--- /dev/null
+/* Copyright (c) 2009 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.engine;\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.util.concurrent.TimeUnit;\r
+\r
+import org.testng.annotations.BeforeTest;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.local.AsyncLocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.runner.msa.Muscle;\r
+\r
+public class FilePullerTester {\r
+\r
+ public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + "TO1381.fasta";\r
+\r
+ String jobId;\r
+ String jobId2;\r
+ String jobId3;\r
+\r
+ @BeforeTest(alwaysRun = true)\r
+ public void init() {\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setInput(test_input);\r
+ Muscle ms = new Muscle().setInput(test_input);\r
+ Muscle ms2 = new Muscle().setInput(test_input);\r
+\r
+ try {\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+ ConfiguredExecutable<Muscle> confms = Configurator\r
+ .configureExecutable(ms, Executable.ExecProvider.Local);\r
+\r
+ ConfiguredExecutable<Muscle> confms2 = Configurator\r
+ .configureExecutable(ms2, Executable.ExecProvider.Local);\r
+\r
+ AsyncLocalRunner as = new AsyncLocalRunner();\r
+ jobId = as.submitJob(confClustal);\r
+ jobId2 = as.submitJob(confms);\r
+ jobId3 = as.submitJob(confms2);\r
+\r
+ ConfiguredExecutable<?> al = as.getResults(jobId);\r
+ ConfiguredExecutable<?> al2 = as.getResults(jobId2);\r
+ ConfiguredExecutable<?> al3 = as.getResults(jobId3);\r
+ assertNotNull(al);\r
+ assertNotNull(al2);\r
+ assertNotNull(al3);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_engine })\r
+ public void testPull() {\r
+ assertNotNull(jobId, "init() method failed!");\r
+ String workDir = Configurator.getWorkDirectory(jobId);\r
+ String statFile = workDir + File.separator + ClustalW.getStatFile();\r
+\r
+ ChunkHolder ch = ProgressGetter.pull(statFile, 0);\r
+ while (ch == null) {\r
+ ch = ProgressGetter.pull(statFile, 0);\r
+ }\r
+ String chunk = "";\r
+ long pos = 0;\r
+ do {\r
+ chunk = ch.getChunk();\r
+ assertNotNull(chunk);\r
+ pos = ch.getNextPosition();\r
+ ch = ProgressGetter.pull(statFile, pos);\r
+ } while (chunk.length() > 0);\r
+\r
+ // All consequent pulls just return empty chunk and same position =\r
+ // file.length\r
+ ch = ProgressGetter.pull(statFile, pos);\r
+ assertNotNull(ch);\r
+ assertEquals(ch.getChunk().length(), 0);\r
+ // Output file size depends on the operation system fs!\r
+ // assertEquals(ch.getNextPosition(), 668);\r
+\r
+ ch = ProgressGetter.pull(statFile, pos);\r
+ assertNotNull(ch);\r
+ assertEquals(ch.getChunk().length(), 0);\r
+ // Output file size depends on the operation system and fs!\r
+ // assertEquals(ch.getNextPosition(), 668);\r
+\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_engine })\r
+ public void testGetDelay() {\r
+ FilePuller fp = FilePuller.newFilePuller(Configurator\r
+ .getWorkDirectory(jobId)\r
+ + File.separator + "stat.log", 256);\r
+ // default delay is 5 minutes\r
+ assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 5 * 60);\r
+ long d = 1000 * 1000 * 1000L * 60; // 1m in nanoseconds\r
+ fp.setDelay(d, TimeUnit.NANOSECONDS);\r
+ assertEquals(fp.getDelayValue(TimeUnit.NANOSECONDS), d);\r
+ assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 60);\r
+ assertEquals(fp.getDelayValue(TimeUnit.MINUTES), 1);\r
+ }\r
+\r
+ @Test(groups = { AllTestSuit.test_group_engine }, dependsOnMethods = { "testPull" })\r
+ public void testCache() {\r
+ assertNotNull(jobId, "init() method failed!");\r
+ assertNotNull(jobId2, "init() method failed!");\r
+ assertEquals(PulledFileCache.getSize(), 1); // One is from previous test\r
+\r
+ String statFile = Configurator.getWorkDirectory(jobId) + File.separator\r
+ + ClustalW.getStatFile();\r
+ String statFile2 = Configurator.getWorkDirectory(jobId2)\r
+ + File.separator + Muscle.getStatFile();\r
+ String statFile3 = Configurator.getWorkDirectory(jobId3)\r
+ + File.separator + Muscle.getStatFile();\r
+\r
+ ChunkHolder ch = ProgressGetter.pull(statFile, 0);\r
+ assertEquals(PulledFileCache.getSize(), 1); // Still one as job has been\r
+ // retrieved from cache\r
+ ChunkHolder ch2 = ProgressGetter\r
+ .pull(statFile2, 0, 5, TimeUnit.SECONDS); // 5\r
+ // second delay\r
+ assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
+\r
+ // Pull the first job completely\r
+ while (ch == null) {\r
+ ch = ProgressGetter.pull(statFile, 0);\r
+ }\r
+ String chunk = "";\r
+ long pos = 0;\r
+ do {\r
+ chunk = ch.getChunk();\r
+ assertNotNull(chunk);\r
+ pos = ch.getNextPosition();\r
+ ch = ProgressGetter.pull(statFile, pos);\r
+ } while (chunk.length() > 0);\r
+\r
+ try {\r
+ Thread.sleep(1000 * 6);\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ // Elements are removed on put operation only\r
+ assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
+ ChunkHolder ch3 = ProgressGetter.pull(statFile3, 0);\r
+ // Now old element was removed, but new added, thus size remains\r
+ // constant\r
+ assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
+\r
+ }\r
+\r
+ @Test\r
+ public void testGet() {\r
+\r
+ FilePuller pp = FilePuller\r
+ .newProgressPuller(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + "percentProgress.txt");\r
+ try {\r
+ assertEquals(pp.getProgress(), 12);\r
+ pp.disconnect();\r
+ } catch (NumberFormatException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / proteocache.git / blobdiff