Parser for DisEMBL results and finished runner, few test cases. DisemblTester has...

[jabaws.git] / testsrc / compbio / runner / disorder / DisemblTester.java

diff --git a/testsrc/compbio/runner/disorder/DisemblTester.java b/testsrc/compbio/runner/disorder/DisemblTester.java
index d77648e..133168e 100644 (file)
--- a/testsrc/compbio/runner/disorder/DisemblTester.java
+++ b/testsrc/compbio/runner/disorder/DisemblTester.java
@@ -31,6 +31,8 @@ import java.io.FileNotFoundException;
 import java.io.IOException;\r
 import java.text.ParseException;\r
 import java.util.HashSet;\r
+import java.util.Map;\r
+import java.util.Set;\r
 \r
 import javax.xml.bind.ValidationException;\r
 \r
@@ -153,7 +155,7 @@ public class DisemblTester {
                                System.out.println("Job Status: " + status);\r
                                Thread.sleep(1000);\r
                                status = aengine.getJobStatus(jobId);\r
-                               ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
+                               ConfiguredExecutable<Disembl> result = (ConfiguredExecutable<Disembl>) aengine\r
                                                .getResults(jobId);\r
                                assertNotNull(result);\r
                                System.out.println("RES:" + result);\r
@@ -188,7 +190,7 @@ public class DisemblTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       HashSet<Score> al2 = confDisembl.getResults();\r
+                       Map<String,Set<Score>> al2 = confDisembl.getResults();\r
                        assertNotNull(al2);\r
                        assertEquals(al2.size(), 3);\r
                        assertEquals(al1.getResults(), al2);\r
@@ -206,51 +208,7 @@ public class DisemblTester {
 \r
        @Test(groups = {AllTestSuit.test_group_runner})\r
        public void readStatistics() {\r
-               try {\r
-                       ConfiguredExecutable<Disembl> confDisembl = Configurator\r
-                                       .configureExecutable(disembl, Executable.ExecProvider.Local);\r
-                       // For local execution use relavive\r
-\r
-                       AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);\r
-                       String jobId = sexec.submitJob(confDisembl);\r
-                       FilePuller fw = FilePuller.newFilePuller(\r
-                                       confDisembl.getWorkDirectory() + File.separator\r
-                                                       + Jronn.getStatFile(),\r
-                                       FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
-                       int count = 0;\r
-                       long position = 0;\r
-                       fw.waitForFile(4);\r
-                       JobStatus status = sexec.getJobStatus(jobId);\r
-                       while (status != JobStatus.FINISHED) {\r
-                               if (fw.hasMoreData()) {\r
-                                       ChunkHolder ch = fw.pull(position);\r
-                                       String chunk = ch.getChunk();\r
-                                       position = ch.getNextPosition();\r
-                               }\r
-                               count++;\r
-                               // Make sure the loop is terminated if the job fails\r
-                               if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
-                                       break;\r
-                               }\r
-                               Thread.sleep(300);\r
-                               status = sexec.getJobStatus(jobId);\r
-                       }\r
-                       assertTrue(count > 1);\r
-                       ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
-                       assertNotNull(al.getResults());\r
-               } catch (JobSubmissionException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               } catch (ResultNotAvailableException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               } catch (IOException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               } catch (InterruptedException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               }\r
+               // No execution statistics is available!\r
        }\r
 \r
        @Test(groups = {AllTestSuit.test_group_runner})\r
@@ -293,11 +251,11 @@ public class DisemblTester {
                        // See in details whether executables are the same\r
                        assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
 \r
-                       ConfiguredExecutable<Disembl> resJronn = Configurator\r
+                       ConfiguredExecutable<Disembl> resDisembl = Configurator\r
                                        .configureExecutable(resurrectedCDisembl.getExecutable(),\r
                                                        Executable.ExecProvider.Local);\r
 \r
-                       sexec = Configurator.getSyncEngine(resJronn,\r
+                       sexec = Configurator.getSyncEngine(resDisembl,\r
                                        Executable.ExecProvider.Local);\r
                        sexec.executeJob();\r
                        al = sexec.waitForResult();\r
@@ -327,7 +285,8 @@ public class DisemblTester {
                        RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
                                        .getRunnerOptions(Disembl.class);\r
                        assertNotNull(disemblConfig);\r
-                       assertTrue(disemblConfig.getArguments().size() > 0);\r
+                       // There is no disembl parameters\r
+                       assertTrue(disemblConfig.getArguments().size() == 0);\r
 \r
                        PresetManager<Disembl> disemblPresets = ConfExecutable\r
                                        .getRunnerPresets(Disembl.class);\r