BAH-3939 | Fix. Update Dependency Versions (#58)

* Parvathy | BAH-3939 | Upgrade Spring Boot Version From 1.5.22.RELEASE To 2.0.0.RELEASE * Parvathy | BAH-3939 | Upgrade Spring Boot Version To 2.0.9. RELEASE * Parvathy | BAH-3939 | Upgrade Spring Boot Version To 2.1.0.RELEASE * Parvathy | BAH-3939 | Upgrade Spring Boot Version To 2.1.18.RELEASE * Parvathy | BAH-3939 | Upgrade Spring Boot Version To 2.2.0.RELEASE * Parvathy | BAH-3939 | Upgrade Spring Boot Version To 2.5.15 * Parvathy | BAH-3939 | Fix. Upgrade mysql-connector-java Version To 8.0.28
Bahmni · Jul 4, 2024 · 284d9ab · 284d9ab
1 parent e6d196d
commit 284d9ab
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Showing 19 changed files with 183 additions and 156 deletions.
diff --git a/build.gradle b/build.gradle
@@ -1,6 +1,6 @@
 buildscript {
     ext {
-        springBootVersion = '1.5.22.RELEASE'
+        springBootVersion = '2.5.15'
         dependencyCheckVersion = '3.1.2'
     }
     repositories {
@@ -13,11 +13,12 @@ buildscript {
 }
 
 plugins {
-    id "nebula.ospackage" version "4.5.1"
+    id "nebula.ospackage" version "8.4.2"
 }
 
 apply plugin: 'java'
 apply plugin: 'org.springframework.boot'
+apply plugin: 'io.spring.dependency-management'
 apply plugin: 'jacoco'
 apply plugin: 'checkstyle'
 apply plugin: 'org.owasp.dependencycheck'
@@ -72,39 +73,40 @@ jacocoTestCoverageVerification {
 check.dependsOn jacocoTestCoverageVerification
 
 dependencies {
-    compile('org.springframework.boot:spring-boot-starter')
-    compile group: 'ch.qos.logback', name: 'logback-classic', version: '1.2.13'
-    compile group: 'ch.qos.logback', name: 'logback-core', version: '1.2.13'
-    compile group: 'org.yaml', name: 'snakeyaml', version: '2.0'
-    compile("org.springframework.boot:spring-boot-starter-batch")
-    compile group: 'org.springframework', name: 'spring-beans', version: '5.3.20'
-    compile group: 'org.springframework', name: 'spring-core', version: '5.3.27'
-    compile group: 'org.springframework', name: 'spring-expression', version: '5.3.27'
-    compile group: 'org.codehaus.jettison', name: 'jettison', version: '1.5.4'
-    compile group: 'com.thoughtworks.xstream', name: 'xstream', version: '1.4.20'
-    compile group: 'com.google.protobuf', name: 'protobuf-java', version: '3.21.7'
-    compile("org.springframework.batch:spring-batch-test")
-    compile group: 'junit', name: 'junit', version: '4.13.1'
-    compile group: 'mysql', name: 'mysql-connector-java', version: '5.1.42'
-    compile group: 'org.postgresql', name: 'postgresql', version: '42.3.9'
-    compile group: 'org.apache.commons', name: 'commons-dbcp2', version: '2.3.0'
-    compile group: 'commons-io', name: 'commons-io', version: '2.7'
-    compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.7'
-    compile group: 'org.freemarker', name: 'freemarker', version: '2.3.23'
-    compile group: 'com.google.code.gson', name: 'gson', version: '2.8.9'
-    compile "com.github.jsqlparser:jsqlparser:1.1"
-    compile 'org.springframework.cloud:spring-cloud-starter-task:1.2.2.RELEASE'
-    compile group: 'org.liquibase', name: 'liquibase-core', version: '4.8.0'
-    compile group: 'org.json', name: 'json', version: '20231013'
-
-    testCompile('org.springframework.boot:spring-boot-starter-test')
-    testCompile group: 'junit', name: 'junit', version: '4.13.1'
-    testCompile group: 'org.mockito', name: 'mockito-core', version: '1.10.19'
-    testCompile group: 'org.powermock', name: 'powermock-core', version: '1.6.4'
-    testCompile "org.powermock:powermock-module-junit4:1.6.4"
-    testCompile "org.powermock:powermock-module-junit4-rule:1.6.4"
-    testCompile "org.powermock:powermock-api-mockito:1.6.4"
-    testCompile group: 'org.hamcrest', name: 'hamcrest-all', version: '1.3'
+    implementation('org.springframework.boot:spring-boot-starter')
+    implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.2.13'
+    implementation group: 'ch.qos.logback', name: 'logback-core', version: '1.2.13'
+    implementation group: 'org.yaml', name: 'snakeyaml', version: '2.0'
+    implementation("org.springframework.boot:spring-boot-starter-batch")
+    implementation group: 'org.springframework', name: 'spring-beans', version: '5.3.20'
+    implementation group: 'org.springframework', name: 'spring-core', version: '5.3.27'
+    implementation group: 'org.springframework', name: 'spring-expression', version: '5.3.27'
+    implementation group: 'org.codehaus.jettison', name: 'jettison', version: '1.5.4'
+    implementation group: 'com.thoughtworks.xstream', name: 'xstream', version: '1.4.20'
+    implementation group: 'com.google.protobuf', name: 'protobuf-java', version: '3.21.7'
+    implementation("org.springframework.batch:spring-batch-test")
+    implementation group: 'junit', name: 'junit', version: '4.13.1'
+    implementation group: 'mysql', name: 'mysql-connector-java', version: '8.0.28'
+    implementation group: 'org.postgresql', name: 'postgresql', version: '42.3.9'
+    implementation group: 'org.apache.commons', name: 'commons-dbcp2', version: '2.3.0'
+    implementation group: 'commons-io', name: 'commons-io', version: '2.7'
+    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.7'
+    implementation group: 'org.freemarker', name: 'freemarker', version: '2.3.23'
+    implementation group: 'com.google.code.gson', name: 'gson', version: '2.8.9'
+    implementation group: 'commons-collections', name: 'commons-collections', version: '3.2.2'
+    implementation "com.github.jsqlparser:jsqlparser:1.1"
+    implementation 'org.springframework.cloud:spring-cloud-starter-task:1.2.2.RELEASE'
+    implementation group: 'org.liquibase', name: 'liquibase-core', version: '4.8.0'
+    implementation group: 'org.json', name: 'json', version: '20231013'
+
+    testImplementation('org.springframework.boot:spring-boot-starter-test')
+    testImplementation group: 'junit', name: 'junit', version: '4.13.1'
+    testImplementation group: 'org.mockito', name: 'mockito-core', version: '1.10.19'
+    testImplementation group: 'org.powermock', name: 'powermock-core', version: '1.6.4'
+    testImplementation "org.powermock:powermock-module-junit4:1.6.4"
+    testImplementation "org.powermock:powermock-module-junit4-rule:1.6.4"
+    testImplementation "org.powermock:powermock-api-mockito:1.6.4"
+    testImplementation group: 'org.hamcrest', name: 'hamcrest-all', version: '1.3'
 }
 
