Merge pull request #32 from ga4gh/release/0.5.7

Release 0.5.7 into main

README.md

@@ -1,2 +1,7 @@
-# ga4gh-starter-kit-common
+# GA4GH Starter Kit Common
 Common utils library for GA4GH Starter Kit web services
+
+## Changelog
+
+### v0.5.7
+* patched log4j dependencies to v2.16.0 to avoid [Log4j Vulnerability](https://www.cisa.gov/uscert/apache-log4j-vulnerability-guidance)

build.gradle

@@ -31,8 +31,16 @@ plugins {
     id 'io.github.gradle-nexus.publish-plugin' version '1.1.0'
 }
 
+configurations.all {
+  resolutionStrategy.eachDependency { DependencyResolveDetails details ->
+    if (details.requested.group == 'org.apache.logging.log4j') {
+      details.useVersion '2.16.0'
+    }
+  }
+}
+
 group 'org.ga4gh'
-version '0.5.6'
+version '0.5.7'
 
 repositories {
     mavenCentral()
@@ -49,6 +57,7 @@ dependencies {
     api 'org.apache.commons:commons-math3:3.6.1'
 
     // implementation 'org.apache.logging.log4j:log4j-core:2.14.1'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.15.0'
     implementation 'com.google.guava:guava:28.1-jre'
     implementation 'org.springframework.boot:spring-boot-starter-web:2.5.0'
     implementation 'commons-cli:commons-cli:1.4'

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.0.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -82,6 +82,7 @@ esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
+
 # Determine the Java command to use to start the JVM.
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
@@ -129,6 +130,7 @@ fi
 if [ "$cygwin" = "true" -o "$msys" = "true" ] ; 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

gradlew.bat

@@ -29,6 +29,9 @@ if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @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="-Xmx64m" "-Xms64m"
 
@@ -37,7 +40,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if "%ERRORLEVEL%" == "0" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -51,7 +54,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -61,28 +64,14 @@ echo location of your Java installation.
 
 goto fail
 
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
 :execute
 @rem Setup the command line
 
 set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
+
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell