Initial commit.

.gitignore

@@ -0,0 +1,9 @@
+.DS_Store
+Thumbs.db
+/SUSHI-GENERATED-FILES.md
+/ig.ini
+/input-cache
+/input
+/output
+/temp
+/template

README.md

@@ -1,2 +1,42 @@
-# synthea-fhir-ig
-Synthea FHIR Implementation Guide
+# Synthea<sup>TM</sup> FHIR Implementation Guide
+
+This repository contains the artifacts required to generate the Synthea<sup>TM</sup> FHIR Implementation Guide (IG) using [SUSHI](http://hl7.org/fhir/uv/shorthand/2020May/sushi.html#step-2-install-sushi) and the HL7 FHIR IG Publisher.
+
+This repository was based on the [FSH Let’s Build Starter Project](https://github.com/standardhealth/fsh-devdays-exercise/releases/tag/v0.0.1).
+
+## Requirements
+
+- [Node.js LTS](https://nodejs.org/en/download/) – needed to install and run SUSHI
+- [SUSHI](http://hl7.org/fhir/uv/shorthand/2020May/sushi.html#step-2-install-sushi) – needed to
+  compile FSH into valid FHIR definitions
+- [OpenJDK 8](https://adoptopenjdk.net/?variant=openjdk8&jvmVariant=hotspot) (or licensed
+  [Oracle JDK](https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html)) – needed
+  to run HL7 IG Publisher
+- [Ruby and Jekyll](https://jekyllrb.com/docs/installation/) – needed to run HL7 IG Publisher
+
+## Build the IG
+
+The first time you run this code, you'll need to execute the `_updatePublisher` script.
+
+```
+sushi
+./_genonce.sh
+```
+
+The final IG will be written to the `./output` folder.
+
+# License
+
+Copyright 2020+ The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

_genonce.bat

@@ -0,0 +1,33 @@
+@ECHO OFF
+REM ***********************************************************************************************
+REM *                              WARNING: DO NOT EDIT THIS FILE                                 *
+REM *                                                                                             *
+REM * This file is generated by SUSHI. Any edits you make to this file will be overwritten.       *
+REM ***********************************************************************************************
+
+SET publisher_jar=org.hl7.fhir.publisher.jar
+SET input_cache_path=%CD%\input-cache
+
+ECHO Checking internet connection...
+PING tx.fhir.org -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 ig.ini %txoption% %*
+) ELSE If exist "..\%publisher_jar%" (
+	JAVA -jar "..\%publisher_jar%" -ig ig.ini %txoption% %*
+) ELSE (
+	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+)
+
+PAUSE

_genonce.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# *************************************************************************************************
+# *                               WARNING: DO NOT EDIT THIS FILE                                  *
+# *                                                                                               *
+# * This file is generated by SUSHI. Any edits you make to this file will be overwritten.         *
+# *************************************************************************************************
+
+publisher_jar=org.hl7.fhir.publisher.jar
+input_cache_path=./input-cache/
+set -e
+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"
+
+publisher=$input_cache_path/$publisher_jar
+if test -f "$publisher"; then
+	java -jar $publisher -ig ig.ini $txoption $*
+
+else
+	publisher=../$publisher_jar
+	if test -f "$publisher"; then
+		java -jar $publisher -ig ig.ini $txoption $*
+	else
+		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+	fi
+fi

_updatePublisher.bat

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+@ECHO OFF
+REM ***********************************************************************************************
+REM *                              WARNING: DO NOT EDIT THIS FILE                                 *
+REM *                                                                                             *
+REM * This file is generated by SUSHI. Any edits you make to this file will be overwritten.       *
+REM ***********************************************************************************************
+
+SETLOCAL
+
+SET dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
+SET publisher_jar=org.hl7.fhir.publisher.jar
+SET input_cache_path=%CD%\input-cache\
+
+:processflags
+SET ARG=%1
+IF DEFINED ARG (
+	IF "%ARG%"=="-f" SET FORCE=true
+	IF "%ARG%"=="--force" SET FORCE=true
+	SHIFT
+	GOTO processflags
+)
+
+FOR %%x IN ("%CD%") DO SET upper_path=%%~dpx
+
+IF NOT EXIST "%input_cache_path%%publisher_jar%" (
+	IF NOT EXIST "%upper_path%%publisher_jar%" (
+		SET jarlocation="%input_cache_path%%publisher_jar%"
+		SET jarlocationname=Input Cache
+		ECHO IG Publisher is not yet in input-cache or parent folder.
+		REM we don't use jarlocation below because it will be empty because we're in a bracketed if statement
+		GOTO create
+	) ELSE (
+		ECHO IG Publisher FOUND in parent folder
+		SET jarlocation="%upper_path%%publisher_jar%"
+		SET jarlocationname=Parent folder
+		GOTO:upgrade
+	)
+) ELSE (
+	ECHO IG Publisher FOUND in input-cache
+	SET jarlocation="%input_cache_path%%publisher_jar%"
+	SET jarlocationname=Input Cache
+	GOTO:upgrade
+)
+
+:create
+IF DEFINED FORCE (
+	MKDIR "%input_cache_path%" 2> NUL
+	GOTO:download
+)
+ECHO Will place publisher jar here: %input_cache_path%%publisher_jar%
+SET /p create="Ok? (Y/N) "
+IF /I "%create%"=="Y" (
+	MKDIR "%input_cache_path%" 2> NUL
+	GOTO:download
+)
+GOTO:done
+
+:upgrade
+IF DEFINED FORCE GOTO:download
+SET /p overwrite="Overwrite %jarlocation%? (Y/N) "
+IF /I "%overwrite%"=="Y" (
+	GOTO:download
+)
+GOTO:done
+
+:download
+ECHO Downloading most recent publisher to %jarlocationname% - it's ~100 MB, so this may take a bit
+
+FOR /f "tokens=4-5 delims=. " %%i IN ('ver') DO SET VERSION=%%i.%%j
+IF "%version%" == "10.0" GOTO win10
+IF "%version%" == "6.3" GOTO win8.1
+IF "%version%" == "6.2" GOTO win8
+IF "%version%" == "6.1" GOTO win7
+IF "%version%" == "6.0" GOTO vista
+
+ECHO Unrecognized version: %version%
+GOTO done
+
+:win10
+CALL POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%dlurl%\",\"%jarlocation%\") } else { Invoke-WebRequest -Uri "%dlurl%" -Outfile "%jarlocation%" }
+
+GOTO done
+
+:win7
+CALL bitsadmin /transfer GetPublisher /download /priority normal "%dlurl%" "%jarlocation%"
+GOTO done
+
+:win8.1
+:win8
+:vista
+ECHO This script does not yet support Windows %winver%.  Please ask for help on http://chat.fhir.org
+GOTO done
+
+:done
+IF NOT DEFINED FORCE PAUSE

