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Merge branch 'main' into dependabot/nuget/System.IdentityModel.Tokens.Jwt-8.3.0
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‎.github/pull_request_template.md

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Original file line numberDiff line numberDiff line change
@@ -13,8 +13,9 @@ Describe how this change was tested.
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- Tag the PR with the type of update: **Bug**, **Build**, **Dependencies**, **Enhancement**, **New-Feature** or **Documentation**
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- Tag the PR with **Open source**, **Azure API for FHIR** (CosmosDB or common code) or **Azure Healthcare APIs** (SQL or common code) to specify where this change is intended to be released.
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- Tag the PR with **Schema Version backward compatible** or **Schema Version backward incompatible** or **Schema Version unchanged** if this adds or updates Sql script which is/is not backward compatible with the code.
16+
- When changing or adding behavior, if your code modifies the system design or changes design assumptions, please create and include an [ADR](https://github.com/microsoft/fhir-server/blob/main/docs/arch).
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- [ ] CI is green before merge [![Build Status](https://microsofthealthoss.visualstudio.com/FhirServer/_apis/build/status/CI%20Build%20%26%20Deploy?branchName=main)](https://microsofthealthoss.visualstudio.com/FhirServer/_build/latest?definitionId=27&branchName=main)
17-
- Review [squash-merge requirements](https://github.com/microsoft/fhir-server/blob/master/SquashMergeRequirements.md)
18+
- Review [squash-merge requirements](https://github.com/microsoft/fhir-server/blob/main/SquashMergeRequirements.md)
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### Semver Change ([docs](https://github.com/microsoft/fhir-server/blob/master/docs/Versioning.md))
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### Semver Change ([docs](https://github.com/microsoft/fhir-server/blob/main/docs/Versioning.md))
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Patch|Skip|Feature|Breaking (reason)

‎CustomAnalysisRules.ruleset

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@@ -2,12 +2,18 @@
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<RuleSet Name="FHIR Analysis Rules" Description="The code analysis rules used for the FHIR server C# source projects." ToolsVersion="17.0">
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<Include Path="minimumrecommendedrules.ruleset" Action="Default" />
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<Include Path="securityrules.ruleset" Action="Default" />
5+
<Rules AnalyzerId="Microsoft.Analyzers.ManagedCodeAnalysis" RuleNamespace="Microsoft.Rules.Managed">
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<Rule Id="CA1852" Action="None" />
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</Rules>
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<Rules AnalyzerId="Microsoft.CodeAnalysis.CSharp.Features" RuleNamespace="Microsoft.CodeAnalysis.CSharp.Features">
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<Rule Id="IDE0003" Action="Warning" />
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<Rule Id="IDE0004" Action="Warning" />
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<Rule Id="IDE0005" Action="Warning" />
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<Rule Id="IDE1005" Action="Warning" />
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</Rules>
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<Rules AnalyzerId="Microsoft.CodeAnalysis.CSharp.NetAnalyzers" RuleNamespace="Microsoft.CodeAnalysis.CSharp.NetAnalyzers">
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<Rule Id="CA1852" Action="None" />
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</Rules>
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<Rules AnalyzerId="Microsoft.CodeAnalysis.NetAnalyzers" RuleNamespace="Microsoft.CodeAnalysis.NetAnalyzers">
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<Rule Id="CA1008" Action="Info" />
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<Rule Id="CA1014" Action="Info" />

‎Directory.Build.props

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@@ -19,7 +19,7 @@
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<PublishRepositoryUrl>true</PublishRepositoryUrl>
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<RepositoryUrl>https://github.com/microsoft/fhir-server</RepositoryUrl>
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<RunSettingsFilePath>$(MSBuildThisFileDirectory)\CodeCoverage.runsettings</RunSettingsFilePath>
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<TargetFrameworks>net8.0;net6.0</TargetFrameworks>
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<TargetFrameworks>net9.0;net8.0</TargetFrameworks>
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<TargetLatestRuntimePatch>true</TargetLatestRuntimePatch>
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<TreatWarningsAsErrors>true</TreatWarningsAsErrors>
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<WarningsAsErrors />

