feat: added FHIR REST operation and only build a single container ima…

…ge (#19)

* build(migrations): moved migration efbundle in same image as the API

* feat: added a first FHIR operations endpoint for creating pseudonyms

.github/workflows/ci.yaml

@@ -19,8 +19,6 @@ jobs:
     outputs:
       api-image-tags: ${{ steps.container_meta.outputs.tags }}
       api-image-version: ${{ steps.container_meta.outputs.version }}
-      migrations-image-tags: ${{ steps.container_migrations_meta.outputs.tags }}
-      migrations-image-version: ${{ steps.container_migrations_meta.outputs.version }}
     steps:
       - name: Checkout
         uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b # tag=v3
@@ -34,13 +32,6 @@ jobs:
           images: |
             ghcr.io/${{ github.repository }}
 
-      - name: Container meta for migrations image
-        id: container_migrations_meta
-        uses: docker/metadata-action@69f6fc9d46f2f8bf0d5491e4aabe0bb8c6a4678a # tag=v4
-        with:
-          images: |
-            ghcr.io/${{ github.repository }}-migrations
-
       - name: Container meta for the unit test image
         id: container_tests_meta
         uses: docker/metadata-action@69f6fc9d46f2f8bf0d5491e4aabe0bb8c6a4678a # tag=v4
@@ -85,17 +76,6 @@ jobs:
           cache-from: type=gha
           cache-to: type=gha,mode=max
 
-      - name: Build and push migrations image
-        uses: docker/build-push-action@c84f38281176d4c9cdb1626ffafcd6b3911b5d94 # tag=v3
-        with:
-          push: ${{ github.event_name != 'pull_request' }}
-          load: ${{ github.event_name == 'pull_request' }}
-          tags: ${{ steps.container_migrations_meta.outputs.tags }}
-          labels: ${{ steps.container_migrations_meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-          target: migrations
-
       - name: Copy unit test coverage reports from container
         env:
           UNIT_TEST_IMAGE: ${{ fromJson(steps.container_tests_meta.outputs.json).tags[0] }}
@@ -127,18 +107,15 @@ jobs:
         if: ${{ github.event_name == 'pull_request' }}
         env:
           API_IMAGE: ${{ fromJson(steps.container_meta.outputs.json).tags[0] }}
-          MIGRATIONS_IMAGE: ${{ fromJson(steps.container_migrations_meta.outputs.json).tags[0] }}
         run: |
           docker save "$API_IMAGE" -o /tmp/api-image.tar
-          docker save "$MIGRATIONS_IMAGE" -o /tmp/migrations-image.tar
 
       - name: Upload container images
         if: ${{ github.event_name == 'pull_request' }}
         uses: actions/upload-artifact@3cea5372237819ed00197afe530f5a7ea3e805c8 # tag=v3.1.0
         with:
           name: container-image-artifacts
           path: |
-            /tmp/migrations-image.tar
             /tmp/api-image.tar
 
   test-api-container:
@@ -167,7 +144,6 @@ jobs:
         if: ${{ github.event_name == 'pull_request' }}
         run: |
           ls -lar /tmp
-          docker load --input /tmp/migrations-image.tar
           docker load --input /tmp/api-image.tar
           docker image ls -a
 
@@ -247,8 +223,8 @@ jobs:
           docker compose --profile=test -f docker-compose.yaml logs
           docker compose --profile=test down --volumes --remove-orphans
 
-  test-migrations-container:
-    name: test migrations container
+  test-migrations:
+    name: test migrations
     runs-on: ubuntu-22.04
     permissions:
       contents: read
@@ -268,7 +244,7 @@ jobs:
       - name: Load migrations image
         if: ${{ github.event_name == 'pull_request' }}
         run: |
-          docker load --input /tmp/migrations-image.tar
+          docker load --input /tmp/api-image.tar
           docker image ls -a
 
       - name: Install .NET
@@ -279,7 +255,7 @@ jobs:
 
