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fix: improved logging and added e2e tests (#7)
* feat: improved logging * test(e2e): added e2e tests * chore: formatted
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,4 @@ | ||
| { | ||
| "$schema": "https://docs.renovatebot.com/renovate-schema.json", | ||
| "extends": [ | ||
| "config:recommended" | ||
| ] | ||
| "extends": ["config:recommended"] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| {"resourceType":"Patient","id":"pid.999","meta":{"source":"#p21"},"identifier":[{"use":"usual","type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"MR"}]},"system":"https://miracum.org/fhir/NamingSystem/identifier/PatientId","value":"pid.999"},{"use":"official","type":{"coding":[{"system":"http://fhir.de/CodeSystem/identifier-type-de-basis","code":"GKV"}]},"system":"http://fhir.de/NamingSystem/gkv/kvid-10","value":"5678","assigner":{"identifier":{"use":"official","system":"http://fhir.de/NamingSystem/arge-ik/iknr","value":"109905113"}}}],"name":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/data-absent-reason","valueCode":"unsupported"}]}],"gender":"unknown","birthDate":"1941-01-01","deceasedDateTime":"2018-08-05T21:28:00+02:00","address":[{"type":"physical","city":"Buschau","postalCode":"12365"}]} | ||
| {"resourceType":"Patient","id":"pid-02cb8631-8342-4343-84d7-cd364e0ab101","identifier":[{"system":"http://example.com/fhir/id","value":"4ca676c2-e2d0-4726-b6dd-83eae57dcf50"}],"name":[{"family":"Wisozk","given":["Mariana"]}],"gender":"male","birthDate":"2005-12-08"} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| {"resourceType":"Patient","id":"pid.999","meta":{"source":"#p21"},"identifier":[{"use":"usual","type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"MR"}]},"system":"https://miracum.org/fhir/NamingSystem/identifier/PatientId","value":"pid.999"},{"use":"official","type":{"coding":[{"system":"http://fhir.de/CodeSystem/identifier-type-de-basis","code":"GKV"}]},"system":"http://fhir.de/NamingSystem/gkv/kvid-10","value":"5678","assigner":{"identifier":{"use":"official","system":"http://fhir.de/NamingSystem/arge-ik/iknr","value":"109905113"}}}],"name":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/data-absent-reason","valueCode":"unsupported"}]}],"gender":"unknown","birthDate":"1941-01-01","deceasedDateTime":"2018-08-05T21:28:00+02:00","address":[{"type":"physical","city":"Buschau","postalCode":"12365"}]} | ||
| {"resourceType":"Patient","id":"new-id-123","identifier":[{"system":"http://example.com/fhir/id","value":"4ca676c2-e2d0-4726-b6dd-83eae57dcf50"}],"name":[{"family":"Wisozk","given":["Mariana"]}],"gender":"male","birthDate":"2005-12-08"} |
26 changes: 26 additions & 0 deletions
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src/PathlingS3Import.Tests.E2E/PathlingS3Import.Tests.E2E.csproj
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| @@ -0,0 +1,26 @@ | ||
| <Project Sdk="Microsoft.NET.Sdk"> | ||
|
|
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| <PropertyGroup> | ||
| <TargetFramework>net8.0</TargetFramework> | ||
| <ImplicitUsings>enable</ImplicitUsings> | ||
| <Nullable>enable</Nullable> | ||
|
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| <IsPackable>false</IsPackable> | ||
| <IsTestProject>true</IsTestProject> | ||
| </PropertyGroup> | ||
|
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| <ItemGroup> | ||
| <PackageReference Include="coverlet.collector" Version="6.0.0" /> | ||
| <PackageReference Include="FluentAssertions" Version="6.12.0" /> | ||
| <PackageReference Include="Hl7.Fhir.R4" Version="5.6.1" /> | ||
| <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.8.0" /> | ||
| <PackageReference Include="Testcontainers" Version="3.7.0" /> | ||
| <PackageReference Include="xunit" Version="2.5.3" /> | ||
| <PackageReference Include="xunit.runner.visualstudio" Version="2.5.3" /> | ||
| </ItemGroup> | ||
|
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| <ItemGroup> | ||
| <Using Include="Xunit" /> | ||
| </ItemGroup> | ||
|
|
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| </Project> |
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| using DotNet.Testcontainers.Builders; | ||
| using FluentAssertions; | ||
| using Hl7.Fhir.Model; | ||
| using Hl7.Fhir.Rest; | ||
| using Xunit.Abstractions; | ||
| using Task = System.Threading.Tasks.Task; | ||
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| namespace PathlingS3Import.Tests.E2E; | ||
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| public class Tests(ITestOutputHelper output) | ||
| { | ||
| private readonly ITestOutputHelper output = output; | ||
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| [Fact] | ||
| public async Task StartImportTool_WithRunningPathlingServerAndMinio_ShouldCreateExpectedNumberOfResources() | ||
| { | ||
| // this test requires the dev fixtures to be running on their default ports as well as | ||
| // a PathlingS3Import image to exist. | ||
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| using var stdoutStream = new MemoryStream(); | ||
| using var stderrStream = new MemoryStream(); | ||
| using var consumer = Consume.RedirectStdoutAndStderrToStream(stdoutStream, stderrStream); | ||
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| var pathlingServerBaseUrl = "http://host.docker.internal:8082/fhir"; | ||
| var resourceType = ResourceType.Patient; | ||
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| string[] args = | ||
| [ | ||
| "--s3-endpoint=http://host.docker.internal:9000", | ||
| $"--pathling-server-base-url={pathlingServerBaseUrl}", | ||
| "--s3-access-key=admin", | ||
| "--s3-secret-key=miniopass", | ||
| "--s3-bucket-name=fhir", | ||
| "--s3-object-name-prefix=staging/", | ||
| $"--import-resource-type={resourceType}", | ||
| "--dry-run=false" | ||
| ]; | ||
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| var testImageTag = | ||
| Environment.GetEnvironmentVariable("PATHLING_S3_IMPORT_IMAGE_TAG") ?? "test"; | ||
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| var testContainer = new ContainerBuilder() | ||
| .WithImage($"ghcr.io/miracum/pathling-s3-import:{testImageTag}") | ||
| .WithCommand(args) | ||
| .WithOutputConsumer(consumer) | ||
| .WithExtraHost("host.docker.internal", "host-gateway") | ||
| .Build(); | ||
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| await testContainer.StartAsync(); | ||
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| var exitCode = await testContainer.GetExitCodeAsync(); | ||
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| output.WriteLine("Test container exited"); | ||
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| consumer.Stdout.Seek(0, SeekOrigin.Begin); | ||
| using var stdoutReader = new StreamReader(consumer.Stdout); | ||
| var stdout = stdoutReader.ReadToEnd(); | ||
| output.WriteLine(stdout); | ||
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| exitCode.Should().Be(0); | ||
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| // use a different base URL since this test isn't run inside | ||
| // a container. Slightly ugly. | ||
| using var fhirClient = new FhirClient( | ||
| "http://localhost:8082/fhir", | ||
| settings: new() | ||
| { | ||
| PreferredFormat = ResourceFormat.Json, | ||
| Timeout = (int)TimeSpan.FromSeconds(60).TotalMilliseconds | ||
| } | ||
| ); | ||
|
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| var response = await fhirClient.SearchAsync( | ||
| resourceType.ToString(), | ||
| summary: SummaryType.Count | ||
| ); | ||
|
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| response.Should().NotBeNull(); | ||
| response!.Total.Should().Be(3); | ||
| } | ||
| } |
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