Merge pull request #84 from WorldHealthOrganization/cleanup

Merge in cleanup branch with Measles and Yellow Fever.

This also includes logical model, questionnaire, and structuremaps for Polio.

.gitignore

@@ -5,4 +5,5 @@ temp
 template
 bundles
 *.jar
-.DS_Store
+.DS_Store
+**/tests-*-bundle.json

_refresh.sh

@@ -1,9 +1,8 @@
 #!/bin/bash
 #DO NOT EDIT WITH WINDOWS
-tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
+tooling_jar=tooling-cli-2.4.0.jar
 input_cache_path=./input-cache
-resources_path=$PWD/input/resources
-ig_ini_path=./ig.ini
+ig_ini_path=$PWD/ig.ini
 
 set -e
 echo Checking internet connection...
@@ -12,7 +11,6 @@ wget -q --spider tx.fhir.org
 if [ $? -eq 0 ]; then
 	echo "Online"
 	fsoption=""
-#"-fs http://cds-sandbox.alphora.com/cqf-ruler-r4/fhir/"
 else
 	echo "Offline"
 	fsoption=""
@@ -22,13 +20,13 @@ echo "$fsoption"
 
 tooling=$input_cache_path/$tooling_jar
 if test -f "$tooling"; then
-	java -Xmx2048M -jar $tooling -RefreshIG -ini="$ig_ini_path" -t -d -p $fsoption
+	java -jar $tooling -RefreshIG -ini="$ig_ini_path" -d -p -t $fsoption
 else
 	tooling=../$tooling_jar
 	echo $tooling
 	if test -f "$tooling"; then
-		java -Xmx2048M -jar $tooling -RefreshIG -ini="$ig_ini_path" -t -d -p $fsoption
+		java -jar $tooling -RefreshIG -ini="$ig_ini_path" -d -p -t $fsoption
 	else
 		echo IG Refresh NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
 	fi
-fi
+fi

_updateCQFTooling.sh

@@ -2,18 +2,17 @@
 #DO NOT EDIT WITH WINDOWS
 #exit 1
 
-r=snapshots
+r=releases
 g=org.opencds.cqf
-a=tooling
-v=1.4.1-SNAPSHOT
-c=jar-with-dependencies
+a=tooling-cli
+v=2.4.0
 
-dlurl='https://oss.sonatype.org/service/local/artifact/maven/redirect?r='${r}'&g='${g}'&a='${a}'&v='${v}'&c='${c}''
+dlurl='https://oss.sonatype.org/service/local/artifact/maven/redirect?r='${r}'&g='${g}'&a='${a}'&v='${v}''
 
 echo ${dlurl}
 
 input_cache_path=./input-cache/
-tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
+tooling_jar=tooling-cli-2.4.0.jar
 
 set -e
 if ! type "curl" > /dev/null; then
@@ -53,10 +52,10 @@ fi
 
 read -r -p "$message" response
 if [[ "$response" =~ ^([yY])$ ]]; then
-	echo "Downloading most recent tooling to $jarlocationname - it's ~170 MB, so this may take a bit"
+	echo "Downloading most recent tooling to $jarlocationname - it's ~110 MB, so this may take a bit"
 #	wget "https://oss.sonatype.org/service/local/repositories/snapshots/content/org/opencds/cqf/tooling/1.0-SNAPSHOT/tooling-1.0-20200107.163002-6-jar-with-dependencies.jar" -O "$jarlocation"
 	curl $dlurl -L -o "$jarlocation" --create-dirs
 	echo "Download complete."
 else
 	echo cancel...
-fi
+fi

_updatePublisher.sh

@@ -117,13 +117,16 @@ if [[ $skipPrompts == true ]] || [[ $response =~ ^[yY].*$ ]]; then
 
   curl -L $gencont_sh_url -o /tmp/_gencontinuous.new
   cp /tmp/_gencontinuous.new _gencontinuous.sh
+  chmod +x _gencontinuous.sh
   rm /tmp/_gencontinuous.new
 
   curl -L $gen_sh_url -o /tmp/_genonce.new
   cp /tmp/_genonce.new _genonce.sh
+  chmod +x _genonce.sh
   rm  /tmp/_genonce.new
 
   curl -L $update_sh_url -o /tmp/_updatePublisher.new
   cp /tmp/_updatePublisher.new _updatePublisher.sh
+  chmod +x _updatePublisher.sh
   rm /tmp/_updatePublisher.new
 fi

ig.ini

@@ -1,7 +1,7 @@
 [IG]
 #ig = input/immz.xml
 ig = fsh-generated/resources/ImplementationGuide-who.fhir.immunization.json
-template = who.fhir.template#current
+template = who.template.root#current
 #template = fhir.base.template
 usage-stats-opt-out = false
-fhir-version = 4.0.1
+fhir-version = 4.0.1