feat: add implementation guide from astacus main repository

.github/workflows/deploy-ig.yaml

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+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy implementation-guide to GitHub pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main", "deploy_ig_pages"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+    # Set up languages framework and libraries
+      - uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '17'
+
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+      - run: npm install -g fsh-sushi
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 3.2
+
+      - name: Install Jekyll
+        run: |
+          gem install jekyll bundler
+    
+      - uses: actions/setup-dotnet@v3
+        with:
+          dotnet-version: '6.0.x'
+
+      - run: dotnet tool install --tool-path ./fhir-cli firely.terminal
+
+    # Build IG
+      - run: gradle buildIG
+        continue-on-error: true
+
+    # Build Fix
+    # TODO remove this and properly fix the build...
+      - run: ./fhir-cli/fhir install hl7.fhir.fr.core 1.1.0
+        continue-on-error: true
+
+      - run: rm package.json package-lock.json
+
+      - run: gradle buildIG
+    # End Of Build Fix
+    # Build IG
+
+    # Upload IG artifact
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - name: Fix permissions
+        run: cp -r ./output _site
+
+      - name: Fix permissions
+        run: |
+          chmod -c -R +rX "_site/" | while read line; do
+            echo "::warning title=Invalid file permissions automatically fixed::$line"
+          done
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

@@ -0,0 +1,17 @@
+.DS_Store
+.idea
+.gradle
+/gradle
+gradlew
+gradlew.bat
+Thumbs.db
+/fsh-generated
+/_input-cache
+input-cache
+/output
+/temp
+/template
+/build
+/node_modules
+package.json
+package-lock.json

README.md

@@ -1,2 +1,69 @@
-# astacus-ig
-Guide d'implémentation FHIR du projet Astacus
+# Astacus IG
+
+
+
+## Building the IG
+
+"Building" the IG means generating a web-based, human-readable representation of the structured information and accompanying documentation defined within this repository. This is done via the [FHIR Implementation Guide Publisher](https://confluence.hl7.org/display/FHIR/IG+Publisher+Documentation) ("IG Publisher"), a Java program provided by the FHIR team for building IGs into a standardized presentation.
+
+If you would like to generate this locally, open command prompt window and navigate to the directory where this repository has been cloned. Then run this command:
+
+- Linux/macOS: `./gradlew buildIG`
+- Windows: `.\gradlew.bat buildIG`
+
+Astacus IG is developed in [FHIR Shorthand (FSH)](http://build.fhir.org/ig/HL7/fhir-shorthand/), a domain-specific language (DSL) for defining the content of FHIR IGs. SUSHI complies FHS files into the JSON files expected by the IG Publisher.
+
+You will need an active internet connection to build the IG. It makes take up to 30 minutes to build for the first time; subsequent builds should be faster (5-7 minutes) on a modern laptop.
+
+When the build finishes, you can open `output/index.html` in your browser to see the locally built IG.
+
+### Dependencies for building the IG
+
+1. You will need to [install java](https://adoptium.net/)
+2. You will need to [install jekyll](https://jekyllrb.com/docs/installation/)
+
+### Running SUSHI independently of the IG Publisher
+
+If you want to run SUSHI without building the entire IG, you can run a gradle task `runSushi`.
+
+### Getting a clean build
+
+While not normally necessary, you can delete the following folders to get a clean build:
+
+- `fsh-generated/` (SUSHI output)
+- `output/` (IG Publisher output)
+- `input-cache/` (IG Publisher local cache; note that deleting this will dramatically increase the length of the next build)
+
+## Key folders & files in the IG
+
+- The FHIR Shorthand (`.fsh`) files defining the resources in this IG are found in `input/fsh/`.
+    - There is an [FSH syntax highlighting extension](https://marketplace.visualstudio.com/items?itemName=kmahalingam.vscode-language-fsh) for [VSCode](https://code.visualstudio.com). The mCODE team generally uses this set of tools for working on FSH files.
+    - The FSH files are prefixed based on what is contained inside.
+
+| Prefix | Description          |
+|--------|----------------------|
+| `AL`   | Aliases              |
+| `DEF`  | Other Definitions    |
+| `EX`   | Examples             |
+| `SD`   | StructureDefinitions |
+| `VS`   | ValueSets            |
+
+- The main pages in the built IG are generated from [Markdown](https://daringfireball.net/projects/markdown/) found in `input/pagecontent/`. These pages must also be included in `sushi-config.yaml` to be compiled to HTML by the IG Publisher.
+- There are a number of other important configuration options in `sushi-config.yaml` including the menu contents of the built IG and the groupings on the [Artifacts Summary page](https://aphp.fr/ig/fhir-astacus-ig/artifacts.html).
+- The source for the UML diagrams in the IG are found in `input/images-source/` and MUST have a `.plantuml` extension. These are automatically converted to SVG by the IG Publisher, and are inserted inline into Markdown files using `{%include some-diagram.svg%}` (which corresponds to `input/images-source/some-diagram.plantuml`).
+
+## Troubleshooting
+
+### Structure Definition is Missing Snapshot Error
+
+Some non-HL7 FHIR packages are distributed without snapshot elements in their profiles. If your IG uses one of these profiles, SUSHI will report an error like the following:
+
+Structure Definition http://interopsante.org/fhir/StructureDefinition/FrPatient is missing snapshot. Snapshot is required for import.
+
+Since SUSHI does not implement its own snapshot generator, you must update the package in your FHIR cache so that its profiles include snapshot elements. Fortunately, the [Firely Terminal](https://fire.ly/products/firely-terminal/) provides a way to do this.
+
+First, you must install [Firely Terminal](https://docs.fire.ly/projects/Firely-Terminal/InstallingFirelyTerminal.html). Then use Firely Terminal to populate the snapshot elements in the dependency package.
+
+1. Run the command: fhir install <package> (<version>), substituting the dependency package ID for <package>. 
+   E.g., fhir install hl7.fhir.fr.core 1.1.0
+2. Run SUSHI again. The error about missing snapshots should no longer be displayed.

