Merge pull request #351 from TheRoddyWMS/fix-localexecutionservice-ig…

…nores-errors

Fix LocalExecutionService ignored errors

.travis.yml

@@ -6,22 +6,18 @@ cache:
   directories:
   - "$HOME/.gradle/caches/"
   - "$HOME/.gradle/wrapper/"
+jdk:
+  - openjdk8
 before_install:
-- curl -s get.sdkman.io | bash
-- source "$HOME/.sdkman/bin/sdkman-init.sh"
-- echo sdkman_auto_answer=true > ~/.sdkman/etc/config
-- source "/home/travis/.sdkman/bin/sdkman-init.sh"
-- sdk install java 8.0.252-open
-- sdk use     java 8.0.252-open
-- export JAVA_HOME="$HOME/.sdkman/candidates/java/current"
-- export JAVA_ROOT="$JAVA_HOME"
-- export JRE_HOME="$JAVA_HOME"
-- export JDK_HOME="$JAVA_HOME"
-- sdk install groovy 2.4.19
-- sdk use     groovy 2.4.19
-- groovy --version
-- git clone https://github.com/eilslabs/Roddy-Default-Plugin.git dist/plugins/DefaultPlugin
-- git clone https://github.com/eilslabs/Roddy-Base-Plugin.git dist/plugins/PluginBase
+  - curl -s get.sdkman.io | bash
+  - source "$HOME/.sdkman/bin/sdkman-init.sh"
+  - echo sdkman_auto_answer=true > ~/.sdkman/etc/config
+  - source "/home/travis/.sdkman/bin/sdkman-init.sh"
+  - sdk install groovy 2.4.19
+  - sdk use     groovy 2.4.19
+  - groovy --version
+  - git clone https://github.com/TheRoddyWMS/Roddy-Default-Plugin.git dist/plugins/DefaultPlugin
+  - git clone https://github.com/TheRoddyWMS/Roddy-Base-Plugin.git dist/plugins/PluginBase
 deploy:
   skip_cleanup: true
   provider: releases

CHANGELIST.md

@@ -1,5 +1,14 @@
 # Changelist
 
+* 3.5.9
+
+  - The LocalExecutionService ignored errors of asychronously executed commands. 
+    Now errors Roddy detects errors and reports their standard and error output.
+  - LocalExecutionService always executes commands via `bash -c` (before it
+    did so only if the process was sychronously executed)
+  - Update of RoddyToolLib to fix error handling in asynchronous execution and
+    with multi-threading and command-output processing (StringBuilder->StringBuffer)
+
 * 3.5.8
 
   - Bugfix: Project XML validation didn't exit != 0 in strict mode

README.md

@@ -1,4 +1,5 @@
-# What is Roddy?
+[![Build Status - Travis](https://travis-ci.org/TheRoddyWMS/Roddy.svg?branch=master)](https://travis-ci.org/TheRoddyWMS/Roddy)
+# What is Roddy? 
 
 Roddy is a framework for development and management of workflows on a batch processing cluster. It has been developed at the German Cancer Research Center (DKFZ) in Heidelberg in the eilslabs group and is used by a number of in-house workflows such as the [PanCancer Alignment Workflow](https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows) and the [ACEseq workflow](https://github.com/eilslabs/ACEseqWorkflow). The development is now continued in the Omics IT and Data Management Core Facility (ODCF) at the DKFZ.
 
@@ -19,7 +20,7 @@ The following workflows have been developed at the DKFZ based on Roddy as workfl
   * [ACEseq workflow](https://github.com/DKFZ-ODCF/ACEseqWorkflow) for copy-number variation calling
   * [InDel-Calling workflow](https://github.com/DKFZ-ODCF/IndelCallingWorkflow) workflow
   * [Sophia workflow](https://github.com/DKFZ-ODCF/SophiaWorkflow) for structural variation calling
-  * RNA-seq workflow (to be published)
+  * [RNA-seq workflow](https://github.com/DKFZ-ODCF/RNAseqWorkflow)
   * CNVkit for copy-number variation calling on exome data (to be published)
   * Leaf-Cutter workflow
   * [Bam-to-FASTQ](https://github.com/TheRoddyWMS/BamToFastqPlugin) plugin

RoddyCore/buildversion.txt

@@ -1,2 +1,2 @@
 3.5
-8
+9

RoddyCore/src/de/dkfz/roddy/Constants.java

@@ -16,8 +16,8 @@ public class Constants {
     // Application constants
     /////////////////////////
 
-    public static final String APP_CURRENT_VERSION_STRING = "3.5.8";
-    public static final String APP_CURRENT_VERSION_BUILD_DATE = "Thu Jun 25 09:14:30 GMT 2020";
+    public static final String APP_CURRENT_VERSION_STRING = "3.5.9";
+    public static final String APP_CURRENT_VERSION_BUILD_DATE = "Wed Oct 21 17:08:57 CEST 2020";
     public static final String APP_PROPERTY_JOB_MANAGER_CLASS = "jobManagerClass";
     public static final String APP_PROPERTY_FILESYSTEM_ACCESS_MANAGER_CLASS = "fileSystemAccessManagerClass";
     public static final String APP_PROPERTY_EXECUTION_SERVICE_CLASS = "executionServiceClass";

RoddyCore/src/de/dkfz/roddy/Roddy.java

@@ -1032,15 +1032,15 @@ public static ShellCommandSet getLocalCommandSet() {
         if (RoddyConversionHelperMethods.isNullOrEmpty(localCommandSet)) {
             logger.postSometimesInfo("Using BashCommandSet, localCommandSet ist not set.");
             BashCommandSet bcs = new BashCommandSet();
-            bcs.validate();
+            bcs.validateShell();
             return bcs;
         }
 
         Class<ShellCommandSet> cls = null;
         try {
             cls = (Class<ShellCommandSet>) LibrariesFactory.getGroovyClassLoader().loadClass(localCommandSet);
             ShellCommandSet shellCommandSet = cls.newInstance();
-            if (shellCommandSet.validate())
+            if (shellCommandSet.validateShell())
                 return shellCommandSet;
             throw new RuntimeException("The selected ShellCommandSet '${localCommandSet}' could not validate.");
         } catch (ClassNotFoundException e) {

RoddyCore/src/de/dkfz/roddy/core/ExecutionContext.groovy

@@ -87,17 +87,17 @@ class ExecutionContext {
      * Keeps a list of errors which happen either on read back or on execution.
      * The list is not stored and rebuilt if necessary, so not all errors might be available.
      */
-    private final List<ExecutionContextError> errors = [].asSynchronized()
+    private final List<ExecutionContextError> errors = ([] as List<ExecutionContextError>).asSynchronized()
     /**
      * Keeps a list of warnings which happen either on read back or on execution.
      * The list is not stored and rebuilt if necessary, so not all errors might be available.
      */
-    private final List<ExecutionContextError> warnings = [].asSynchronized()
+    private final List<ExecutionContextError> warnings = ([] as List<ExecutionContextError>).asSynchronized()
     /**
      * Keeps a list of info entries which happen either on read back or on execution.
      * The list is not stored and rebuilt if necessary, so not all errors might be available.
      */
-    private final List<ExecutionContextError> infos = [].asSynchronized()
+    private final List<ExecutionContextError> infos = ([] as List<ExecutionContextError>).asSynchronized()
 
     /**
      * The timestamp of this context object