Tests for AACon loader

[jabaws.git] / testsrc / compbio / runner / conservation / AAConTester.java

diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java
index 033555a..fbb9720 100644 (file)
--- a/testsrc/compbio/runner/conservation/AAConTester.java
+++ b/testsrc/compbio/runner/conservation/AAConTester.java
@@ -20,7 +20,6 @@ package compbio.runner.conservation;
 import static org.testng.Assert.assertEquals;\r
 import static org.testng.Assert.assertFalse;\r
 import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertNull;\r
 import static org.testng.Assert.assertTrue;\r
 import static org.testng.Assert.fail;\r
 \r
@@ -29,6 +28,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
 import java.text.ParseException;\r
+import java.util.Arrays;\r
 \r
 import javax.xml.bind.ValidationException;\r
 \r
@@ -56,9 +56,11 @@ import compbio.metadata.JobExecutionException;
 import compbio.metadata.JobStatus;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.LimitsManager;\r
+import compbio.metadata.Preset;\r
 import compbio.metadata.PresetManager;\r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.RunnerConfig;\r
+import compbio.runner.Util;\r
 import compbio.util.FileWatcher;\r
 import compbio.util.SysPrefs;\r
 \r
@@ -188,7 +190,38 @@ public class AAConTester {
                        assertNotNull(al1.getResults());\r
                        MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
                        assertNotNull(annotations);\r
-                       assertEquals(annotations.getAnnotations().size(), 18);\r
+                       assertEquals(annotations.getAnnotations().size(), 1);\r
+                       assertEquals(al1.getResults(), annotations);\r
+               } catch (JobSubmissionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (ResultNotAvailableException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (JobExecutionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               }\r
+       }\r
+\r
+       @Test()\r
+       public void testRunLocallyWithPreset() {\r
+               try {\r
+                       PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);\r
+                       assert aaconPresets != null;\r
+                       ConfiguredExecutable<AACon> confAAcon = Configurator\r
+                                       .configureExecutable(aacon, Executable.ExecProvider.Local);\r
+                       Preset<AACon> quick = aaconPresets\r
+                                       .getPresetByName("Quick conservation");\r
+                       confAAcon.addParameters(quick.getOptions());\r
+                       // For local execution use relative\r
+                       LocalRunner lr = new LocalRunner(confAAcon);\r
+                       lr.executeJob();\r
+                       ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+                       assertNotNull(al1.getResults());\r
+                       MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+                       assertNotNull(annotations);\r
+                       assertEquals(annotations.getAnnotations().size(), 13);\r
                        assertEquals(al1.getResults(), annotations);\r
                } catch (JobSubmissionException e) {\r
                        e.printStackTrace();\r
@@ -205,18 +238,23 @@ public class AAConTester {
        @Test()\r
        public void testRunLocallyOnTwoCpu() {\r
                try {\r
+                       aacon = new AACon();\r
+                       aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
+\r
                        aacon.setNCore(2);\r
                        ConfiguredExecutable<AACon> confAAcon = Configurator\r
                                        .configureExecutable(aacon, Executable.ExecProvider.Local);\r
-\r
+                       confAAcon.addParameters(Arrays.asList("-m=KABAT,JORES"));\r
+                       confAAcon.addParameters(Arrays.asList("-m=TAYLOR_GAPS"));\r
                        // For local execution use relative\r
                        LocalRunner lr = new LocalRunner(confAAcon);\r
+\r
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
                        MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
                        assertNotNull(annotations);\r
-                       assertEquals(annotations.getAnnotations().size(), 18);\r
+                       assertEquals(annotations.getAnnotations().size(), 3);\r
                        assertEquals(al1.getResults(), annotations);\r
                } catch (JobSubmissionException e) {\r
                        e.printStackTrace();\r
@@ -229,7 +267,6 @@ public class AAConTester {
                        fail(e.getLocalizedMessage());\r
                }\r
        }\r
-\r
        @Test()\r
        public void readStatistics() {\r
                try {\r
@@ -358,7 +395,7 @@ public class AAConTester {
 \r
                        PresetManager<AACon> aaconPresets = ConfExecutable\r
                                        .getRunnerPresets(AACon.class);\r
-                       assertNull(aaconPresets); // there is no presets\r
+                       assertNotNull(aaconPresets);\r
 \r
                        LimitsManager<AACon> jronnLimits = ConfExecutable\r
                                        .getRunnerLimits(AACon.class);\r