Merge pull request #115 from cqframework/develop

Develop

.gitignore

@@ -10,3 +10,9 @@
 /resources/ig-new.xml
 /org.hl7.fhir.publisher.jar
 template
+input-cache/*
+!/input-cache/txcache
+input/ig-expansion-parameters.json
+input/ig-new.json
+input/ig-new.xml
+input/ig-validation-parameters.json

_createValueSetsFromSpreadSheets.bat

@@ -1,5 +1,5 @@
 @ECHO OFF
-SET tooling_jar=tooling-1.0.4-SNAPSHOT-jar-with-dependencies.jar
+SET tooling_jar=tooling-1.1.0-SNAPSHOT-jar-with-dependencies.jar
 SET input_cache_path=%~dp0input-cache
 SET spreadsheet_directory_path=%~dp0input\vocabulary\valueset\spreadsheets
 SET output_path=%~dp0input\vocabulary\valueset

_genonce.bat

@@ -0,0 +1,27 @@
+@ECHO OFF
+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.json %txoption% %*
+) ELSE If exist "..\%publisher_jar%" (
+	JAVA -jar ..\%publisher_jar% -ig ig.json %txoption% %*
+) ELSE (
+	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+)
+
+PAUSE

_genonce.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+publisher_jar=org.hl7.fhir.publisher.jar
+input_cache_path=./input-cache/
+set -e
+echo Checking internet connection...
+wget -q --spider tx.fhir.org
+
+if [ $? -eq 0 ]; then
+	echo "Online"
+	txoption=""
+else
+	echo "Offline"
+	txoption="-tx n/a"
+fi
+txoption="-tx n/a"
+echo "$txoption"
+
+publisher=$input_cache_path/$publisher_jar
+if test -f "$publisher"; then
+	JAVA -jar $publisher -ig ig.json $txoption $*
+
+else
+	publisher=../$publisher_jar
+	echo $publisher
+	if test -f "$publisher"; then
+		JAVA -jar $publisher -ig ig.json $txoption $*
+	else
+		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
+	fi
+fi

_refresh.bat

@@ -0,0 +1,31 @@
+@ECHO OFF
+SET tooling_jar=tooling-1.1.0-SNAPSHOT-jar-with-dependencies.jar
+SET input_cache_path=%~dp0input-cache
+SET resources_path=%~dp0/input/resources
+SET ig_resource_path=%~dp0/input/opioid-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=
+
+: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 -ip=%~dp0 -rp="%resources_path%" -igrp="%ig_resource_path%" -iv=fhir3 -t -d -p %fsoption%
+	JAVA -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -ip=%~dp0 -rp="%resources_path%" -igrp="%ig_resource_path%" -iv=fhir3 -t -d -p %fsoption%
+) ELSE If exist "..\%tooling_jar%" (
+	ECHO running: JAVA -jar "..\%tooling_jar%" -RefreshIG -ip=%~dp0 -rp="%resources_path%" -igrp="%ig_resource_path%" -iv=fhir3 -t -d -p %fsoption%
+	JAVA -jar "..\%tooling_jar%" -RefreshIG -ip=%~dp0 -rp="%resources_path%" -igrp="%ig_resource_path%" -iv=fhir3 -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-1.1.0-SNAPSHOT-jar-with-dependencies.jar
+input_cache_path=./input-cache
+resources_path=$PWD/input/resources
+ig_resource_path=./input/opioid-cds.xml
+
+set -e
+echo Checking internet connection...
+wget -q --spider tx.fhir.org
+
+if [ $? -eq 0 ]; then
+	echo "Online"
+	fsoption=""
+	#"-fs http://cds-sandbox.alphora.com/cqf-ruler-dstu3/fhir/"
+else
+	echo "Offline"
+	fsoption=""
+fi
+
+echo "$fsoption"
+
+tooling=$input_cache_path/$tooling_jar
+if test -f "$tooling"; then
+	JAVA -jar $tooling -RefreshIG -ip="$PWD" -igrp="$ig_resource_path" -rp="$resources_path" -iv=fhir3 -t -d -p $fsoption
+else
+	tooling=../$tooling_jar
+	echo $tooling
+	if test -f "$tooling"; then
+		JAVA -jar $tooling -RefreshIG -ip="$PWD" -igrp="$ig_resource_path" -rp="$resources_path" -iv=fhir3 -t -d -p $fsoption
+	else
+		echo IG Refresh NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
+	fi
+fi

_updateRefreshIG.bat → _updateCQFTooling.bat

@@ -1,7 +1,7 @@
 @ECHO OFF
 
-SET "dlurl=https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=org.opencds.cqf&a=tooling&v=1.0.4-SNAPSHOT&c=jar-with-dependencies"
-SET tooling_jar=tooling-1.0.4-SNAPSHOT-jar-with-dependencies.jar
+SET "dlurl=https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=org.opencds.cqf&a=tooling&v=1.1.0-SNAPSHOT&c=jar-with-dependencies"
+SET tooling_jar=tooling-1.1.0-SNAPSHOT-jar-with-dependencies.jar
 SET input_cache_path=%~dp0input-cache\
 
