Merge pull request #50 from ga4gh/release/0.2.2

Release 0.2.2 into main

README.md

@@ -182,4 +182,9 @@ Multiple datasets are currently contained in this repo for development and testi
   - see the [datasets page](./DATASETS.md#htsjdk) for a list of `DRS IDs` for `DrsObjects` in the htsjdk dataset
 * Open dataset of 384 Phenopackets: [Paper](https://pubmed.ncbi.nlm.nih.gov/32755546/), [Dataset homepage](https://zenodo.org/record/3905420#.YArkBzpKhPZ)
 
-  - see the [datasets page](./DATASETS.md#Phenopackets) for a list of `DRS IDs` for `DrsObjects` in the Phenopackets dataset
+  - see the [datasets page](./DATASETS.md#Phenopackets) for a list of `DRS IDs` for `DrsObjects` in the Phenopackets dataset
+
+## Changelog
+
+### v0.2.2
+* patched log4j dependencies to v2.16.0 to avoid [Log4j Vulnerability](https://www.cisa.gov/uscert/apache-log4j-vulnerability-guidance)

build.gradle

@@ -26,9 +26,17 @@ plugins {
     id 'io.codearte.nexus-staging' version '0.30.0'
 }
 
+configurations.all {
+  resolutionStrategy.eachDependency { DependencyResolveDetails details ->
+    if (details.requested.group == 'org.apache.logging.log4j') {
+      details.useVersion '2.16.0'
+    }
+  }
+}
+
 archivesBaseName = 'ga4gh-starter-kit-drs'
 group 'org.ga4gh'
-version '0.2.1'
+version '0.2.2'
 
 repositories {
     // Use jcenter for resolving dependencies.
@@ -54,7 +62,7 @@ dependencies {
     implementation 'javax.xml.bind:jaxb-api:2.2.8'
     implementation 'org.springdoc:springdoc-openapi-ui:1.2.33'
     implementation 'org.xerial:sqlite-jdbc:3.8.11.2'
-    implementation 'org.ga4gh:ga4gh-starter-kit-common:0.5.4'
+    implementation 'org.ga4gh:ga4gh-starter-kit-common:0.5.6'
 
     testImplementation 'org.testng:testng:7.0.0'
     testImplementation 'org.springframework.boot:spring-boot-starter-test:2.5.0'

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-7.3.2-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

src/main/java/org/ga4gh/starterkit/drs/app/DrsServer.java

@@ -29,6 +29,7 @@ public static void main(String[] args) {
 
     private static boolean setup(String[] args) {
         Options options = new DrsServerSpringConfig().getCommandLineOptions();
-        return ServerPropertySetter.setServerProperties(DrsServerYamlConfigContainer.class, args, options, "config");
+        ServerPropertySetter setter = new ServerPropertySetter();
+        return setter.setServerProperties(DrsServerYamlConfigContainer.class, args, options, "config");
     }
 }

src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java

@@ -153,7 +153,8 @@ public DrsServerYamlConfigContainer mergedDrsConfigContainer(
         @Qualifier(DrsServerConstants.DEFAULT_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer defaultContainer,
         @Qualifier(DrsServerConstants.USER_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer userContainer
     ) {
-        DeepObjectMerger.merge(userContainer, defaultContainer);
+        DeepObjectMerger merger = new DeepObjectMerger();
+        merger.merge(userContainer, defaultContainer);
         return defaultContainer;
     }
 

src/main/java/org/ga4gh/starterkit/drs/constant/DrsServiceInfoDefaults.java

@@ -54,7 +54,7 @@ public class DrsServiceInfoDefaults {
     /**
      * Default service version
      */
-    public static final String VERSION = "0.2.1";
+    public static final String VERSION = "0.2.2";
 
     /**
      * Default service organization name

src/main/java/org/ga4gh/starterkit/drs/model/DrsServiceInfo.java

@@ -10,16 +10,14 @@
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.UPDATED_AT;
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ENVIRONMENT;
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.VERSION;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ORGANIZATION_NAME;
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ORGANIZATION_URL;
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_GROUP;
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_ARTIFACT;
 import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_VERSION;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.PropertyNamingStrategies;
+import com.fasterxml.jackson.databind.annotation.JsonNaming;
 
 /**
  * Extension of the GA4GH base service info specification to include DRS-specific

src/test/resources/responses/service-info/show/00.json

@@ -1 +1 @@
-{"id":"org.ga4gh.starterkit.drs","name":"GA4GH Starter Kit DRS Service","description":"An open source, community-driven implementation of the GA4GH Data Repository Service (DRS) API specification.","contactUrl":"mailto:[email protected]","documentationUrl":"https://github.com/ga4gh/ga4gh-starter-kit-drs","createdAt":"2020-01-15T12:00:00Z","updatedAt":"2020-01-15T12:00:00Z","environment":"test","version":"0.2.1","type":{"group":"org.ga4gh","artifact":"drs","version":"1.1.0"},"organization":{"name":"Global Alliance for Genomics and Health","url":"https://ga4gh.org"}}
+{"id":"org.ga4gh.starterkit.drs","name":"GA4GH Starter Kit DRS Service","description":"An open source, community-driven implementation of the GA4GH Data Repository Service (DRS) API specification.","contactUrl":"mailto:[email protected]","documentationUrl":"https://github.com/ga4gh/ga4gh-starter-kit-drs","createdAt":"2020-01-15T12:00:00Z","updatedAt":"2020-01-15T12:00:00Z","environment":"test","version":"0.2.2","type":{"group":"org.ga4gh","artifact":"drs","version":"1.1.0"},"organization":{"name":"Global Alliance for Genomics and Health","url":"https://ga4gh.org"}}