_updatePublisher.sh

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+#!/bin/bash
+
+# *************************************************************************************************
+# *                               WARNING: DO NOT EDIT THIS FILE                                  *
+# *                                                                                               *
+# * This file is generated by SUSHI. Any edits you make to this file will be overwritten.         *
+# *************************************************************************************************
+
+dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
+publisher_jar=org.hl7.fhir.publisher.jar
+input_cache_path=./input-cache/
+
+set -e
+if ! type "curl" > /dev/null; then
+	echo "ERROR: Script needs curl to download latest IG Publisher. Please install curl."
+	exit 1
+fi
+
+FORCE=false
+
+while :; do
+    case $1 in
+        -f|--force) FORCE=true ;;
+        --)
+            shift
+            break
+            ;;
+        *) break
+    esac
+    shift
+done
+
+publisher="$input_cache_path$publisher_jar"
+if test -f "$publisher"; then
+	echo "IG Publisher FOUND in input-cache"
+	jarlocation="$publisher"
+	jarlocationname="Input Cache"
+	upgrade=true
+else
+	publisher="../$publisher_jar"
+	upgrade=true
+	if test -f "$publisher"; then
+		echo "IG Publisher FOUND in parent folder"
+		jarlocation="$publisher"
+		jarlocationname="Parent Folder"
+		upgrade=true
+	else
+		echo IG Publisher NOT FOUND in input-cache or parent folder...
+		jarlocation=$input_cache_path$publisher_jar
+		jarlocationname="Input Cache"
+		upgrade=false
+	fi
+fi
+
+if [[ "$FORCE" != true ]]; then
+  if "$upgrade"; then
+    message="Overwrite $jarlocation? (Y/N) "
+  else
+    echo Will place publisher jar here: "$jarlocation"
+    message="Ok? (Y/N) "
+  fi
+  read -r -p "$message" response
+fi
+
+if [[ "$FORCE" == true ]] || [[ "$response" =~ ^([yY])$ ]]; then
+	echo "Downloading most recent publisher to $jarlocationname - it's ~100 MB, so this may take a bit"
+#	wget "https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar" -O "$jarlocation"
+	curl $dlurl -o "$jarlocation" --create-dirs
+else
+	echo cancel...
+fi

fsh/config.yaml

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+id: synthea.fhir
+canonical: http://synthetichealth.github.io/synthea
+name: Synthea
+status: active
+version: 1.0.0
+fhirVersion: 4.0.1
+copyrightYear: 2020+
+releaseLabel: Build CI
+publisher:
+  name: The MITRE Corporation
+  url: http://synthea.mitre.org
+template: fhir.base.template#0.1.0
+
+menu:
+  Home: index.html
+  Artifacts: artifacts.html
+
+parameters:
+  apply-contact: true
+  apply-jurisdiction: false
+  apply-publisher: true

fsh/ig-data/input/pagecontent/index.md

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+# Synthea<sup>TM</sup> Implementation Guide
+
+Welcome to the Synthea<sup>TM</sup> Implementation Guide (IG).
+
+[Synthea](https://github.com/synthetichealth/synthea) is an open-source Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats, including HL7 FHIR.
+
+This simple FHIR IG defines a small set of optional [artifacts](artifacts.html).

fsh/patient.fsh

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+// Synthea Patient profile.
+Profile: SyntheaPatient
+Parent: Patient
+Id: synthea-patient
+Title: "Synthea Patient Profile"
+Description: "Synthea outputs additional extensions on Patient resources, notably `quality-adjusted-life-years` and `disability-adjusted-life-years`."
+* extension contains QALY named quality-adjusted-life-years 0..1
+* extension contains DALY named disability-adjusted-life-years 0..1
+
+// QALY Extension
+Extension: QALY
+Id: quality-adjusted-life-years
+Title: "Quality Adjusted Life Years"
+Description: "Quality Adjusted Life Years as defined in the literature and summarized at <a href=\"https://en.wikipedia.org/wiki/Quality-adjusted_life_year\"/>."
+* value[x] only decimal
+
+// DALY Extension
+Extension: DALY
+Id: disability-adjusted-life-years
+Title: "Disability Adjusted Life Years"
+Description: "Disability Adjusted Life Years as defined in the literature and summarized at <a href=\"https://en.wikipedia.org/wiki/Disability-adjusted_life_year\"/>."
+* value[x] only decimal