoc plugin setting file +*.GhostDoc.xml + +# Node.js Tools for Visual Studio +.ntvs_analysis.dat +node_modules/ + +# Visual Studio 6 build log +*.plg + +# Visual Studio 6 workspace options file +*.opt + +# Visual Studio 6 auto-generated workspace file (contains which files were open etc.) +*.vbw + +# Visual Studio 6 auto-generated project file (contains which files were open etc.) +*.vbp + +# Visual Studio 6 workspace and project file (working project files containing files to include in project) +*.dsw +*.dsp + +# Visual Studio 6 technical files +*.ncb +*.aps + +# Visual Studio LightSwitch build output +**/*.HTMLClient/GeneratedArtifacts +**/*.DesktopClient/GeneratedArtifacts +**/*.DesktopClient/ModelManifest.xml +**/*.Server/GeneratedArtifacts +**/*.Server/ModelManifest.xml +_Pvt_Extensions + +# Paket dependency manager +.paket/paket.exe +paket-files/ + +# FAKE - F# Make +.fake/ + +# CodeRush personal settings +.cr/personal + +# Python Tools for Visual Studio (PTVS) +__pycache__/ +*.pyc + +# Cake - Uncomment if you are using it +# tools/** +# !tools/packages.config + +# Tabs Studio +*.tss + +# Telerik's JustMock configuration file +*.jmconfig + +# BizTalk build output +*.btp.cs +*.btm.cs +*.odx.cs +*.xsd.cs + +# OpenCover UI analysis results +OpenCover/ + +# Azure Stream Analytics local run output +ASALocalRun/ + +# MSBuild Binary and Structured Log +*.binlog + +# NVidia Nsight GPU debugger configuration file +*.nvuser + +# MFractors (Xamarin productivity tool) working folder +.mfractor/ + +# Local History for Visual Studio +.localhistory/ + +# Visual Studio History (VSHistory) files +.vshistory/ + +# BeatPulse healthcheck temp database +healthchecksdb + +# Backup folder for Package Reference Convert tool in Visual Studio 2017 +MigrationBackup/ + +# Ionide (cross platform F# VS Code tools) working folder +.ionide/ + +# Fody - auto-generated XML schema +FodyWeavers.xsd + +# VS Code files for those working on multiple tools +.vscode/* +!.vscode/settings.json +!.vscode/tasks.json +!.vscode/launch.json +!.vscode/extensions.json +*.code-workspace + +# Local History for Visual Studio Code +.history/ + +# Windows Installer files from build outputs +*.cab +*.msi +*.msix +*.msm +*.msp + +# JetBrains Rider +*.sln.iml +.idea + +## +## Visual studio for Mac +## + + +# globs +Makefile.in +*.userprefs +*.usertasks +config.make +config.status +aclocal.m4 +install-sh +autom4te.cache/ +*.tar.gz +tarballs/ +test-results/ + +# Mac bundle stuff +*.dmg +*.app + +# content below from: https://github.com/github/gitignore/blob/master/Global/macOS.gitignore +# General +.DS_Store +.AppleDouble +.LSOverride + +# Icon must end with two \r +Icon + + +# Thumbnails +._* + +# Files that might appear in the root of a volume +.DocumentRevisions-V100 +.fseventsd +.Spotlight-V100 +.TemporaryItems +.Trashes +.VolumeIcon.icns +.com.apple.timemachine.donotpresent + +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk + +# content below from: https://github.com/github/gitignore/blob/master/Global/Windows.gitignore +# Windows thumbnail cache files +Thumbs.db +ehthumbs.db +ehthumbs_vista.db + +# Dump file +*.stackdump + +# Folder config file +[Dd]esktop.ini + +# Recycle Bin used on file shares +$RECYCLE.BIN/ + +# Windows Installer files +*.cab +*.msi +*.msix +*.msm +*.msp + +# Windows shortcuts +*.lnk + +# Vim temporary swap files +*.swp diff --git a/.mega-linter.yml b/.mega-linter.yml new file mode 100644 index 0000000..9e27172 --- /dev/null +++ b/.mega-linter.yml @@ -0,0 +1,30 @@ +# Configuration file for MegaLinter +# See all available variables at https://oxsecurity.github.io/megalinter/configuration/ and in linters documentation + +APPLY_FIXES: none # all, none, or list of linter keys +# ENABLE: # If you use ENABLE variable, all other languages/formats/tooling-formats will be disabled by default +# ENABLE_LINTERS: # If you use ENABLE_LINTERS variable, all other linters will be disabled by default +DISABLE: + - COPYPASTE # Comment to enable checks of excessive copy-pastes + - SPELL # Comment to enable checks of spelling mistakes + +DISABLE_LINTERS: + - REPOSITORY_DEVSKIM + - MARKDOWN_MARKDOWN_TABLE_FORMATTER + - CSHARP_DOTNET_FORMAT + - MARKDOWN_MARKDOWN_LINK_CHECK + +SHOW_ELAPSED_TIME: true +FILEIO_REPORTER: false +# DISABLE_ERRORS: true # Uncomment if you want MegaLinter to detect errors but not block CI to pass + +BASH_SHFMT_ARGUMENTS: + - "--indent=2" + +REPOSITORY_TRIVY_ARGUMENTS: + - "--severity=HIGH,CRITICAL" + +IGNORE_GITIGNORED_FILES: true + +REPOSITORY_KICS_ARGUMENTS: + - --fail-on=HIGH diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..c7e9712 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,34 @@ +{ + "version": "0.2.0", + "configurations": [ + { + // Use IntelliSense to find out which attributes exist for C# debugging + // Use hover for the description of the existing attributes + // For further information visit https://github.com/dotnet/vscode-csharp/blob/main/debugger-launchjson.md + "name": ".NET Core Launch (console)", + "type": "coreclr", + "request": "launch", + "preLaunchTask": "build", + // If you have changed target frameworks, make sure to update the program path. + "program": "${workspaceFolder}/src/PathlingS3Import/bin/Debug/net8.0/PathlingS3Import.dll", + "args": [ + "--s3-endpoint=http://localhost:9000", + "--pathling-server-base-url=http://localhost:8082/fhir", + "--s3-access-key=admin", + "--s3-secret-key=miniopass", + "--s3-bucket-name=fhir", + "--s3-object-name-prefix=staging/" + ], + "env": {}, + "cwd": "${workspaceFolder}/src/PathlingS3Import", + // For more information about the 'console' field, see https://aka.ms/VSCode-CS-LaunchJson-Console + "console": "internalConsole", + "stopAtEntry": false + }, + { + "name": ".NET Core Attach", + "type": "coreclr", + "request": "attach" + } + ] +} diff --git a/.vscode/tasks.json b/.vscode/tasks.json new file mode 100644 index 0000000..da75242 --- /dev/null +++ b/.vscode/tasks.json @@ -0,0 +1,41 @@ +{ + "version": "2.0.0", + "tasks": [ + { + "label": "build", + "command": "dotnet", + "type": "process", + "args": [ + "build", + "${workspaceFolder}/PathlingS3Import.sln", + "/property:GenerateFullPaths=true", + "/consoleloggerparameters:NoSummary;ForceNoAlign" + ], + "problemMatcher": "$msCompile" + }, + { + "label": "publish", + "command": "dotnet", + "type": "process", + "args": [ + "publish", + "${workspaceFolder}/PathlingS3Import.sln", + "/property:GenerateFullPaths=true", + "/consoleloggerparameters:NoSummary;ForceNoAlign" + ], + "problemMatcher": "$msCompile" + }, + { + "label": "watch", + "command": "dotnet", + "type": "process", + "args": [ + "watch", + "run", + "--project", + "${workspaceFolder}/PathlingS3Import.sln" + ], + "problemMatcher": "$msCompile" + } + ] +} diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..43c6a0a --- /dev/null +++ b/Dockerfile @@ -0,0 +1,24 @@ +FROM mcr.microsoft.com/dotnet/sdk:8.0.201-jammy@sha256:dc273e23006f85ef4bf154844a3147325c50adc4b5dac9191238bed4931743ac AS build +WORKDIR /build +ENV DOTNET_CLI_TELEMETRY_OPTOUT=1 + +COPY src/PathlingS3Import/PathlingS3Import.csproj . +COPY src/PathlingS3Import/packages.lock.json . + +RUN dotnet restore --locked-mode +COPY . . + +RUN dotnet publish \ + -c Release \ + -o /build/publish \ + src/PathlingS3Import/PathlingS3Import.csproj + +FROM mcr.microsoft.com/dotnet/runtime:8.0.2-jammy@sha256:8a8b6038864efd998525050d8dc16cec2825648d587747c30d1d6b4280a39880 AS runtime +WORKDIR /opt/pathling-s3-import +USER 65534:65534 +ENV DOTNET_ENVIRONMENT="Production" \ + DOTNET_CLI_TELEMETRY_OPTOUT=1 + +COPY --from=build /build/publish . +ENTRYPOINT ["/bin/bash", "-c"] +CMD [ "/opt/pathling-s3-import/PathlingS3Import --help"] diff --git a/PathlingS3Import.sln b/PathlingS3Import.sln new file mode 100644 index 0000000..32a88c4 --- /dev/null +++ b/PathlingS3Import.sln @@ -0,0 +1,27 @@ + +Microsoft Visual Studio Solution File, Format Version 12.00 +# Visual Studio Version 17 +VisualStudioVersion = 17.0.31903.59 +MinimumVisualStudioVersion = 10.0.40219.1 +Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{7C72D930-9EE6-4CA3-8F01-40429262EE29}" +EndProject +Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "PathlingS3Import", "src\PathlingS3Import\PathlingS3Import.csproj", "{1B97F255-F56D-4AE5-A25A-2C9C2AFEBFAB}" +EndProject +Global + GlobalSection(SolutionConfigurationPlatforms) = preSolution + Debug|Any CPU = Debug|Any CPU + Release|Any CPU = Release|Any CPU + EndGlobalSection + GlobalSection(SolutionProperties) = preSolution + HideSolutionNode = FALSE + EndGlobalSection + GlobalSection(ProjectConfigurationPlatforms) = postSolution + {1B97F255-F56D-4AE5-A25A-2C9C2AFEBFAB}.Debug|Any CPU.ActiveCfg = Debug|Any CPU + {1B97F255-F56D-4AE5-A25A-2C9C2AFEBFAB}.Debug|Any CPU.Build.0 = Debug|Any CPU + {1B97F255-F56D-4AE5-A25A-2C9C2AFEBFAB}.Release|Any CPU.ActiveCfg = Release|Any CPU + {1B97F255-F56D-4AE5-A25A-2C9C2AFEBFAB}.Release|Any CPU.Build.0 = Release|Any CPU + EndGlobalSection + GlobalSection(NestedProjects) = preSolution + {1B97F255-F56D-4AE5-A25A-2C9C2AFEBFAB} = {7C72D930-9EE6-4CA3-8F01-40429262EE29} + EndGlobalSection +EndGlobal diff --git a/compose.yaml b/compose.yaml new file mode 100644 index 0000000..021c727 --- /dev/null +++ b/compose.yaml @@ -0,0 +1,11 @@ +services: + minio: + image: docker.io/bitnami/minio:2024.2.17-debian-12-r2@sha256:4d04a41f9d385d51ecd9be8dafca13fe9d56be2cc1c5ea8f98e6cfb235d87ae5 + environment: + MINIO_ROOT_USER: "admin" + # kics-scan ignore-line + MINIO_ROOT_PASSWORD: "miniopass" # gitleaks:allow + MINIO_DEFAULT_BUCKETS: "fhir" + ports: + - "127.0.0.1:9000:9000" + - "127.0.0.1:9001:9001" diff --git a/src/PathlingS3Import/PathlingS3Import.csproj b/src/PathlingS3Import/PathlingS3Import.csproj new file mode 100644 index 0000000..171d3d9 --- /dev/null +++ b/src/PathlingS3Import/PathlingS3Import.csproj @@ -0,0 +1,17 @@ + + + + Exe + net8.0 + enable + enable + true + + + + + + + + + diff --git a/src/PathlingS3Import/Program.cs b/src/PathlingS3Import/Program.cs new file mode 100644 index 0000000..6b5a9ec --- /dev/null +++ b/src/PathlingS3Import/Program.cs @@ -0,0 +1,140 @@ +using System.Reactive.Linq; +using DotMake.CommandLine; +using Hl7.Fhir.Model; +using Hl7.Fhir.Rest; +using Hl7.Fhir.Serialization; +using Minio; +using Minio.DataModel.Args; + +return Cli.Run(args); + +// Create a simple class like this to define your root command: +[CliCommand(Description = "The import command")] +public class ImportCliCommand +{ + [CliOption(Description = "The S3 endpoint URI", Name = "--s3-endpoint")] + public Uri? S3Endpoint { get; set; } + + [CliOption(Description = "The S3 access key", Name = "--s3-access-key")] + public string? S3AccessKey { get; set; } + + [CliOption(Description = "The S3 secret key", Name = "--s3-secret-key")] + public string? S3SecretKey { get; set; } + + [CliOption( + Description = "The name of the bucket containing the resources to import", + Name = "--s3-bucket-name" + )] + public string? S3BucketName { get; set; } = "fhir"; + + [CliOption( + Description = "The S3 object name prefix. Corresponds to kafka-fhir-to-server's `S3_OBJECT_NAME_PREFIX`", + Name = "--s3-object-name-prefix" + )] + public string? S3ObjectNamePrefix { get; set; } = ""; + + [CliOption(Description = "The FHIR base URL of the Pathling server")] + public Uri? PathlingServerBaseUrl { get; set; } + + [CliOption(Description = "The type of FHIR resource to import")] + public ResourceType ImportResourceType { get; set; } = ResourceType.Patient; + + public void Run() + { + Console.WriteLine($@"Handler for '{GetType().FullName}' is run:"); + Console.WriteLine($@"Value for {nameof(S3Endpoint)} property is '{S3Endpoint}'"); + Console.WriteLine( + $@"Value for {nameof(PathlingServerBaseUrl)} property is '{PathlingServerBaseUrl}'" + ); + Console.WriteLine(); + + DoAsync().Wait(); + } + + private async System.Threading.Tasks.Task DoAsync() + { + var fhirClient = new FhirClient( + PathlingServerBaseUrl, + settings: new FhirClientSettings + { + PreferredFormat = ResourceFormat.Json, + // TODO: change once we implement it client-side + UseAsync = false, + Timeout = (int)TimeSpan.FromMinutes(30).TotalMilliseconds, + } + ); + + var minio = new MinioClient() + .WithEndpoint(S3Endpoint) + .WithCredentials(S3AccessKey, S3SecretKey) + .Build(); + + var bucketExistsArgs = new BucketExistsArgs().WithBucket(S3BucketName); + bool found = await minio.BucketExistsAsync(bucketExistsArgs); + if (!found) + { + throw new ArgumentException($"Bucket {S3BucketName} doesn't exist."); + } + + var prefix = $"{S3ObjectNamePrefix}{ImportResourceType}/"; + + Console.WriteLine($"Listing objects in {S3BucketName}/{prefix}."); + + var listArgs = new ListObjectsArgs() + .WithBucket(S3BucketName) + .WithPrefix(prefix) + .WithRecursive(false); + + var observable = minio.ListObjectsAsync(listArgs); + + var allObjects = new List(); + + using var subscription = observable.Subscribe( + item => + { + Console.WriteLine("OnNext: {0}", item.Key); + allObjects.Add(item); + }, + ex => Console.WriteLine("OnError: {0}", ex.Message), + () => Console.WriteLine("Finished listing.") + ); + + observable.Wait(); + + foreach (var item in allObjects) + { + var parameter = new Parameters.ParameterComponent() + { + Name = "source", + Part = + [ + new Parameters.ParameterComponent() + { + Name = "resourceType", + Value = new Code(ImportResourceType.ToString()) + }, + new Parameters.ParameterComponent() + { + Name = "mode", + Value = new Code("merge") + }, + new Parameters.ParameterComponent() + { + Name = "url", + Value = new FhirUrl($"s3://{S3BucketName}/{item.Key}") + } + ] + }; + + var importParameters = new Parameters(); + // for now, create one Import request per file. In the future, + // we might want to add multiple ndjson files at once in batches. + importParameters.Parameter.Add(parameter); + + Console.WriteLine(importParameters.ToJson()); + + var response = await fhirClient.WholeSystemOperationAsync("import", importParameters); + Console.WriteLine(response.ToJson()); + } + } +} diff --git a/src/PathlingS3Import/packages.lock.json b/src/PathlingS3Import/packages.lock.json new file mode 100644 index 0000000..d201428 --- /dev/null +++ b/src/PathlingS3Import/packages.lock.json @@ -0,0 +1,134 @@ +{ + "version": 1, + "dependencies": { + "net8.0": { + "DotMake.CommandLine": { + "type": "Direct", + "requested": "[1.8.1, )", + "resolved": "1.8.1", + "contentHash": "FRbfKWmp90SGPpN4DSJmCxF29RYDpkxeUWK2Sz9kdQTvI3L4sBAvwatjAuG/65aC8K6xqaQ7EVOpKpCVWSE0jw==" + }, + "Hl7.Fhir.R4": { + "type": "Direct", + "requested": "[5.6.1, )", + "resolved": "5.6.1", + "contentHash": "t7CclUNoIJowULFwArxZzc7SVLkQzqMjL79b5bxQI57Ar3Dkh8iz7dTtQNs/KZlFHXhE44DXfuzNayExH269xA==", + "dependencies": { + "Hl7.Fhir.Conformance": "5.6.1" + } + }, + "Minio": { + "type": "Direct", + "requested": "[6.0.2, )", + "resolved": "6.0.2", + "contentHash": "4Od4uGANX5X0AL90WV0viBNzpE2+jDHro6CGvR4//MVj5SiTTwR5SUikXgd/2G2PtYyXw4b/IBpo7Kt5cCCndA==", + "dependencies": { + "CommunityToolkit.HighPerformance": "8.2.2", + "Microsoft.Extensions.DependencyInjection.Abstractions": "8.0.0", + "Microsoft.Extensions.Logging": "8.0.0", + "System.IO.Hashing": "8.0.0", + "System.Reactive": "6.0.0" + } + }, + "CommunityToolkit.HighPerformance": { + "type": "Transitive", + "resolved": "8.2.2", + "contentHash": "+zIp8d3sbtYaRbM6hqDs4Ui/z34j7DcUmleruZlYLE4CVxXq+MO8XJyIs42vzeTYFX+k0Iq1dEbBUnQ4z/Gnrw==" + }, + "Fhir.Metrics": { + "type": "Transitive", + "resolved": "1.2.2", + "contentHash": "600yqTbqREfogkwWH+MrXwq7fFI/gO5xn1+f7EYHlN69kXZhEpyG3V574PJiErfMQS1IpDNs4QT0aAu3KGlGFQ==" + }, + "Hl7.Fhir.Base": { + "type": "Transitive", + "resolved": "5.6.1", + "contentHash": "vhtdt2hx/Jd6tarNF82Yi+ieSmm13YFXUx8kv02bq83dWOJ3uLCMDBeVTtcLI0pe7a9DqTP1PQgAIBfY2rQiFA==", + "dependencies": { + "Fhir.Metrics": "1.2.2", + "Newtonsoft.Json": "13.0.3", + "System.ComponentModel.Annotations": "5.0.0", + "System.Reflection.Emit.Lightweight": "4.7.0" + } + }, + "Hl7.Fhir.Conformance": { + "type": "Transitive", + "resolved": "5.6.1", + "contentHash": "mQ//YjQrD+255TsYnVuC3qKFYagD8wHfNQLc5bd2tuSmpWbd8nQJJO/MZBMK98OsEO9uVg2b5rkYRMW3BD23Ug==", + "dependencies": { + "Hl7.Fhir.Base": "5.6.1" + } + }, + "Microsoft.Extensions.DependencyInjection": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "V8S3bsm50ig6JSyrbcJJ8bW2b9QLGouz+G1miK3UTaOWmMtFwNNNzUf4AleyDWUmTrWMLNnFSLEQtxmxgNQnNQ==", + "dependencies": { + "Microsoft.Extensions.DependencyInjection.Abstractions": "8.0.0" + } + }, + "Microsoft.Extensions.DependencyInjection.Abstractions": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "cjWrLkJXK0rs4zofsK4bSdg+jhDLTaxrkXu4gS6Y7MAlCvRyNNgwY/lJi5RDlQOnSZweHqoyvgvbdvQsRIW+hg==" + }, + "Microsoft.Extensions.Logging": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "tvRkov9tAJ3xP51LCv3FJ2zINmv1P8Hi8lhhtcKGqM+ImiTCC84uOPEI4z8Cdq2C3o9e+Aa0Gw0rmrsJD77W+w==", + "dependencies": { + "Microsoft.Extensions.DependencyInjection": "8.0.0", + "Microsoft.Extensions.Logging.Abstractions": "8.0.0", + "Microsoft.Extensions.Options": "8.0.0" + } + }, + "Microsoft.Extensions.Logging.Abstractions": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "arDBqTgFCyS0EvRV7O3MZturChstm50OJ0y9bDJvAcmEPJm0FFpFyjU/JLYyStNGGey081DvnQYlncNX5SJJGA==", + "dependencies": { + "Microsoft.Extensions.DependencyInjection.Abstractions": "8.0.0" + } + }, + "Microsoft.Extensions.Options": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "JOVOfqpnqlVLUzINQ2fox8evY2SKLYJ3BV8QDe/Jyp21u1T7r45x/R/5QdteURMR5r01GxeJSBBUOCOyaNXA3g==", + "dependencies": { + "Microsoft.Extensions.DependencyInjection.Abstractions": "8.0.0", + "Microsoft.Extensions.Primitives": "8.0.0" + } + }, + "Microsoft.Extensions.Primitives": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "bXJEZrW9ny8vjMF1JV253WeLhpEVzFo1lyaZu1vQ4ZxWUlVvknZ/+ftFgVheLubb4eZPSwwxBeqS1JkCOjxd8g==" + }, + "Newtonsoft.Json": { + "type": "Transitive", + "resolved": "13.0.3", + "contentHash": "HrC5BXdl00IP9zeV+0Z848QWPAoCr9P3bDEZguI+gkLcBKAOxix/tLEAAHC+UvDNPv4a2d18lOReHMOagPa+zQ==" + }, + "System.ComponentModel.Annotations": { + "type": "Transitive", + "resolved": "5.0.0", + "contentHash": "dMkqfy2el8A8/I76n2Hi1oBFEbG1SfxD2l5nhwXV3XjlnOmwxJlQbYpJH4W51odnU9sARCSAgv7S3CyAFMkpYg==" + }, + "System.IO.Hashing": { + "type": "Transitive", + "resolved": "8.0.0", + "contentHash": "ne1843evDugl0md7Fjzy6QjJrzsjh46ZKbhf8GwBXb5f/gw97J4bxMs0NQKifDuThh/f0bZ0e62NPl1jzTuRqA==" + }, + "System.Reactive": { + "type": "Transitive", + "resolved": "6.0.0", + "contentHash": "31kfaW4ZupZzPsI5PVe77VhnvFF55qgma7KZr/E0iFTs6fmdhhG8j0mgEx620iLTey1EynOkEfnyTjtNEpJzGw==" + }, + "System.Reflection.Emit.Lightweight": { + "type": "Transitive", + "resolved": "4.7.0", + "contentHash": "a4OLB4IITxAXJeV74MDx49Oq2+PsF6Sml54XAFv+2RyWwtDBcabzoxiiJRhdhx+gaohLh4hEGCLQyBozXoQPqA==" + } + } + } +} \ No newline at end of file