       - name: Run migrations tests
         env:
-          VFPS_MIGRATIONS_IMAGE_TAG: ${{ needs.build.outputs.migrations-image-version }}
+          VFPS_IMAGE_TAG: ${{ needs.build.outputs.api-image-version }}
         run: dotnet test src/Vfps.IntegrationTests --configuration=Release -l "console;verbosity=detailed"
 
   run-iter8-tests:
@@ -313,9 +289,6 @@ jobs:
           # vfps api image
           kind load image-archive /tmp/api-image.tar
 
-          # vfps migrations image
-          kind load image-archive /tmp/migrations-image.tar
-
       - name: List images in cluster
         run: docker exec kind-control-plane crictl images
 
@@ -326,7 +299,6 @@ jobs:
           helm repo add chgl https://chgl.github.io/charts
           helm install \
             --set="image.tag=${IMAGE_TAG}" \
-            --set="migrationsJob.image.tag=${IMAGE_TAG}" \
             -f tests/iter8/values.yaml \
             --wait \
             --timeout=10m \
@@ -393,7 +365,7 @@ jobs:
     if: ${{ github.event_name != 'pull_request' }}
     needs:
       - build
-      - test-migrations-container
+      - test-migrations
       - test-api-container
     permissions:
       contents: read
@@ -410,7 +382,7 @@ jobs:
       - name: Install Cosign
         uses: sigstore/cosign-installer@f3c664df7af409cb4873aa5068053ba9d61a57b6 # tag=v2.6.0
 
-      - name: Sign api image
+      - name: Sign vfps image
         env:
           COSIGN_EXPERIMENTAL: "true"
           IMAGES: ${{ needs.build.outputs.api-image-tags }}
@@ -423,17 +395,3 @@ jobs:
             echo "Signing '$image' using keyless approach"
             cosign sign "$image"
           done <<< "$IMAGES"
-
-      - name: Sign migrations image
-        env:
-          COSIGN_EXPERIMENTAL: "true"
-          IMAGES: ${{ needs.build.outputs.migrations-image-tags }}
-        run: |
-          while read -r image; do
-            if [[ $image = quay.io/* ]]; then
-              echo "Skipping '$image' hosted on quay.io"
-              continue
-            fi
-            echo "Signing '$image' using keyless approach"
-            cosign sign "$image"
-          done <<< "$IMAGES"

Dockerfile

@@ -1,13 +1,18 @@
 # syntax=docker/dockerfile:1.4
 FROM mcr.microsoft.com/dotnet/nightly/aspnet:7.0.0-rc.1-jammy-chiseled@sha256:4011e4c1b5781ac8d48a322ee0b80f1742b8b5d1b50b8287e6c38ecaecd5575b AS runtime
+WORKDIR /opt/vfps
+EXPOSE 8080/tcp 8081/tcp
+USER 65532:65532
 ENV DOTNET_ENVIRONMENT="Production" \
     DOTNET_SYSTEM_GLOBALIZATION_INVARIANT=1 \
-    DOTNET_CLI_TELEMETRY_OPTOUT=1
-USER 65532:65532
+    DOTNET_CLI_TELEMETRY_OPTOUT=1 \
+    ASPNETCORE_URLS="" \
+    DOTNET_BUNDLE_EXTRACT_BASE_DIR=/tmp
 
 FROM mcr.microsoft.com/dotnet/sdk:7.0.100-rc.1-jammy@sha256:5f968241760ea2469f029d769aec5c5f03ef55c608c63cfd74c7509757a3813a AS build
 WORKDIR /build
-ENV DOTNET_CLI_TELEMETRY_OPTOUT=1
+ENV DOTNET_CLI_TELEMETRY_OPTOUT=1 \
+    PATH="/root/.dotnet/tools:${PATH}"
 
