Merge branch 'develop'

integrationTest.properties

@@ -0,0 +1,25 @@
+lsf.rest.host=
+lsf.rest.account=
+lsf.rest.password=
+
+lsf.host=
+lsf.account=
+
+pbs.host=
+pbs.account=
+
+sge.host=
+sge.account=
+
+slurm.host=
+slurm.account=
+
+# set test script to run, default: 'ls'
+testscript=
+
+# set absolute path for test script on cluster node. It needs to be set to run tests with file. e.g. /path/to/file/testscript.sh
+remoteToolPath=
+
+# set absolute log path, e.g. /path/to/logfile/test.out. default: no log file is created.
+logpath=
+

src/main/groovy/de/dkfz/roddy/AvailableClusterSystems.groovy

@@ -9,6 +9,7 @@ package de.dkfz.roddy
 import de.dkfz.roddy.execution.jobs.cluster.lsf.LSFJobManager
 import de.dkfz.roddy.execution.jobs.cluster.lsf.rest.LSFRestJobManager
 import de.dkfz.roddy.execution.jobs.cluster.pbs.PBSJobManager
+import de.dkfz.roddy.execution.jobs.cluster.sge.SGEJobManager
 import de.dkfz.roddy.execution.jobs.direct.synchronousexecution.DirectSynchronousExecutionJobManager
 import de.dkfz.roddy.execution.jobs.BatchEuphoriaJobManager
 import groovy.transform.CompileStatic
@@ -20,7 +21,7 @@ import groovy.transform.CompileStatic
  */
 @CompileStatic
 enum AvailableClusterSystems {
-    direct(DirectSynchronousExecutionJobManager.class), pbs(PBSJobManager.class), sge("de.dkfz.eilslabs.batcheuphoria.execution.cluster.sge.SGEJobManager"), slurm("de.dkfz.eilslabs.batcheuphoria.execution.cluster.slurm.SlurmJobManager"), lsf(LSFJobManager.class), lsfrest(LSFRestJobManager.class)
+    direct(DirectSynchronousExecutionJobManager.class), pbs(PBSJobManager.class), sge(SGEJobManager.class), slurm("de.dkfz.eilslabs.batcheuphoria.execution.cluster.slurm.SlurmJobManager"), lsf(LSFJobManager.class), lsfrest(LSFRestJobManager.class)
 
     final String className
 

src/main/groovy/de/dkfz/roddy/execution/jobs/GenericJobInfo.groovy

@@ -31,7 +31,7 @@ class GenericJobInfo {
     LocalDateTime endTime;
     LocalDateTime eligibleTime; // when all conditions like job dependencies full filled, it is qu
 
-    String executionHosts;
+    List<String> executionHosts;
     String submissionHost;
     String priority;
 
@@ -57,7 +57,7 @@ class GenericJobInfo {
     String pendReason;
     String execHome;
     String execUserName;
-    String pidStr;
+    List<String> pidStr;
     String pgidStr; // Currently active process group ID in a job.
     Integer exitCode; // UNIX exit status of the job
     String jobGroup;

src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/ClusterJobManager.groovy

@@ -28,7 +28,7 @@ abstract class ClusterJobManager<C extends Command> extends BatchEuphoriaJobMana
         super(executionService, parms)
     }
 
-    protected static <T> T catchExceptionAndLog(final Closure<T> closure) {
+    protected static <T> T catchAndLogExceptions(final Closure<T> closure) {
         try {
             return closure.call()
         } catch (Exception e) {