init

.gitignore

@@ -0,0 +1,8 @@
+indicators/ind1
+input-cache
+output
+input/tests/results/*.txt
+temp/
+template/
+*.jar
+.DS_Store

LICENSE.md

@@ -0,0 +1,33 @@
+> CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
+
+
+----------
+
+
+### <em>Statement of Purpose</em>
+The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work").
+
+Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others.
+
+For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights.
+
+**1. Copyright and Related Rights**. A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following:
+<ol type="i"><li>the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; </li>
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+<li>other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof.</li>
+</ol>
+
+**2. Waiver**. To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose.
+
+**3. Public License Fallback**. Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose.
+
+**4. Limitations and Disclaimers**.
+<ol type="a"><li>No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document</li>
+<li>Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law.</li>
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+<li>Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work.</li>
+</ol>

README.md

@@ -0,0 +1,49 @@
+# WHO Immunization Implementation Guide (FHIR R4 (4.0.1))
+
+This implementation guide defines core data element profiles for use for the World Health Organization (WHO) Immunization computable guideline content.
+
+The current draft of the implementation guide is available [here](http://build.fhir.org/ig/WorldHealthOrganization/smart-immunization/).
+
+The guide is published under a Creative Commons [license](LICENSE.md).
+
+## Change Management
+
+Feedback and issues can be submitted via the [issues](issues) page, and will be incorporated into subsequent releases as time and resources allow.
+
+## Roadmap
+### Completed
+* PlanDefinitions
+
+### In Progress
+* Measures 
+
+### ToDo 
+* ActivityDefinitions
+
+## Repository and Build Information
+
+This repository contains the source for the WHO Core Implementation Guide, and uses the [FHIR Implementation Guide publisher](http://wiki.hl7.org/index.php?title=IG_Publisher_Documentation) to produce a FHIR Implementation Guide.
+
+Commits to this repository will automatically trigger a new build of the IG, which will then be published to the following location:
+
+[http://build.fhir.org/ig/WorldHealthOrganization/smart-immunization/](http://build.fhir.org/ig/WorldHealthOrganization/smart-immunization/)
+
+Build log is available here:
+
+[http://build.fhir.org.s3-website-us-east-1.amazonaws.com/logs/WorldHealthOrganization/smart-immunization](http://build.fhir.org.s3-website-us-east-1.amazonaws.com/logs/WorldHealthOrganization/smart-immunization)
+
+Debugging information is available here:
+
+[http://build.fhir.org/ig/WorldHealthOrganization/smart-immunization/debug.tgz](http://build.fhir.org/ig/WorldHealthOrganization/smart-immunization/debug.tgz)
+
+### Local Build
+
+The HL7 IG Publisher can be downloaded locally to make building as easy as possible. To build locally, download the publisher tooling locally using the _updatePublisher script:
+
+    _updatePublisher
+
+Once the publication tooling is cached locally, use the _genOnce script to build locally:
+
+    _genOnce
+
+The output will be available in the `output` folder.

_autoPublish.bat

@@ -0,0 +1,32 @@
+@ECHO off
+SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET input_cache_path=%~dp0input-cache
+SET resources_path=%~dp0input/resources
+SET ig_resource_path=input/core.xml
+SET fsoption=http://localhost:8080/cqf-ruler-r4/fhir/
+SET publisher_jar=publisher.jar
+SET test_path=D:\Projects\connectathon\fhir401\input\tests
+SET fhir_version=4.0.1
+SET ini_file=ig.ini
+
+    cmd /c _updatePublisher.bat /f
+    ECHO Done with updatePublisher
+
+    cmd /c _updateCQFTooling.bat /f
+    ECHO Done with updateCQFTooling
+
+    cmd /c _processDataDictionary.bat
+    ECHO Done with ProcessAcceleratorKit
+
+    JAVA -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp=%resources_path% -ip=%ig_resource_path% -t -d -p -fs=%fsoption%
+    ECHO Done with -RefreshIG
+
+    JAVA -jar "%input_cache_path%\%tooling_jar%" -TestIG -ini=%ini_file% -root-dir=%~dp0 -fv=%fhir_version% -tcp=%test_path% -fs=%fsoption%
+    ECHO Done with -TestIGOperation
+
+    REM from _genonce.bat
+    JAVA -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption%
+
+REM TODO - PUBLISH to "web site"  copy output dir to another location
+    ECHO  Done with publish to web site
+    ECHO 