‎Directory.Packages.props

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Original file line numberDiff line numberDiff line change
@@ -1,58 +1,74 @@
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<Project>
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<!-- Shared dependencies versions.-->
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<PropertyGroup>
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<HealthcareSharedPackageVersion>7.1.183</HealthcareSharedPackageVersion>
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<Hl7FhirVersion>4.3.0</Hl7FhirVersion>
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<HealthcareSharedPackageVersion>8.0.33</HealthcareSharedPackageVersion>
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<Hl7FhirVersion>5.11.3</Hl7FhirVersion>
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<Hl7FhirLegacyVersion>5.11.0</Hl7FhirLegacyVersion>
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</PropertyGroup>
7-
<ItemGroup Label="CVE Mitigation">
8-
<!--Please include the CGA id if possible-->
9-
<PackageVersion Include="System.Security.Cryptography.Xml" Version="8.0.2" />
10-
<!--CVE-2023-29331-->
11-
<PackageVersion Include="System.Security.Cryptography.Pkcs" Version="8.0.1" />
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<!-- CVE-2021-26701 -->
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<PackageVersion Include="System.Text.Encodings.Web" Version="8.0.0" />
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<!-- CVE-2020-1045 -->
15-
<PackageVersion Include="Microsoft.AspNetCore.Http" Version="2.2.2" />
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<!-- CVE-2022-26907 -->
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<PackageVersion Include="Microsoft.Rest.ClientRuntime" Version="2.3.24" />
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</ItemGroup>
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<!-- SDK Packages -->
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<Choose>
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<When Condition="'$(TargetFramework)' == 'net8.0'">
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<PropertyGroup>
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<AspNetPackageVersion>8.0.0</AspNetPackageVersion>
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<!-- >= 12.2.0 MediatR started depending on 8.x Microsoft.Extension.* libraries -->
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<MediatRVersion>12.4.1</MediatRVersion>
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<LoggingVersion>8.0.2</LoggingVersion>
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<ConsoleLoggingVersion>8.0.1</ConsoleLoggingVersion>
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<SdkPackageVersion>8.0</SdkPackageVersion>
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<AspNetPackageVersion>8.0.12</AspNetPackageVersion>
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</PropertyGroup>
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</When>
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<Otherwise>
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<PropertyGroup>
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<AspNetPackageVersion>6.0.23</AspNetPackageVersion>
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<MediatRVersion>12.4.1</MediatRVersion>
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<LoggingVersion>9.0.1</LoggingVersion>
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<ConsoleLoggingVersion>9.0.1</ConsoleLoggingVersion>
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<SdkPackageVersion>9.0</SdkPackageVersion>
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<AspNetPackageVersion>9.0.1</AspNetPackageVersion>
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</PropertyGroup>
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</Otherwise>
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</Choose>
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<ItemGroup Label="CVE Mitigation">
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<!--Please include the CGA id if possible-->
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<PackageVersion Include="System.Security.Cryptography.Xml" Version="8.0.2" />
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<!--CVE-2023-29331-->
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<PackageVersion Include="System.Security.Cryptography.Pkcs" Version="8.0.1" />
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<!-- CVE-2021-26701 -->
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<PackageVersion Include="System.Text.Encodings.Web" Version="9.0.1" />
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<!-- CVE-2020-1045 -->
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<PackageVersion Include="Microsoft.AspNetCore.Http" Version="2.2.2" />
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<!-- CVE-2022-26907 -->
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<PackageVersion Include="Microsoft.Rest.ClientRuntime" Version="2.3.24" />
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</ItemGroup>
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<ItemGroup>
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<PackageVersion Include="AngleSharp" Version="1.1.2" />
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<PackageVersion Include="Azure.Identity" Version="1.13.1" />
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<PackageVersion Include="Azure.Identity" Version="1.13.2" />
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<PackageVersion Include="Azure.ResourceManager.CosmosDB" Version="1.3.2" />
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<PackageVersion Include="Azure.Extensions.AspNetCore.Configuration.Secrets" Version="1.3.2" />
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<PackageVersion Include="Azure.Monitor.OpenTelemetry.AspNetCore" Version="1.2.0" />