 FOR %%x IN ("%CD%") DO SET upper_path=%%~dpx

_updateRefreshIG.sh → _updateCQFTooling.sh

@@ -5,15 +5,15 @@
 r=snapshots
 g=org.opencds.cqf
 a=tooling
-v=1.0.2-SNAPSHOT
+v=1.1.0-SNAPSHOT
 c=jar-with-dependencies
 
 dlurl='https://oss.sonatype.org/service/local/artifact/maven/redirect?r='${r}'&g='${g}'&a='${a}'&v='${v}'&c='${c}''
 
 echo ${dlurl}
 
 input_cache_path=./input-cache/
-tooling_jar=tooling-1.0.2-SNAPSHOT-jar-with-dependencies.jar
+tooling_jar=tooling-1.1.0-SNAPSHOT-jar-with-dependencies.jar
 
 set -e
 if ! type "curl" > /dev/null; then

_updatePublisher.bat

@@ -0,0 +1,131 @@
+@ECHO OFF
+
+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\
+SET skipPrompts=false
+
+set update_bat_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_updatePublisher.bat
+set gen_bat_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_genonce.bat
+set gencont_bat_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_gencontinuous.bat
+set gencont_sh_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_gencontinuous.sh
+set gen_sh_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_genonce.sh
+set update_sh_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_updatePublisher.sh
+
+IF "%~1"=="/f" SET skipPrompts=true
+
+ECHO "%skipPrompts%"
+
+
+: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%
+IF "%skipPrompts%"=="true" (
+	SET create="Y"
+) ELSE (
+	SET /p create="Ok? (Y/N) "
+)
+IF /I %create%=="Y" (
+	MKDIR "%input_cache_path%" 2> NUL
+	GOTO:download
+)
+GOTO:done
+
+:upgrade
+IF "%skipPrompts%"=="true" (
+	SET overwrite="Y"
+) ELSE (
+	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
+
+REM Download all batch files (and this one with a new name)
+
+SETLOCAL DisableDelayedExpansion
+
+REM ==== For getting the sources online...
+rem POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%update_bat_url%\",\"_updatePublisher.new.bat\") } else { Invoke-WebRequest -Uri "%update_bat_url%" -Outfile "_updatePublisher.new.bat" }
+rem POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gen_bat_url%\",\"_genonce.bat\") } else { Invoke-WebRequest -Uri "%gen_bat_url%" -Outfile "_genonce.bat" }
+rem POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gencont_bat_url%\",\"_gencontinuous.bat\") } else { Invoke-WebRequest -Uri "%gencont_bat_url%" -Outfile "_gencontinuous.bat" }
+
+rem POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%update_sh_url%\",\"_updatePublisher.sh\") } else { Invoke-WebRequest -Uri "%update_sh_url%" -Outfile "_updatePublisher.new.sh" }
+rem POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gen_sh_url%\",\"_genonce.sh\") } else { Invoke-WebRequest -Uri "%gen_sh_url%" -Outfile "_genonce.sh" }
+rem POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gencont_sh_url%\",\"_gencontinuous.sh\") } else { Invoke-WebRequest -Uri "%gencont_sh_url%" -Outfile "_gencontinuous.sh" }
+
+rem ECHO Updating this file...
+rem start copy /y "_updatePublisher.new.bat" "_updatePublisher.bat" ^&^& del "_updatePublisher.new.bat" ^&^& exit
+REM ============================
+
+IF "%skipPrompts%"=="true" (
+  PAUSE
+}

_updatePublisher.sh

@@ -1,19 +1,33 @@
 #!/bin/bash
-dlurl=https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar
+dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
 publisher_jar=org.hl7.fhir.publisher.jar
-root_path=./
+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
 
-publisher="$root_path$publisher_jar"
+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 root"
+	echo "IG Publisher FOUND in input-cache"
 	jarlocation="$publisher"
-	jarlocationname="Root"
+	jarlocationname="Input Cache"
 	upgrade=true
 else
 	publisher="../$publisher_jar"
@@ -25,22 +39,23 @@ else
 		upgrade=true
 	else
 		echo IG Publisher NOT FOUND in input-cache or parent folder...
-		jarlocation="$root_path$publisher_jar"
-		jarlocationname="Root"
+		jarlocation=$input_cache_path$publisher_jar
+		jarlocationname="Input Cache"
 		upgrade=false
 	fi
 fi
 
-if $upgrade ; then
-	message="Overwrite $jarlocation? [Y/N] "
-else
-	#echo Will place publisher jar here: $root_path$publisher_jar
-	echo Will place publisher jar here: $jarlocation
-	message="Ok? [Y/N]"
+if [[ "$FORCE" != true ]]; then
+  if "$upgrade"; then
+    message="Overwrite $jarlocation? (Y/N) "
+  else
+    echo Will place publisher jar here: "$jarlocation"
+    message="Ok (enter 'y' or 'Y' to continue, any other key to cancel)?"
+  fi
+  read -r -p "$message" response
 fi
 
-read -r -p "$message" response
-if [[ "$response" =~ ^([yY])$ ]]; then
+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