_gencontinuous.bat

@@ -0,0 +1,2 @@
+@ECHO OFF
+CALL ./_genonce.bat -watch

_gencontinuous.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+./_genonce.sh -watch

_genonce.bat

@@ -0,0 +1,27 @@
+@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

@@ -0,0 +1,28 @@
+#!/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"
+
+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

_processDataDictionary.bat

@@ -0,0 +1,22 @@
+@ECHO off
+SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET input_cache_path=%~dp0input-cache
+SET datadictionary_directory=input/datadictionary/
+SET datadictionary_filename=%datadictionary_directory%\IMZDAKDataDictionaryDRAFT.xlsx
+SET datadictionary_sheetname=Master-1.0
+SET scope=Core
+SET tooling=%input_cache_path%\%tooling_jar%
+SET upper_path=%%~dpx
+
+if EXIST "%tooling%" (
+	JAVA -jar "%tooling%" -ProcessAcceleratorKit -s="%scope%" -pts="%datadictionary_filename%" -dep="%datadictionary_sheetname%" -op=.
+) ELSE (
+	ECHO "%tooling%"
+	if EXIST "%tooling%" (
+		JAVA -jar $tooling -ProcessAcceleratorKit -s=$scope -pts=./input/datadictionary/$datadictionary_filename -dep=$datadictionary_sheetname -op=.
+	) ELSE (
+		ECHO  ProcessAcceloratorKit NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
+		ECHO 
+    )
+)
+

_processDataDictionary.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#DO NOT EDIT WITH WINDOWS
+tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+input_cache_path=./input-cache
+datadictionary_filename="IMZDAKDataDictionaryDRAFT.xlsx"
+datadictionary_sheetname="Master-1.0"
+scope="Core"
+
+set -e
+
+tooling=$input_cache_path/$tooling_jar
+if test -f "$tooling"; then
+	JAVA -jar $tooling -ProcessAcceleratorKit -s=$scope -pts=./input/datadictionary/$datadictionary_filename -dep=$datadictionary_sheetname -op=.
+else
+	tooling=../$tooling_jar
+	echo $tooling
+	if test -f "$tooling"; then
+		JAVA -jar $tooling -ProcessAcceleratorKit -s=$scope -pts=./input/datadictionary/$datadictionary_filename -dep=$datadictionary_sheetname -op=.
+	else
+		echo ProcessAcceloratorKit NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
+	fi
+fi

_refresh.bat

@@ -0,0 +1,31 @@
+@ECHO OFF
+SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET input_cache_path=%~dp0input-cache
+SET resources_path=%~dp0input/resources
+SET ig_resource_path=input/anc-cds.xml
+
+ECHO Checking internet connection...
+PING tx.fhir.org -n 1 -w 1000 | FINDSTR TTL && GOTO isonline
+ECHO We're offline...
+SET fsoption=
+GOTO igpublish
+
+:isonline
+ECHO We're online, setting publish to the Connectathon sandbox FHIR server
+SET fsoption=-fs http://localhost:8080/cqf-ruler-r4/fhir/
+
+:igpublish
+
+SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
+
+IF EXIST "%input_cache_path%\%tooling_jar%" (
+	ECHO running: JAVA -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption%
+	JAVA -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption%
+) ELSE If exist "..\%tooling_jar%" (
+	ECHO running: JAVA -jar "..\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption%
+	JAVA -jar "..\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption%
+) ELSE (
+	ECHO IG Refresh NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
+)
+
+PAUSE