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<PackageVersion Include="Azure.Storage.Blobs" Version="12.21.2" />
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<PackageVersion Include="coverlet.collector" Version="6.0.2" />
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<PackageVersion Include="coverlet.collector" Version="6.0.4" />
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<PackageVersion Include="DotNet.ReproducibleBuilds" Version="1.2.25" />
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<PackageVersion Include="Ensure.That" Version="10.1.0" />
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<PackageVersion Include="FluentValidation" Version="11.10.0" />
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<PackageVersion Include="FluentValidation" Version="11.11.0" />
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<PackageVersion Include="Hl7.Fhir.Base" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.STU3" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.R4" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.R4B" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.R5" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Serialization" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Validation.Legacy.STU3" Version="$(Hl7FhirLegacyVersion)" />
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<PackageVersion Include="Hl7.Fhir.Validation.Legacy.R4" Version="$(Hl7FhirLegacyVersion)" />
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<PackageVersion Include="Hl7.Fhir.Validation.Legacy.R4B" Version="$(Hl7FhirLegacyVersion)" />
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<PackageVersion Include="Hl7.Fhir.Validation.Legacy.R5" Version="$(Hl7FhirLegacyVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.Data.STU3" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.Data.R4" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.Data.R4B" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.Data.R5" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.STU3" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.R4" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.R4B" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.R5" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Specification.STU3" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.STU3" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.Fhir.Support.Poco" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="Hl7.FhirPath" Version="$(Hl7FhirVersion)" />
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<PackageVersion Include="IdentityServer4" Version="4.1.2" />
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<PackageVersion Include="MediatR" Version="12.4.1" />
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<PackageVersion Include="MediatR" Version="$(MediatRVersion)" />
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<PackageVersion Include="Microsoft.ApplicationInsights.AspNetCore" Version="2.22.0" />
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<PackageVersion Include="Microsoft.AspNetCore.Authentication.JwtBearer" Version="$(AspNetPackageVersion)" />
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<PackageVersion Include="Microsoft.AspNetCore.JsonPatch" Version="$(AspNetPackageVersion)" />
@@ -63,42 +79,43 @@
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<PackageVersion Include="Microsoft.Azure.ContainerRegistry" Version="1.0.0-preview.2" />
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<PackageVersion Include="Microsoft.Azure.Cosmos" Version="3.45.2" />
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<PackageVersion Include="Microsoft.Azure.Storage.Blob" Version="11.2.3" />
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<PackageVersion Include="Microsoft.Extensions.Configuration.Binder" Version="8.0.1" />
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<PackageVersion Include="Microsoft.Extensions.Configuration.CommandLine" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Configuration.Json" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Configuration" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions" Version="8.0.8" />
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<PackageVersion Include="Microsoft.Extensions.Diagnostics.HealthChecks" Version="8.0.7" />
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<PackageVersion Include="Microsoft.Extensions.FileProviders.Embedded" Version="8.0.10" />
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<PackageVersion Include="Microsoft.Extensions.Hosting.Abstractions" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Http.Polly" Version="8.0.8" />
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<PackageVersion Include="Microsoft.Extensions.Http" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Logging.Abstractions" Version="8.0.1" />
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<PackageVersion Include="Microsoft.Data.SqlClient" Version="5.2.2" />
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<PackageVersion Include="Microsoft.Extensions.Configuration.Binder" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Configuration.CommandLine" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Configuration.Json" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Configuration" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Diagnostics.HealthChecks" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.FileProviders.Embedded" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Hosting.Abstractions" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Http.Polly" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Http" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Logging.Abstractions" Version="$(LoggingVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Logging.ApplicationInsights" Version="2.22.0" />
