Feature/devops automation (#106)

Update Feature Branche with recent main-developments:

* fix: Remove manual slice creation

* feat: Run workflow on every PR and Branch

* feat: Bump CI versions

* fix: Remove unused attributes

* Commit from GitHub Actions (CI (FHIR Validation))

* devcontainer for docker hosting of environment

* workflow for automated image rendering

* ignore when push (also merged) to main

* use default default author

* auto-generated diagrams by GitHub Action after source code change

---------

Co-authored-by: Yannick Börner <[email protected]>
Co-authored-by: ylboerner <[email protected]>
Co-authored-by: Alexander Zautke <[email protected]>
Co-authored-by: MaxMTheilig <[email protected]>

.devcontainer/Dockerfile

@@ -0,0 +1,59 @@
+FROM mcr.microsoft.com/devcontainers/base:alpine-3.18
+
+# Setzen der Umgebungsvariablen
+ENV FIRELY_TERMINAL_VERSION=3.1.0
+ENV JAVA_VALIDATOR_VERSION=6.0.11
+ENV SUSHI_VERSION=3.5.0
+
+# Installieren der notwendige Tools
+# Add Microsoft's .NET SDK repository and install .NET SDK
+RUN wget https://dot.net/v1/dotnet-install.sh \
+    && chmod +x dotnet-install.sh \
+    && ./dotnet-install.sh --channel 6.0 --install-dir /usr/share/dotnet \
+    && ln -s /usr/share/dotnet/dotnet /usr/local/bin \
+    && rm dotnet-install.sh
+
+# Install ICU libraries
+RUN apk add --no-cache icu-libs
+
+# Install Node.js and npm
+RUN apk add --no-cache nodejs npm
+
+# Install Java (OpenJDK)
+RUN apk add --no-cache openjdk11
+
+# Install Firely Terminal as vscode user
+# Switch to the vscode user
+USER vscode
+
+# Install Firely Terminal
+RUN dotnet tool install --global Firely.Terminal --version $FIRELY_TERMINAL_VERSION
+
+# Add .NET tools to PATH for vscode user
+ENV PATH="/home/vscode/.dotnet/tools:${PATH}"
+
+# Switch back to root user to perform remaining installations
+USER root
+
+RUN npm install -g fsh-sushi@$SUSHI_VERSION
+
+# Installieren der zusätzliche Abhängigkeiten
+RUN apk update && apk add --no-cache jq findutils curl ca-certificates
+
+# Setup for FHIR Validator
+RUN mkdir -p /home/vscode/.fhir/validators/
+RUN wget -q https://github.com/hapifhir/org.hl7.fhir.core/releases/download/$JAVA_VALIDATOR_VERSION/validator_cli.jar -O /home/vscode/.fhir/validators/validator_cli.jar
+
+# Set ownership
+RUN mkdir -p /home/vscode/.fhir/packages && \
+    chown -R vscode:vscode /home/vscode/.fhir/packages
+
+RUN mkdir -p /home/vscode/.fhir/settings/
+COPY codfsh-config.yaml /home/vscode/.fhir/settings/codfsh-config.yaml
+
+# Setzen des Arbeitsverzeichnis
+WORKDIR /workspace
+
+COPY . /workspace
+
+CMD [ "/bin/bash" ]

.devcontainer/codfsh-config.yaml

@@ -0,0 +1,9 @@
+sushi:
+  min_version: "3.5.0"
+hapi:
+  min_version: "3.0.0"
+  parameters: 
+    jurisdiction: DE
+    locale: de-DE
+    tx: "n/a"
+    debug: true

.devcontainer/devcontainer.json

@@ -0,0 +1,34 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/alpine
+{
+	"name": "FHIR Development Container",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"gematikde.codfsh",
+				"MITRE-Health.vscode-language-fsh",
+				"ms-azuretools.vscode-docker"
+			],
+			"settings": {
+				"codfsh.HapiValidator.Executable": "/home/vscode/.fhir/validators/validator_cli.jar",
+				"codfsh.HapiValidator.Settings.SettingsFile": "/home/vscode/.fhir/settings/codfsh-config.yaml"
+			}
+		}
+	}
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "uname -a",
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.github/workflows/RenderAllDiagrams.yml

