initial commit

.bumpversion.cfg

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+[bumpversion]
+current_version = 1.2.1-snapshot
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>\S+))?
+serialize =
+	{major}.{minor}.{patch}-{release}
+	{major}.{minor}.{patch}
+commit = False
+tag = False
+
+[bumpversion:part:release]
+optional_value = release
+values =
+	snapshot
+	release
+
+[bumpversion:file:sushi-config.yaml]
+search = version: {current_version}
+replace = version: {new_version}

.fsh-validator.yml

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+exclude_code_systems:
+  - http://fhir.de/CodeSystem/bfarm/icd-10-gm

.github/workflows/fhir-validate.yml

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+name: FHIR Validation
+
+on:
+  push:
+    branches:
+      - main
+      - master
+      - staging
+  pull_request:
+    branches:
+      - main
+      - master
+      - staging
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  LANG: "en_US.UTF-8"
+
+jobs:
+
+  fsh-fhir-validation:
+    runs-on: ubuntu-latest
+    steps:
+
+        # locale must be set explicitly, otherwise fhir validator 5.7.75 fails
+      - name: set locale
+        run: |
+          sudo locale-gen en_US.UTF-8
+          sudo update-locale LANG=en_US.UTF-8
+
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install Python dependencies
+        uses: py-actions/py-dependency-install@v2
+
+      - name: Setup Java JDK
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+
+      - name: Setup NodeJS
+        uses: actions/setup-node@v3
+        with:
+          node-version: '18'
+
+      - name: Prepare environment
+        run: ./scripts/prepare-environment.sh
+
+      - name: Execute validator
+        run: fsh-validator --all

.github/workflows/ig-publish.yml

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+name: ImplementationGuide Publisher
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the main or master branch
+  push:
+    branches:
+      - main
+      - master
+      - staging
+  pull_request:
+    branches:
+      - main
+      - master
+      - staging
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  run-publisher:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      # read id, version and canonical from sushi-config.yaml
+      - name: Run read-yaml action
+        id: yaml-data
+        uses: CumulusDS/get-yaml-paths-action@v1.0.1
+        with:
+          file: sushi-config.yaml
+          version: version
+          canonical: canonical
+          id: id
+
+      # display outputs from read-yaml action
+      - name: Display read-yaml output
+        run: |
+          echo "id: ${{ steps.yaml-data.outputs.id }}"
+          echo "target url: ${{ steps.yaml-data.outputs.canonical }}"
+          echo "version: ${{ steps.yaml-data.outputs.version }}"
+
+      - name: Run the IG publisher
+        uses: docker://hl7fhir/ig-publisher-base:latest
+        with:
+          args: ./scripts/run-ig-publisher.sh
+
+
+      # deploy implementation guide to github pages
+      - name: Deploy
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main')
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./output
+          force_orphan: true
+
+      # upload binaries to release
+      - name: Upload binaries to release
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main')
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: ./output/package.tgz
+          asset_name: ${{ steps.yaml-data.outputs.id }}-${{ steps.yaml-data.outputs.version }}.tgz
+          tag: v${{ steps.yaml-data.outputs.version }}
+          release_name: Release v${{ steps.yaml-data.outputs.version }}
+          overwrite: true

.gitignore

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+# Temporary folders #
+#####################
+temp
+template
+output
+input-cache
+fsh-generated
+_preprocessed
+notes
+notebooks
+
+# IG publisher files #
+###########################################
+validator_cli.jar
+publisher.jar
+_gencontinuous.bat
+_gencontinuous.sh
+
+# OS generated files #
+###########################
+.DS_Store
+Thumbs.db
+
+# IDE folders and files
+###########################
+.vscode
+*.code-workspace
+.idea
+
+# nodejs files/directories
+###########################
+package-lock.json
+node_modules/
+package.json
+
+# cache folders
+###########################
+__pycache__/
+
+# generated files
+###########################
+*-generated.md

.pre-commit-config.yaml

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+exclude: '^docs/'
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: mixed-line-ending
+    -   id: check-json
+    -   id: pretty-format-json
+        args: ['--autofix', '--no-sort-keys']

.zshrc

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+
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/Users/lisav/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/Users/lisav/miniconda3/etc/profile.d/conda.sh" ]; then
+        . "/Users/lisav/miniconda3/etc/profile.d/conda.sh"
+    else
+        export PATH="/Users/lisav/miniconda3/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/Users/lisav/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/Users/lisav/miniconda3/etc/profile.d/conda.sh" ]; then
+        . "/Users/lisav/miniconda3/etc/profile.d/conda.sh"
+    else
+        export PATH="/Users/lisav/miniconda3/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+
+export PATH=$PATH:/opt/sushi/bin
+
+
+export PATH=$PATH:/opt/sushi/bin

README.md

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+# Template for CPG-on-EBMonFHIR machine-readable clinical practice guidelines# CICU

_genonce.bat

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+@ECHO OFF
+SET publisher_jar=publisher.jar
+SET input_cache_path=%CD%\input-cache
+
+ECHO Checking internet connection...
+PING tx.fhir.org -4 -n 1 -w 1000 | FINDSTR TTL && GOTO isonline
+ECHO We're offline...
+SET txoption=-tx n/a
+GOTO igpublish
+
+:isonline
+ECHO We're online
+SET txoption=
+
+:igpublish
+
+SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
+
+IF EXIST "%input_cache_path%\%publisher_jar%" (
+	JAVA -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption% %*
+) ELSE If exist "..\%publisher_jar%" (
+	JAVA -jar "..\%publisher_jar%" -ig . %txoption% %*
+) ELSE (
+	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+)
+
+PAUSE

_genonce.sh

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+#!/bin/bash
+publisher_jar=publisher.jar
+input_cache_path=./input-cache/
+echo Checking internet connection...
+curl -sSf tx.fhir.org > /dev/null
+
+if [ $? -eq 0 ]; then
+	echo "Online"
+	txoption=""
+else
+	echo "Offline"
+	txoption="-tx n/a"
+fi
+
+echo "$txoption"
+
+export JAVA_TOOL_OPTIONS="$JAVA_TOOL_OPTIONS -Dfile.encoding=UTF-8"
+
+publisher=$input_cache_path/$publisher_jar
+if test -f "$publisher"; then
+	java -jar $publisher -ig . $txoption $*
+
+else
+	publisher=../$publisher_jar
+	if test -f "$publisher"; then
+		java -jar $publisher -ig . $txoption $*
+	else
+		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+	fi
+fi