_refresh.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+#DO NOT EDIT WITH WINDOWS
+tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+input_cache_path=./input-cache
+resources_path=$PWD/input/resources
+ig_ini_path=./ig.ini
+
+set -e
+echo Checking internet connection...
+wget -q --spider tx.fhir.org
+
+if [ $? -eq 0 ]; then
+	echo "Online"
+	fsoption=""
+#"-fs http://cds-sandbox.alphora.com/cqf-ruler-r4/fhir/"
+else
+	echo "Offline"
+	fsoption=""
+fi
+
+echo "$fsoption"
+
+tooling=$input_cache_path/$tooling_jar
+if test -f "$tooling"; then
+	JAVA -jar $tooling -RefreshIG -ini="$ig_ini_path" -t -d -p $fsoption
+else
+	tooling=../$tooling_jar
+	echo $tooling
+	if test -f "$tooling"; then
+		JAVA -jar $tooling -RefreshIG -ini="$ig_ini_path" -t -d -p $fsoption
+	else
+		echo IG Refresh NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
+	fi
+fi

_updateCQFTooling.bat

@@ -0,0 +1,89 @@
+@ECHO OFF
+
+SET "dlurl=https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=org.opencds.cqf&a=tooling&v=1.3.1-SNAPSHOT&c=jar-with-dependencies"
+SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET input_cache_path=%~dp0input-cache\
+SET skipPrompts=false
+IF "%~1"=="/f" SET skipPrompts=true
+
+FOR %%x IN ("%CD%") DO SET upper_path=%%~dpx
+
+IF NOT EXIST "%input_cache_path%%tooling_jar%" (
+	IF NOT EXIST "%upper_path%%tooling_jar%" (
+		SET jarlocation=%input_cache_path%%tooling_jar%
+		SET jarlocationname=Input Cache
+		ECHO IG Refresh 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 RefreshFOUND in parent folder
+		SET jarlocation=%upper_path%%tooling_jar%
+		SET jarlocationname=Parent folder
+		GOTO:upgrade
+	)
+) ELSE (
+	ECHO IG Refresh FOUND in input-cache
+	SET jarlocation=%input_cache_path%%tooling_jar%
+	SET jarlocationname=Input Cache
+	GOTO:upgrade
+)
+
+:create
+ECHO Will place refresh jar here: %input_cache_path%%tooling_jar%
+IF "%skipPrompts%"=="false" (
+    SET /p create="Ok? (Y/N)"
+    IF /I "%create%"=="Y" (
+        MKDIR "%input_cache_path%" 2> NUL
+        GOTO:download
+    )
+) ELSE (
+    MKDIR "%input_cache_path%" 2> NUL
+    GOTO:download
+)
+
+GOTO:done
+
+:upgrade
+IF "%skipPrompts%"=="false" (
+    SET /p overwrite="Overwrite %jarlocation%? (Y/N)"
+    IF /I "%overwrite%"=="Y" (
+        GOTO:download
+    )
+) ELSE (
+    GOTO:download
+)
+GOTO:done
+
+:download
+ECHO Downloading most recent refresh to %jarlocationname% - it's ~70 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
+POWERSHELL -command "if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile('%dlurl%','%jarlocation%') } else { Invoke-WebRequest -Uri '%dlurl%' -Outfile '%jarlocation%' }"
+ECHO Download complete.
+GOTO done
+
+:win7
+bitsadmin /transfer GetRefresh /download /priority normal "%dlurl%" "%jarlocation%"
+ECHO Download complete.
+GOTO done
+
+:win8.1
+:win8
+:vista
+ECHO This script does not yet support Windows %winver%.  Please ask for help on https://chat.fhir.org/#narrow/stream/179207-connectathon-mgmt/topic/Clinical.20Reasoning.20Track
+GOTO done
+
+:done
+IF "%skipPrompts%"=="false" (
+    PAUSE
+)