@@ -0,0 +1,97 @@
+name: Render All Diagrams
+
+on:
+  push:
+    paths:
+    - '**/Material/imgsrc/**/*.puml'
+    - '**/Material/imgsrc/**/*.drawio'
+    branches-ignore:
+    - main**
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Installs Java distribution for running the plantUML jar
+      - name: Install Java
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '17'
+          check-latest: true
+
+      # Install graphviz for plantuml     
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v1
+
+      # Download plantUML jar 
+      - name: Download plantuml file
+        run: |
+          wget -O plantuml.jar "https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar" 
+                                
+       # Clean Folder
+      - name: Ensure and clean folder
+        run: |
+          img_dir=ImplementationGuide/images/diagrams
+          mkdir -p $img_dir
+          rm -rf ImplementationGuide/images/diagrams/*.svg
+
+      # Generate the SVGs from PUML
+      - name: Render PUML to SVG and Move files
+        run: |
+          FileNamePaths=$(find . -path "*/imgsrc/*/*.puml" -exec dirname {} \; | sort -u)
+          for dir in $FileNamePaths
+          do
+            # Render SVGs from PUMLs
+            find $dir -name "*.puml" -exec java -jar plantuml.jar -tsvg {} \;
+          done
+
+      # Generate the SVGs from DrawIO
+      - name: Render DrawIO to SVG with predefined action
+        uses: rlespinasse/drawio-export-action@v2
+        with:
+          path: ./Material/imgsrc/drawio/ 
+          remove-page-suffix: true
+          output: .
+          format: svg
+          action-mode: all
+
+      # copies the created png & svg files to the images/diagrams folder and deletes the drawio files
+      - name: Move SVGs to target image folder
+        run: |
+          img_dir=ImplementationGuide/images/diagrams
+          # Find all unique directories containing *.svg files under any /imgsrc/ folder
+          FileNamePaths=$(find . -path "*/imgsrc/*/*.svg" -exec dirname {} \; | sort -u)
+          for dir in $FileNamePaths
+          do
+            # Move SVGs to out directory
+            find $dir -name "*.svg" -exec mv {} $img_dir \;
+          done
+      
+      ## add and commit the new generated files
+      #- name: Create Pull Request
+      #  uses: peter-evans/create-pull-request@v5
+      #  with:
+      #    branch: auto/images-generation
+      #    commit-message: Generated Images from source Code by GitHub Action
+      #    title: Generated Images from GitHub Action
+      #    assignees: ${{ github.actor }}
+      #    reviewers: ${{ github.actor }}
+      #    delete-branch: true
+      #    labels: automated pr
+
+      - name: Commit rendered files
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_user_name: GitHub Actions Bot
+          commit_user_email: [email protected]
+          commit_message: auto-generated diagrams by GitHub Action after source code change

.github/workflows/main.yml

@@ -6,9 +6,7 @@ name: CI (FHIR Validation)
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
-    branches: [ master ]
   pull_request:
-    branches: [ master ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -29,7 +27,7 @@ jobs:
       # Java and .NET are already installed on ubuntu-latest
 
       - name: Firely.Terminal (GitHub Actions)
-        uses: FirelyTeam/firely-terminal-pipeline@v0.3.5
+        uses: FirelyTeam/firely-terminal-pipeline@v0.4.0
         with:
           PATH_TO_CONFORMANCE_RESOURCES: Resources/fsh-generated/resources/
           #PATH_TO_EXAMPLES: Examples
@@ -42,7 +40,7 @@ jobs:
           SIMPLIFIER_PASSWORD: ${{ secrets.SIMPLIFIER_PASSWORD }}
           SUSHI_ENABLED: true
           SUSHI_OPTIONS: Resources/
-          SUSHI_VERSION: 2.10.2
+          SUSHI_VERSION: 3.5.0
           EXPECTED_FAILS: VALIDATION_CONFORMANCE_DOTNET VALIDATION_CONFORMANCE_JAVA VALIDATION_EXAMPLES_JAVA
 
       - name: Add & Commit

Resources/fsh-generated/resources/Medication-ExampleISiKMedikament2.json

@@ -8,15 +8,6 @@
   },
   "ingredient": [
     {
-      "extension": [
-        {
-          "valueCoding": {
-            "system": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/CodeSystem/wirkstofftyp",
-            "code": "IN"
-          },
-          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/wirkstofftyp"
-        }
-      ],
       "strength": {
         "numerator": {
           "system": "http://unitsofmeasure.org",
@@ -31,6 +22,15 @@
           "code": "mL"
         }
       },
+      "extension": [
+        {
+          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/wirkstofftyp",
+          "valueCoding": {
+            "system": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/CodeSystem/wirkstofftyp",
+            "code": "IN"
+          }
+        }
+      ],
       "itemCodeableConcept": {
         "coding": [
           {