build.gradle.kts

@@ -0,0 +1,151 @@
+import org.gradle.nativeplatform.platform.internal.DefaultNativePlatform
+import com.github.gradle.node.npm.task.NpmTask
+import com.github.gradle.node.npm.task.NpxTask
+import java.nio.file.Files
+import java.io.FileOutputStream
+import java.net.URI
+import java.nio.channels.Channels
+import java.nio.file.Paths
+
+plugins {
+    id("java")
+    id("com.github.node-gradle.node") version "3.5.1"
+}
+
+val rootDir = Paths.get(
+    projectDir.absolutePath
+)
+    .toUri()
+    .path
+    .substringAfter("/")
+    .substringBeforeLast("/")
+
+val currentOperatingSystem = DefaultNativePlatform.getCurrentOperatingSystem()!!
+project.ext.set(
+    "os",
+    when {
+        currentOperatingSystem.isWindows -> "win"
+        currentOperatingSystem.isLinux -> "linux"
+        currentOperatingSystem.isMacOsX -> "darwin"
+        currentOperatingSystem.isSolaris -> ""
+        currentOperatingSystem.isFreeBSD -> ""
+        else -> ""
+    }
+)
+
+val currentArchitecture = DefaultNativePlatform.getCurrentArchitecture()!!
+project.ext.set(
+    "arch",
+    when {
+        currentArchitecture.isAmd64 -> "x64"
+        currentArchitecture.isArm -> "arm64"
+        currentArchitecture.isI386 -> ""
+        currentArchitecture.isIa64 -> ""
+        else -> ""
+    }
+)
+
+group = "fr.aphp"
+version = "0.0.1-SNAPSHOT"
+
+node {
+    download.set(true)
+    version.set(properties["nodeVersion"] as? String)
+}
+
+defaultTasks("cleanIG", "buildIG")
+
+val sushiInstall = tasks.register<NpmTask>("sushiInstall") {
+    args.set(
+        listOf(
+            "install",
+            "fsh-sushi@${properties["sushiVersion"]}"
+        )
+    )
+    dependsOn(
+        tasks.nodeSetup,
+        tasks.npmSetup,
+        tasks.npmInstall
+    )
+}
+
+val sushiBuild = tasks.register<NpxTask>("sushiBuild") {
+    command.set("sushi")
+    args.set(
+        listOf(
+            "build",
+            "."
+        )
+    )
+    dependsOn(
+        sushiInstall
+    )
+}
+
+val igPublisherInstall = tasks.register<Task>("igPublisherInstall") {
+    group = "build setup"
+    doLast {
+        val inputCacheDir = file("input-cache").toPath()
+        val publisherJar = file("input-cache/publisher.jar").toPath()
+
+        if (!Files.exists(inputCacheDir)) {
+            Files.createDirectory(inputCacheDir)
+        }
+
+        if (!Files.exists(publisherJar)) {
+            URI.create("https://github.com/HL7/fhir-ig-publisher/releases/download/${properties["publisherVersion"]}/publisher.jar")
+                .toURL().openStream().use {
+                    Channels.newChannel(it).use { rbc ->
+                        FileOutputStream("input-cache/publisher.jar").use { fos ->
+                            fos.channel.transferFrom(rbc, 0, Long.MAX_VALUE)
+                        }
+                    }
+                }
+        }
+    }
+}
+
+val buildIG = tasks.register<JavaExec>("buildIG") {
+    group = "build"
+
+    environment(
+        "PATH",
+        listOf(
+            System.getenv("PATH"),
+            "$rootDir/.gradle/nodejs/node-v${properties["nodeVersion"]}-${project.ext.get("os")}-${project.ext.get("arch")}",
+            "$rootDir/node_modules/.bin"
+        ).joinToString(
+            System.getProperties().getProperty("path.separator")
+        )
+    )
+    jvmArgs(
+        "-Xmx6144m",
+        "-Dfile.encoding=UTF-8"
+    )
+    classpath("input-cache/publisher.jar")
+    args = listOf(
+        "-no-sushi",
+        "-ig",
+        "."
+    )
+    dependsOn(
+            tasks.nodeSetup,
+            tasks.npmSetup,
+            tasks.npmInstall,
+            sushiBuild,
+            igPublisherInstall
+    )
+}
+
+val cleanIG = tasks.register<Delete>("cleanIG") {
+    group = "build"
+    delete(
+            "fsh-generated",
+            "output",
+            "temp",
+            "template",
+            "input-cache/schemas",
+            "input-cache/txcache",
+            "input-cache/publisher.jar"
+    )
+}

gradle.properties

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+nodeVersion = 18.18.2
+sushiVersion = 3.3.3
+publisherVersion = 1.4.6

ig.ini

@@ -0,0 +1,3 @@
+[IG]
+ig = fsh-generated/resources/ImplementationGuide-aphp.fhir.fr.astacus.json
+template = fhir.base.template#current