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<PackageVersion Include="Microsoft.Extensions.Logging.Console" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Logging" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.TimeProvider.Testing" Version="8.10.0" />
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<PackageVersion Include="Microsoft.Extensions.Options.ConfigurationExtensions" Version="8.0.0" />
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<PackageVersion Include="Microsoft.Extensions.Logging.Console" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Logging" Version="$(ConsoleLoggingVersion)" />
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<PackageVersion Include="Microsoft.Extensions.TimeProvider.Testing" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Extensions.Options.ConfigurationExtensions" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Abstractions" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Api" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Client" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Core" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Encryption" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Extensions.BuildTimeCodeGenerator" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Extensions.DependencyInjection" Version="$(HealthcareSharedPackageVersion)" />
89-
<PackageVersion Include="Microsoft.Health.Fhir.Anonymizer.R4.Core" Version="3.1.0.62" />
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<PackageVersion Include="Microsoft.Health.Fhir.Anonymizer.Stu3.Core" Version="3.1.0.62" />
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<PackageVersion Include="Microsoft.Health.Fhir.Anonymizer.R4.Core" Version="4.1.1.3" />
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<PackageVersion Include="Microsoft.Health.Fhir.Anonymizer.Stu3.Core" Version="4.1.1.3" />
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<PackageVersion Include="Microsoft.Health.Fhir.Liquid.Converter" Version="7.0.1" />
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<PackageVersion Include="Microsoft.Health.SqlServer.Api" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.SqlServer" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Test.Utilities" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Health.Tools.Sql.Tasks" Version="$(HealthcareSharedPackageVersion)" />
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<PackageVersion Include="Microsoft.Identity.Web" Version="2.13.3" />
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<PackageVersion Include="Microsoft.IO.RecyclableMemoryStream" Version="3.0.1" />
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<PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
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<PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.12.0" />
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<PackageVersion Include="Microsoft.SourceLink.GitHub" Version="8.0.0" />
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<PackageVersion Include="Microsoft.SqlServer.DACFx" Version="162.0.52" />
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<PackageVersion Include="Microsoft.SqlServer.SqlManagementObjects" Version="171.30.0" />
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<PackageVersion Include="Microsoft.SqlServer.SqlManagementObjects" Version="172.52.0" />
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<PackageVersion Include="Newtonsoft.Json.Schema" Version="4.0.1" />
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<PackageVersion Include="Newtonsoft.Json" Version="13.0.3" />
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<PackageVersion Include="NSubstitute" Version="5.3.0" />
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<PackageVersion Include="System.Collections.Immutable" Version="8.0.0" />
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<PackageVersion Include="System.CommandLine.NamingConventionBinder" Version="2.0.0-beta4.22272.1" />
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<PackageVersion Include="System.CommandLine" Version="2.0.0-beta4.22272.1" />
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<PackageVersion Include="System.Configuration.ConfigurationManager" Version="8.0.0" />
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<PackageVersion Include="System.Data.SqlClient" Version="4.8.6" />
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<PackageVersion Include="System.Diagnostics.PerformanceCounter" Version="8.0.0" />
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<PackageVersion Include="System.IdentityModel.Tokens.Jwt" Version="8.3.0" />
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<PackageVersion Include="System.Configuration.ConfigurationManager" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="System.Diagnostics.PerformanceCounter" Version="$(SdkPackageVersion)" />
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<PackageVersion Include="System.IO.FileSystem.AccessControl" Version="5.0.0" />
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<PackageVersion Include="System.Net.Http" Version="4.3.4" />
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<PackageVersion Include="System.Private.ServiceModel" Version="4.10.3" />
@@ -124,5 +141,6 @@
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<PackageVersion Include="xunit.runner.visualstudio" Version="2.8.2" />
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<PackageVersion Include="System.Drawing.Common" Version="8.0.8" />
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<PackageVersion Include="Moq" Version="4.20.69" />
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<PackageVersion Include="System.Text.RegularExpressions" Version="4.3.1" />
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</ItemGroup>
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</Project>

