Merge pull request #35 from TheRoddyWMS/library-version-bumps-and-gro…

…ovification

Bumped libraries and fixed a test

.gitignore

@@ -15,3 +15,7 @@ gradle-app.setting
 ### IntelliJ
 .idea
 /out/
+
+.classpath
+.project
+.settings

README.md

@@ -25,6 +25,13 @@ where you substitute the correct proxies and ports required for your environment
 
 ## Changelog
 
+* 2.4.1
+
+   - Patch: Library update
+   - Patch: Changed one logging message
+   - Patch: Fixed a unit test
+   - Patch: Code layout refactorings and groovification
+
 * 2.4.0
 
   - Minor: Improved reporting of stdout and stderr for executed commands

build.gradle

@@ -30,10 +30,10 @@ repositories {
 }
 
 dependencies {
-    compile 'org.codehaus.groovy:groovy-all:2.4.9'
-    testCompile 'junit:junit:4.12'
+    compile 'org.codehaus.groovy:groovy-all:2.4.21'
+    testCompile 'junit:junit:4.13.1'
     testCompile 'org.spockframework:spock-core:1.1-groovy-2.4'
-    compile group: 'commons-codec', name: 'commons-codec', version: '1.9'
+    compile group: 'commons-codec', name: 'commons-codec', version: '1.13'
     compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
 }
 

src/main/groovy/de/dkfz/roddy/execution/io/LocalExecutionHelper.groovy

@@ -147,7 +147,7 @@ class LocalExecutionHelper {
             OutputStream outputStream = null,
             ExecutorService executorService = executorService) {
         List<String> bashCommand = ["bash", "-c", command]
-        logger.postRareInfo("Executing the command ${bashCommand} locally.")
+        logger.postRareInfo("Executing command locally: ${bashCommand}")
         ProcessBuilder processBuilder = new ProcessBuilder(bashCommand)
         Process process = processBuilder.start()
         CompletableFuture<List<String>> stdoutF

src/main/groovy/de/dkfz/roddy/tools/BufferValue.groovy

@@ -15,7 +15,7 @@ package de.dkfz.roddy.tools
  * However floating point values can be parsed and will be rounded to their Integers.
  * Created by heinold on 10.11.15.
  */
-public class BufferValue {
+class BufferValue {
 
 /**
      * The stored value aligned to KiloByte