import java.io.IOException;\r
import java.text.ParseException;\r
import java.util.Arrays;\r
import java.io.IOException;\r
import java.text.ParseException;\r
import java.util.Arrays;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.FilePuller;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.FilePuller;\r
import compbio.engine.cluster.drmaa.JobRunner;\r
import compbio.engine.cluster.drmaa.StatisticManager;\r
import compbio.engine.local.LocalRunner;\r
import compbio.engine.cluster.drmaa.JobRunner;\r
import compbio.engine.cluster.drmaa.StatisticManager;\r
import compbio.engine.local.LocalRunner;\r
import compbio.metadata.ChunkHolder;\r
import compbio.metadata.JobExecutionException;\r
import compbio.metadata.JobStatus;\r
import compbio.metadata.ChunkHolder;\r
import compbio.metadata.JobExecutionException;\r
import compbio.metadata.JobStatus;\r
public void testRunOnCluster() {\r
assertFalse(SysPrefs.isWindows,\r
"Cluster execution can only be in unix environment");\r
public void testRunOnCluster() {\r
assertFalse(SysPrefs.isWindows,\r
"Cluster execution can only be in unix environment");\r
* This tests fails from time to time depending on the cluster load or some\r
* other factors. Any client code has to adjust for this issue\r
*/\r
* This tests fails from time to time depending on the cluster load or some\r
* other factors. Any client code has to adjust for this issue\r
*/\r
public void testRunOnClusterAsync() {\r
assertFalse(SysPrefs.isWindows,\r
"Cluster execution can only be in unix environment");\r
public void testRunOnClusterAsync() {\r
assertFalse(SysPrefs.isWindows,\r
"Cluster execution can only be in unix environment");\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
public void testRunLocallyWithPreset() {\r
try {\r
PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);\r
public void testRunLocallyWithPreset() {\r
try {\r
PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
assertEquals(al1.getResults(), annotations);\r
\r
} catch (JobSubmissionException e) {\r
assertEquals(al1.getResults(), annotations);\r
\r
} catch (JobSubmissionException e) {\r