 # TODO: remove "prerelease" once .NET 7 is officially released
 RUN dotnet tool install --global dotnet-ef --prerelease
@@ -28,6 +33,14 @@ dotnet publish src/Vfps/Vfps.csproj \
     --no-build \
     --configuration=Release \
     -o /build/publish
+
+dotnet ef migrations bundle \
+    --project=src/Vfps/Vfps.csproj \
+    --startup-project=src/Vfps/Vfps.csproj \
+    --configuration=Release \
+    --runtime=linux-x64 \
+    --verbose \
+    -o /build/efbundle
 EOF
 
 FROM build AS unit-test
@@ -39,35 +52,7 @@ RUN dotnet test \
     -l "console;verbosity=detailed" \
     --settings=runsettings.xml
 
-FROM build AS build-migrations
-WORKDIR /build
-ENV PATH="/root/.dotnet/tools:${PATH}"
-ENV DOTNET_CLI_TELEMETRY_OPTOUT=1
-
-COPY --from=build /build .
-
-RUN dotnet ef migrations bundle \
-    --project=src/Vfps/Vfps.csproj \
-    --startup-project=src/Vfps/Vfps.csproj \
-    --configuration=Release \
-    --runtime=linux-x64 \
-    --verbose \
-    -o /build/efbundle
-
-FROM runtime AS migrations
-WORKDIR /opt/vfps-database-migrations
-ENV DOTNET_BUNDLE_EXTRACT_BASE_DIR=/tmp
-
-COPY --chown=65532:65532 --from=build-migrations /build/src/Vfps/appsettings.json .
-COPY --chown=65532:65532 --from=build-migrations /build/efbundle .
-
-ENTRYPOINT ["/opt/vfps-database-migrations/efbundle"]
-
 FROM runtime
-WORKDIR /opt/vfps
-ENV ASPNETCORE_URLS=""
-EXPOSE 8080/tcp 8081/tcp
-
 COPY --chown=65532:65532 --from=build /build/publish .
-
+COPY --chown=65532:65532 --from=build /build/efbundle .
 ENTRYPOINT ["dotnet", "/opt/vfps/Vfps.dll"]

README.md

@@ -54,6 +54,49 @@ See <https://github.com/chgl/charts/tree/master/charts/vfps> for a production-gr
 The service exports metrics in Prometheus format on `/metrics`.
 Health-, readiness-, and liveness-probes are exposed at `/healthz`, `/readyz`, and `/livez` respectively.
 
+## FHIR operations
+
+The service also exposes a FHIR operations endpoint. Sending a FHIR Parameters resource to `/v1/fhir/$create-pseudonym`
+of the following schema:
+
+```json
+{
+  "resourceType": "Parameters",
+  "parameter": [
+    {
+      "name": "namespace",
+      "valueString": "test"
+    },
+    {
+      "name": "originalValue",
+      "valueString": "hello world"
+    }
+  ]
+}
+```
+
+will create a pseudonym in the `test` namespace. The expected response looks as follows:
+
+```json
+{
+  "resourceType": "Parameters",
+  "parameter": [
+    {
+      "name": "namespace",
+      "valueString": "test"
+    },
+    {
+      "name": "originalValue",
+      "valueString": "hello world"
+    },
+    {
+      "name": "pseudonymValue",
+      "valueString": "8KWwnm3TXR5R9iUDVVKD-jUezE4DEyeydOeq4v_a_b5ejSLmqOlT8g"
+    }
+  ]
+}
+```
+
 ## Development
 
 ### Prerequisites
@@ -121,20 +164,12 @@ reportgenerator -reports:"./coverage/*/coverage.cobertura.xml" -targetdir:"cover
 rm -rf coverage/
 ```
 
-### Build container images
-
-#### Main VFPS service
+### Build container image
 
