import java.io.IOException;\r
import java.text.ParseException;\r
import java.util.Arrays;\r
+import java.util.HashSet;\r
\r
import javax.xml.bind.ValidationException;\r
\r
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.conservation.Method;\r
-import compbio.data.sequence.MultiAnnotatedSequence;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\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.metadata.AllTestSuit;\r
import compbio.metadata.ChunkHolder;\r
import compbio.metadata.JobExecutionException;\r
import compbio.metadata.JobStatus;\r
aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
}\r
\r
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner})\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
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_cluster})\r
public void testRunOnClusterAsync() {\r
assertFalse(SysPrefs.isWindows,\r
"Cluster execution can only be in unix environment");\r
}\r
}\r
\r
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testRunLocally() {\r
try {\r
ConfiguredExecutable<AACon> confAAcon = Configurator\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+ ScoreManager annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 1);\r
+ assertEquals(annotations.asSet().size(), 18);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
}\r
}\r
\r
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testRunLocallyWithPreset() {\r
try {\r
PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+ ScoreManager annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 13);\r
+ assertEquals(annotations.asSet().size(), 13);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
}\r
}\r
\r
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testRunLocallyOnTwoCpu() {\r
try {\r
aacon = new AACon();\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+ ScoreManager annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 3);\r
+ assertEquals(annotations.asSet().size(), 3);\r
assertEquals(al1.getResults(), annotations);\r
\r
} catch (JobSubmissionException e) {\r
fail(e.getLocalizedMessage());\r
}\r
}\r
- @Test()\r
+ \r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void readStatistics() {\r
try {\r
ConfiguredExecutable<AACon> confAAcon = Configurator\r
}\r
}\r
\r
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testPersistance() {\r
try {\r
AACon aacon = new AACon();\r
}\r
}\r
\r
- @Test()\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testConfigurationLoading() {\r
try {\r
RunnerConfig<AACon> aaconConfig = ConfExecutable\r