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Commit 15d75e66 authored by AAZIBOU EL GERRAB Nabila's avatar AAZIBOU EL GERRAB Nabila
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add script for xehealth project

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2 merge requests!52release 3.2.0,!51release 3.2.0
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hl7templates/hl7templates-packager-jar/src/main/resources/assemble-scripts/xehealthGeneration.sh
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#!/bin/bash #!/bin/bash
#################################### ####################################
# SEQUOIA Generation & Adaptation Script # Xehealth Generation Script
# Created by Achraf Achkari - 09 Nov 2021 # Created by Nabila Aazibou - 03 Aout 2023
# Last revision - 09 Nov 2021 # Last revision - 03 Aout 2023
# Version 1.0.0 # Version 3.5.1
##################################### #####################################
#Colors definitions for terminal #Colors definitions for terminal
RED='\033[0;31m' RED='\033[0;31m'
GREEN='\033[0;32m' GREEN='\033[0;32m'
ORANGE='\033[0;33m' ORANGE='\033[0;33m'
NC='\033[0m' NC='\033[0m'
#SEQUOIA Validators
MU3="HL7 - C-CDA R2.1 - Meaningful Use Stage 3" ## FUNCTIONS DEFINITION
USCDI="HL7 - C-CDA R2.1 - USCDI"
CCDA_R_1="HL7 - C-CDA R1.1" function readBBR {
read -r bbrPath
isAbsPath=`echo "${bbrPath}" | grep ^/.* | wc -l`
if [ $isAbsPath -eq 0 ]; then
echo -e "${RED}[ ${bbrPath} ] is not an absolute path${NC}"
exit 1
fi
if [ ! -f $bbrPath ]; then
echo -e "${RED}[ ${bbrPath} ] is not a file or doesn't exist !${NC}"
exit 1
fi
}
#UNCOMENT THIS TO OVERRIDE DEFAULT JAVA VERSION USED BY SYSTEM #UNCOMENT THIS TO OVERRIDE DEFAULT JAVA VERSION USED BY SYSTEM
...@@ -37,20 +50,22 @@ if [ -z "$javaVersion" ]; then ...@@ -37,20 +50,22 @@ if [ -z "$javaVersion" ]; then
exit 1 exit 1
fi fi
## JAR DETECTION
# Try to get the jar of GOC automatically # Try to get the jar of GOC automatically
jarPath=$(ls -l | grep -oh -e "[^ ]*-jar-with-dependencies\.jar") jarPath=`ls -l | grep -oh -e "[^ ]*-jar-with-dependencies\.jar"`
if [ -z "$jarPath" ]; then if [ -z $jarPath ]; then
echo -e "${ORANGE}Could not detect the JAR of GOC, please provide the path manually${NC}" echo -e "${ORANGE}Could not detect the JAR of GOC, please provide the path manually${NC}"
read -r jarPath read -r jarPath
else else
absJarPath=$(realpath "$jarPath") absJarPath=`realpath $jarPath`
echo -e "${GREEN}A GOC JAR has been detected at: (${jarPath}) want you to use it?${NC}" echo -e "${GREEN}A GOC JAR has been detected at: (${jarPath}) want you to use it?${NC}"
printf "hit enter for yes, enter an other path to change it: " printf "hit enter for yes, provide an other path to change it: "
read -r newJarPath read -r newJarPath
if [ ! -z "$newJarPath" ]; then if [ ! -z $newJarPath ]; then