 jar {
@@ -165,8 +167,8 @@ buildRpm {
     postUninstall file("${projectDir}/scripts/builds/postuninstall.sh")
 }
 
-task wrapper(type: Wrapper) {
-    gradleVersion = '4.5.1'
+wrapper {
+    gradleVersion = '6.8.3'
 }
 
 checkstyle {

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,5 @@
-#Tue May 24 11:00:15 IST 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.8.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.5.1-bin.zip
diff --git a/gradlew b/gradlew
@@ -1,25 +1,43 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 
 ##############################################################################
 ##
 ##  Gradle start up script for UN*X
 ##
 ##############################################################################
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
 
 APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
-warn ( ) {
+warn () {
     echo "$*"
 }
 
-die ( ) {
+die () {
     echo
     echo "$*"
     echo
@@ -30,6 +48,7 @@ die ( ) {
 cygwin=false
 msys=false
 darwin=false
+nonstop=false
 case "`uname`" in
   CYGWIN* )
     cygwin=true
@@ -40,31 +59,11 @@ case "`uname`" in
   MINGW* )
     msys=true
     ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
 esac
 
-# For Cygwin, ensure paths are in UNIX format before anything is touched.
-if $cygwin ; then
-    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-fi
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >&-
-APP_HOME="`pwd -P`"
-cd "$SAVED" >&-
-
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
 # Determine the Java command to use to start the JVM.
@@ -90,7 +89,7 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
     MAX_FD_LIMIT=`ulimit -H -n`
     if [ $? -eq 0 ] ; then
         if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
@@ -114,6 +113,7 @@ fi
 if $cygwin ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
 
     # We build the pattern for arguments to be converted via cygpath
     ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
@@ -154,11 +154,19 @@ if $cygwin ; then
     esac
 fi
 
-# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
-function splitJvmOpts() {
-    JVM_OPTS=("$@")
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
 }
-eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
-JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
 
-exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
+exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
@@ -8,14 +8,14 @@
 @rem Set local scope for the variables with windows NT shell
 if "%OS%"=="Windows_NT" setlocal
 
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
-
 set DIRNAME=%~dp0
 if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
@@ -46,10 +46,9 @@ echo location of your Java installation.
 goto fail
 
 :init
-@rem Get command-line arguments, handling Windowz variants
+@rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line

diff --git a/package/docker/files/application.properties b/package/docker/files/application.properties
@@ -1,18 +1,20 @@
-
-spring.datasource.url=jdbc:postgresql://${MART_DB_HOST}/${MART_DB_NAME}
+spring.datasource.jdbc-url=jdbc:postgresql://${MART_DB_HOST}/${MART_DB_NAME}
 spring.datasource.username=${MART_DB_USERNAME}
 spring.datasource.password=${MART_DB_PASSWORD}
 spring.datasource.driver-class-name=org.postgresql.Driver
 