 ```sh
 docker build -t ghcr.io/chgl/vfps:latest .
 ```
 
-#### VFPS database migration container
-
-```sh
-docker build -t ghcr.io/chgl/vfps-migrations:latest --target=migrations .
-```
-
 ## Benchmarks
 
 ### Micro benchmarks

src/Vfps.IntegrationTests/MigrationsTests.cs

@@ -12,16 +12,15 @@ public class MigrationsTests : IAsyncLifetime, IClassFixture<NetworkFixture>
 
     private readonly TestcontainerDatabase postgresqlContainer;
 
-    private readonly NetworkFixture networkFixture;
-
     private readonly string connectionString;
 
     private readonly string migrationsImage;
 
+    private readonly ITestcontainersBuilder<TestcontainersContainer> migrationsContainerBuilder;
+
     public MigrationsTests(ITestOutputHelper output, NetworkFixture networkFixture)
     {
         this.output = output;
-        this.networkFixture = networkFixture;
 
         postgresqlContainer = new TestcontainersBuilder<PostgreSqlTestcontainer>()
             .WithDatabase(new PostgreSqlTestcontainerConfiguration("docker.io/bitnami/postgresql:14.5.0-debian-11-r17")
@@ -38,23 +37,25 @@ public MigrationsTests(ITestOutputHelper output, NetworkFixture networkFixture)
 
         this.connectionString = "Server=postgres;Port=5432;Database=vfps;User Id=postgres;Password=postgres;";
 
-        var migrationsImageTag = Environment.GetEnvironmentVariable("VFPS_MIGRATIONS_IMAGE_TAG") ?? "latest";
-        this.migrationsImage = $"ghcr.io/chgl/vfps-migrations:{migrationsImageTag}";
+        var migrationsImageTag = Environment.GetEnvironmentVariable("VFPS_IMAGE_TAG") ?? "latest";
+        this.migrationsImage = $"ghcr.io/chgl/vfps:{migrationsImageTag}";
+
+        migrationsContainerBuilder = new TestcontainersBuilder<TestcontainersContainer>()
+            .WithImage(migrationsImage)
+            .WithName("migrations")
+            .WithNetwork(networkFixture.Network.Id, networkFixture.Network.Name)
+            .WithEntrypoint("/opt/vfps/efbundle")
+            .WithCommand("--verbose", $"--connection={connectionString}");
     }
 
     [Fact]
     public async Task RunMigrationsContainer_WithCorrectConnectionString_ShouldSucceed()
     {
         using var consumer = Consume.RedirectStdoutAndStderrToStream(new MemoryStream(), new MemoryStream());
 
-        var migrationsContainerBuilder = new TestcontainersBuilder<TestcontainersContainer>()
-            .WithImage(migrationsImage)
-            .WithName("migrations")
+        await using var migrationsContainer = migrationsContainerBuilder
             .WithOutputConsumer(consumer)
-            .WithNetwork(networkFixture.Network.Id, networkFixture.Network.Name)
-            .WithCommand("--verbose", $"--connection={connectionString}");
-
-        await using var migrationsContainer = migrationsContainerBuilder.Build();
+            .Build();
 
         await migrationsContainer.StartAsync();
 
@@ -74,14 +75,10 @@ public async Task RunMigrationsContainer_WithWrongConnectionString_ShouldFail()
     {
         using var consumer = Consume.RedirectStdoutAndStderrToStream(new MemoryStream(), new MemoryStream());
 
-        var migrationsContainerBuilder = new TestcontainersBuilder<TestcontainersContainer>()
-            .WithImage(migrationsImage)
-            .WithName("migrations")
+        await using var migrationsContainer = migrationsContainerBuilder
             .WithOutputConsumer(consumer)
-            .WithNetwork(networkFixture.Network.Id, networkFixture.Network.Name)
-            .WithCommand("--verbose", "--connection=Server=not-postgres;Port=5432;Database=vfps;User Id=postgres;Password=postgres;");
-
-        await using var migrationsContainer = migrationsContainerBuilder.Build();
+            .WithCommand("--verbose", "--connection=Server=not-postgres;Port=5432;Database=vfps;User Id=postgres;Password=postgres;")
+            .Build();
 
         await migrationsContainer.StartAsync();