isAbsPath=$(echo "${newJarPath}" | grep -c "^/.*") isAbsPath=`echo "${newJarPath}" | grep ^/.* | wc -l`
if [ "$isAbsPath" -eq 0 ]; then if [ $isAbsPath -eq 0 ]; then
echo -e "${RED}[ ${newJarPath} ] is not an absolute path${NC}" echo -e "${RED}[ ${newJarPath} ] is not an absolute path${NC}"
exit 1 exit 1
fi fi
...@@ -58,10 +73,10 @@ else ...@@ -58,10 +73,10 @@ else
fi fi
fi fi
## MAVEN VERIFICATION
#Try to use maven wrapper #Try to use maven wrapper
if [ -f ./classes/maven-wrapper/mvnw ];then if [ -f ./classes/maven-wrapper/mvnw ];then
# base_dir=$(realpath ./classes/maven-wrapper)
mavenPath=$(realpath "./classes/maven-wrapper/mvnw") mavenPath=$(realpath "./classes/maven-wrapper/mvnw")
testMaven=$($mavenPath -v) testMaven=$($mavenPath -v)
if [ ! -z "$testMaven" ]; then if [ ! -z "$testMaven" ]; then
...@@ -121,109 +136,65 @@ fi; ...@@ -121,109 +136,65 @@ fi;
echo -e "${GREEN}Using maven at: ${mavenPath}${NC}" echo -e "${GREEN}Using maven at: ${mavenPath}${NC}"
## BBR READING
printf "Please enter a path to your BBR (Absolute Path) : " printf "Please enter a path to your BBR (Absolute Path) : "
read -r bbrPath readBBR
isAbsPath=$(echo "${bbrPath}" | grep ^/.* | wc -l) validator="xehealth"
if [ "$isAbsPath" -eq 0 ]; then
echo -e "${RED}[ ${bbrPath} ] is not an absolute path${NC}"
exit 1
fi
if [ ! -f "$bbrPath" ]; then
echo -e "${RED}[ ${bbrPath} ] is not a file or doesn't exist !${NC}"
exit 1
fi
printf "Please choose the kind of validator you want to generate: \n"
printf "\t 1- $MU3\n"
printf "\t 2- $USCDI\n"
printf "\t 3- $CCDA_R_1\n"
printf "your choice: "
read -r choice
if [ "$choice" -gt 3 -o "$choice" -lt 1 ]; then
echo "${RED}Wrong choice, please repeat and choose between 1 and 3${NC}"
exit 1
fi
versionLabel=""
case $choice in
1)
echo -e "${GREEN}generating ${MU3// /}${NC}"
validator=${MU3// /}
versionLabel="2.1"
;;
esac
printf "Please enter workspace path (where you want to generate the validator): " printf "Please enter workspace path (where you want to generate the validator): "
read -r workspaceDir read -r workspaceDir
if [ ! -d "$workspaceDir" ]; then if [ ! -d $workspaceDir ]; then
echo "${RED}The provided workspace is not a valid directory" echo "${RED}The provided workspace is not a valid directory"
exit 1 exit 0
fi fi
isAbsPath=$(echo "${workspaceDir}" | grep -c "^/.*") isAbsPath=`echo "${workspaceDir}" | grep ^/.* | wc -l`
if [ "$isAbsPath" -eq 0 ]; then if [ $isAbsPath -eq 0 ]; then
echo -e "${RED}[ ${workspaceDir} ] is not an absolute path" echo -e "${RED}[ ${workspaceDir} ] is not an absolute path"
exit 1 exit 0
fi fi
_currDate=$(date +%Y-%m-%d-%H-%M-%S) _currDate=`date +%Y-%m-%d-%H-%M-%S`
printf "Please enter the folder name of your validator: (output-${validator}-${_currDate})?: " printf "Please enter the folder name of your validator: (output-${validator}-${_currDate})?"