‎README.md

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@@ -55,6 +55,7 @@ To see what is releasing in the FHIR Server, please refer to the [releases](http
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- [SMART on FHIR Proxy tutorial](docs/SMARTonFHIR.md): Describes how to use the proxy to enable SMART on FHIR applications with the FHIR Server.
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- [FHIR Postman tutorial](https://docs.microsoft.com/azure/healthcare-apis/access-fhir-postman-tutorial): Describes how to access a FHIR API using Postman.
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- [Debugging](docs/HowToDebug.md): Describes how to debug FHIR Server for Azure using Visual Studio.
58+
- [Connect to SQL Database](docs/HowToConnectSQLDatabase.md): Describes how to connect to SQL Database.
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## Blog Posts
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* Blog: [FHIR Server for Azure, an open source project for modern healthcare](https://cloudblogs.microsoft.com/industry-blog/health/2018/11/12/fhir-server-for-azure-an-open-source-project-for-cloud-based-health-solutions/).

‎build/build-variables.yml

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@@ -5,7 +5,7 @@ variables:
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buildConfiguration: 'Release'
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publicDockerImagePlatforms: 'linux/amd64,linux/arm64'
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testDockerImagePlatforms: 'linux/amd64'
8-
defaultBuildFramework: 'net8.0'
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defaultBuildFramework: 'net9.0'
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azureSubscriptionEndpoint: 'docker-build'
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azureContainerRegistryName: 'healthplatformregistry'
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azureContainerRegistry: '$(azureContainerRegistryName).azurecr.io'

‎build/ci-pipeline.yml

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@@ -65,7 +65,7 @@ stages:
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majorMinorPatch: $[stageDependencies.UpdateVersion.Semver.outputs['SetVariablesFromGitVersion.majorMinorPatch']]
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nuGetVersion: $[stageDependencies.UpdateVersion.Semver.outputs['SetVariablesFromGitVersion.nuGetVersion']]
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jobs:
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- job: Windows_dotnet8
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- job: Windows_dotnet9
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pool:
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name: '$(DefaultWindowsPool)'
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steps:
@@ -74,14 +74,14 @@ stages:
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targetBuildFramework: $(defaultBuildFramework)
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unitTest: false
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codeCoverage: true
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- job: Linux_dotnet6
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- job: Linux_dotnet8
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pool:
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name: '$(DefaultLinuxPool)'
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vmImage: '$(LinuxVmImage)'
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steps:
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- template: ./jobs/build.yml
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parameters:
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targetBuildFramework: 'net6.0'
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targetBuildFramework: 'net8.0'
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- stage: BuildArtifacts
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displayName: 'Build artifacts'

‎build/docker/Dockerfile

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@@ -1,11 +1,9 @@
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# --platform tells docker to always use the host platform for the build not the target platform. Runtime container will use target platform.
2-
FROM --platform=$BUILDPLATFORM mcr.microsoft.com/dotnet/sdk:8.0.403-cbl-mariner2.0 AS build
2+
FROM --platform=$BUILDPLATFORM mcr.microsoft.com/dotnet/sdk:9.0.102-azurelinux3.0 AS build
33
ARG TARGETARCH
44
ARG FHIR_VERSION
55
ARG ASSEMBLY_VER
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7-
RUN groupadd nonroot -g 1000 && useradd -r -M -s /sbin/nologin -g nonroot -c nonroot nonroot -u 998
8-
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WORKDIR /repo
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COPY .editorconfig \
@@ -76,10 +74,10 @@ RUN dotnet restore ./src/Microsoft.Health.Fhir.${FHIR_VERSION}.Web/Microsoft.Hea
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COPY . .
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RUN dotnet publish /repo/src/Microsoft.Health.Fhir.${FHIR_VERSION}.Web/Microsoft.Health.Fhir.${FHIR_VERSION}.Web.csproj -o "/build" --no-restore -p:AssemblyVersion="${ASSEMBLY_VER}" -p:FileVersion="${ASSEMBLY_VER}" -p:Version="${ASSEMBLY_VER}" -f net8.0 -a $TARGETARCH
77+
RUN dotnet publish /repo/src/Microsoft.Health.Fhir.${FHIR_VERSION}.Web/Microsoft.Health.Fhir.${FHIR_VERSION}.Web.csproj -o "/build" --no-restore -p:AssemblyVersion="${ASSEMBLY_VER}" -p:FileVersion="${ASSEMBLY_VER}" -p:Version="${ASSEMBLY_VER}" -f net9.0 -a $TARGETARCH
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# Implicitly uses the target platform for the runtime image.
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FROM mcr.microsoft.com/dotnet/aspnet:8.0.11-cbl-mariner2.0 AS runtime
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FROM mcr.microsoft.com/dotnet/aspnet:9.0.1-azurelinux3.0 AS runtime
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ARG FHIR_VERSION
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@@ -90,9 +88,6 @@ RUN tdnf clean all && tdnf repolist --refresh && tdnf update -y && tdnf clean al
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RUN tdnf install icu -y && \
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tdnf clean all
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COPY --from=build /etc/group /etc/group
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COPY --from=build /etc/passwd /etc/passwd
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ENV DOTNET_SYSTEM_GLOBALIZATION_INVARIANT=false \
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ASPNETCORE_URLS=http://+:8080
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