-spring.ds_openmrs.url=jdbc:mysql://${OPENMRS_DB_HOST}/${OPENMRS_DB_NAME}
-spring.ds_openmrs.username=${OPENMRS_DB_USERNAME}
-spring.ds_openmrs.password=${OPENMRS_DB_PASSWORD}
-spring.ds_openmrs.driver-class-name=com.mysql.jdbc.Driver
+spring.ds-openmrs.jdbc-url=jdbc:mysql://${OPENMRS_DB_HOST}/${OPENMRS_DB_NAME}
+spring.ds-openmrs.username=${OPENMRS_DB_USERNAME}
+spring.ds-openmrs.password=${OPENMRS_DB_PASSWORD}
+spring.ds-openmrs.driver-class-name=com.mysql.cj.jdbc.Driver
+
+spring.ds-mart.jdbc-url=jdbc:postgresql://${MART_DB_HOST}/${MART_DB_NAME}
+spring.ds-mart.username=${MART_DB_USERNAME}
+spring.ds-mart.password=${MART_DB_PASSWORD}
+spring.ds-mart.driver-class-name=org.postgresql.Driver
 
-spring.ds_mart.url=jdbc:postgresql://${MART_DB_HOST}/${MART_DB_NAME}
-spring.ds_mart.username=${MART_DB_USERNAME}
-spring.ds_mart.password=${MART_DB_PASSWORD}
-spring.ds_mart.driver-class-name=org.postgresql.Driver
+spring.batch.initialize-schema=always
+spring.main.allow-bean-definition-overriding=true
 
 bahmniMartConfigFile=file:/bahmni-mart/conf/bahmni-mart.json
 defaultConfigPath=/bahmni-mart/conf/app.json
@@ -21,11 +23,11 @@ defaultExtensionConfigPath=/bahmni-mart/conf/extension.json
 implementationExtensionConfigPath=""
 logging.level.org.bahmni=INFO
 
-liquibase.enabled=true
-liquibase.change-log=file:/bahmni-mart/conf/liquibase.xml
-liquibase.url=jdbc:postgresql://${MART_DB_HOST}/${MART_DB_NAME}
-liquibase.user=${MART_DB_USERNAME}
-liquibase.password=${MART_DB_PASSWORD}
+spring.liquibase.enabled=true
+spring.liquibase.change-log=file:/bahmni-mart/conf/liquibase.xml
+spring.liquibase.url=jdbc:postgresql://${MART_DB_HOST}/${MART_DB_NAME}
+spring.liquibase.user=${MART_DB_USERNAME}
+spring.liquibase.password=${MART_DB_PASSWORD}
 
 # Notifications config
 bahmni-mart.mail.subject=""

diff --git a/src/main/java/org/bahmni/mart/BatchUtils.java b/src/main/java/org/bahmni/mart/BatchUtils.java
@@ -33,6 +33,12 @@ public static String getPostgresCompatibleValue(String value, String dataType) {
           case "timestamp":
           case "time":
               return getStringForPsql(value);
+          case "BIT":
+              if ("true".equalsIgnoreCase(value)) {
+                  return "B'1'";
+              } else {
+                  return "B'0'";
+              }
           default:
               return value;
         }

diff --git a/src/main/java/org/bahmni/mart/dbconfig/DatabaseConfiguration.java b/src/main/java/org/bahmni/mart/dbconfig/DatabaseConfiguration.java
@@ -4,9 +4,9 @@
 import org.postgresql.copy.CopyManager;
 import org.postgresql.core.BaseConnection;
 import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.boot.autoconfigure.batch.BatchDatabaseInitializer;
+import org.springframework.boot.autoconfigure.batch.BatchDataSourceInitializer;
 import org.springframework.boot.autoconfigure.batch.BatchProperties;
-import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
+import org.springframework.boot.jdbc.DataSourceBuilder;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -23,7 +23,7 @@ public class DatabaseConfiguration {
 
     @Primary
     @Bean(name = "openmrsDb")
-    @ConfigurationProperties(prefix = "spring.ds_openmrs")
+    @ConfigurationProperties(prefix = "spring.ds-openmrs")
     public DataSource openmrsDataSource() {
         return DataSourceBuilder.create().build();
     }
@@ -34,7 +34,7 @@ public JdbcTemplate openmrsJdbcTemplate(@Qualifier("openmrsDb") DataSource dsOpe
     }
 
     @Bean(name = "martDb")
-    @ConfigurationProperties(prefix = "spring.ds_mart")
+    @ConfigurationProperties(prefix = "spring.ds-mart")
     public DataSource martDataSource() {
         return DataSourceBuilder.create().build();
     }
@@ -66,9 +66,9 @@ public DataSource dataSource() {
     }
 
     @Bean
-    public BatchDatabaseInitializer batchDatabaseInitializer(final BatchProperties properties,
+    public BatchDataSourceInitializer batchDataSourceInitializer(final BatchProperties properties,
                                                              @Qualifier("scdfDb") final DataSource dataSource,
                                                              final ResourceLoader resourceLoader) {
-        return new BatchDatabaseInitializer(dataSource, resourceLoader, properties);
+        return new BatchDataSourceInitializer(dataSource, resourceLoader, properties);
     }
 }