read -r folderName read -r folderName
if [ -z "$folderName" ]; then if [ -z $folderName ]; then
folderName="output-${validator}-${_currDate}" folderName="output-${validator}-${_currDate}"
fi; fi;
echo -e "${GREEN}your validator will be generated in: ${workspaceDir}/${folderName}${NC}" echo -e "${GREEN}your validator will be generated in: ${workspaceDir}/${folderName}${NC}"
######## GENERATION COMMAND ######## ######## GENERATION COMMAND ########
$JAVA_HOME/bin/java -jar "$absJarPath" -bbr "$bbrPath" -out "${workspaceDir}/${folderName}" -mvn "$mavenPath" -serviceName "$validator" -versionLabel "$versionLabel" -ignoreTemplateIdRequirements -ignoreCdaBasicRequirements $JAVA_HOME/bin/java -jar $jarPath -bbr $bbrPath -out "${workspaceDir}/${folderName}" -mvn $mavenPath -serviceName $validator -HL7TEMP_CDACONFFOLDERNAME cdaxehealth -ignoreCdaBasicRequirements
#################################### ####################################
if [ $? != 0 ]; then #Replacing XSD
echo "${RED}Generation Failed${NC}" pathToResources=""
exit 1 if [ -d ./classes/xehealth-resources/xsd ]; then
fi pathToResources=$(realpath "./classes/xehealth-resources/xsd")
echo -e "${GREEN}XSD Resources found at $pathToResources${NC}"
echo -e "${GREEN}Validator generated successfully${NC}" else
echo -e "${ORANGE}Could not find resources, please provide the path to the XSD folder manually${NC}"
echo -e "${NC}Start SVS Adaptations..." echo -e "${ORANGE}be careful, the directory should contain correct XSD files for the validator to run. This is not checked by the script!${NC}"
read -r pathToResources
if [ ! -f ./xehealthGeneration.sh ]; then if [ ! -d $pathToResources ]; then
echo -e "${RED}Could not find the xehealthGeneration script, please recompile GOC and rerun this script" echo -e "${RED} invalid path to directory"
exit 1; exit 1;
fi;
# adapt only if version is higher than 1.1
if [ "$versionLabel" != "1.1" ]; then
pathToResources=''
if [ ! -d ./classes/xehealth-resources.xsd ]; then
echo -e "${RED}Resources for adaptations not found, please provide a path manually"
read -r $pathToResources
else
pathToResources=$(realpath ./classes/xehealth-resources.xsd)
fi
if [ ! -x ./xehealthGeneration.sh ]; then
chmod +x xehealthGeneration.sh
fi; fi;
fi;
env JAVA_HOME=$JAVA_HOME M2_BIN=$mavenPath ./xehealthGeneration.sh "$workspaceDir/$folderName" $pathToResources pathToXSD=$(realpath $(find "${workspaceDir}/${folderName}" -type d -name "xsd" | grep -e ".*-app/.*"))
echo "$pathToXSD"
XSDDirname=$(dirname "$pathToXSD")
echo "$XSDDirname"
rm -r "$pathToXSD"
cp -r "$pathToResources" "$XSDDirname"
if [ $? != 0 ]; then
echo "${RED}Adaptations failed"
exit 1
fi
fi;
#Zip validator #Zip validator
#move to bin path #move to app path
appassemblerPath=$(realpath $(find $workspaceDir/$folderName -type d -wholename */appassembler)) appPath=$(realpath $(find $workspaceDir/$folderName -type d -wholename *validator-app))
cd $appassemblerPath cd $appPath
#Create bbr folder #Create bbr folder
mkdir "bbr" || echo "File already exist, that won't affect next steps" mkdir "bbr" || echo "File already exist, that won't affect next steps"
...@@ -231,7 +202,7 @@ cp $bbrPath bbr ...@@ -231,7 +202,7 @@ cp $bbrPath bbr
#create documentation folder #create documentation folder
documentationPath=$(realpath $(find $workspaceDir/$folderName -type d -wholename "*/documentation")) documentationPath=$(realpath $(find $workspaceDir/$folderName -type d -wholename "*/documentation"))
cp -r $documentationPath $appassemblerPath cp -r $documentationPath $appPath
#Zipping #Zipping
zip -r "validator-$_currDate.zip" bbr/ documentation/ repo/ bin/ zip -r "validator-$_currDate.zip" bbr/ documentation/ repo/ bin/
\ No newline at end of file
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