testsrc/compbio/engine/FilePullerTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.engine;\r
  20 \r
  21 import static org.testng.Assert.assertEquals;\r
  22 import static org.testng.Assert.assertNotNull;\r
  23 import static org.testng.Assert.fail;\r
  24 \r
  25 import java.io.File;\r
  26 import java.io.IOException;\r
  27 import java.util.concurrent.TimeUnit;\r
  28 \r
  29 import org.testng.annotations.BeforeTest;\r
  30 import org.testng.annotations.Test;\r
  31 \r
  32 import compbio.engine.client.ConfiguredExecutable;\r
  33 import compbio.engine.client.Executable;\r
  34 import compbio.engine.local.AsyncLocalRunner;\r
  35 import compbio.metadata.AllTestSuit;\r
  36 import compbio.metadata.ChunkHolder;\r
  37 import compbio.metadata.JobSubmissionException;\r
  38 import compbio.metadata.ResultNotAvailableException;\r
  39 import compbio.runner.msa.ClustalW;\r
  40 import compbio.runner.msa.Muscle;\r
  41 \r
  42 public class FilePullerTester {\r
  43 \r
  44         public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  45                         + "TO1381.fasta";\r
  46 \r
  47         String jobId;\r
  48         String jobId2;\r
  49         String jobId3;\r
  50 \r
  51         @BeforeTest(alwaysRun = true)\r
  52         public void init() {\r
  53                 ClustalW clustal = new ClustalW();\r
  54                 clustal.setInput(test_input);\r
  55                 Muscle ms = new Muscle().setInput(test_input);\r
  56                 Muscle ms2 = new Muscle().setInput(test_input);\r
  57 \r
  58                 try {\r
  59                         // For local execution use relavive\r
  60                         ConfiguredExecutable<ClustalW> confClustal = Configurator\r
  61                                         .configureExecutable(clustal, Executable.ExecProvider.Local);\r
  62                         ConfiguredExecutable<Muscle> confms = Configurator\r
  63                                         .configureExecutable(ms, Executable.ExecProvider.Local);\r
  64 \r
  65                         ConfiguredExecutable<Muscle> confms2 = Configurator\r
  66                                         .configureExecutable(ms2, Executable.ExecProvider.Local);\r
  67 \r
  68                         AsyncLocalRunner as = new AsyncLocalRunner();\r
  69                         jobId = as.submitJob(confClustal);\r
  70                         jobId2 = as.submitJob(confms);\r
  71                         jobId3 = as.submitJob(confms2);\r
  72 \r
  73                         ConfiguredExecutable<?> al = as.getResults(jobId);\r
  74                         ConfiguredExecutable<?> al2 = as.getResults(jobId2);\r
  75                         ConfiguredExecutable<?> al3 = as.getResults(jobId3);\r
  76                         assertNotNull(al);\r
  77                         assertNotNull(al2);\r
  78                         assertNotNull(al3);\r
  79                 } catch (JobSubmissionException e) {\r
  80                         e.printStackTrace();\r
  81                         fail(e.getLocalizedMessage());\r
  82                 } catch (ResultNotAvailableException e) {\r
  83                         e.printStackTrace();\r
  84                         fail(e.getLocalizedMessage());\r
  85                 }\r
  86         }\r
  87 \r
  88         @Test(groups = { AllTestSuit.test_group_engine })\r
  89         public void testPull() {\r
  90                 assertNotNull(jobId, "init() method failed!");\r
  91                 String workDir = Configurator.getWorkDirectory(jobId);\r
  92                 String statFile = workDir + File.separator + ClustalW.getStatFile();\r
  93 \r
  94                 ChunkHolder ch = ProgressGetter.pull(statFile, 0);\r
  95                 while (ch == null) {\r
  96                         ch = ProgressGetter.pull(statFile, 0);\r
  97                 }\r
  98                 String chunk = "";\r
  99                 long pos = 0;\r
 100                 do {\r
 101                         chunk = ch.getChunk();\r
 102                         assertNotNull(chunk);\r
 103                         pos = ch.getNextPosition();\r
 104                         ch = ProgressGetter.pull(statFile, pos);\r
 105                 } while (chunk.length() > 0);\r
 106 \r
 107                 // All consequent pulls just return empty chunk and same position =\r
 108                 // file.length\r
 109                 ch = ProgressGetter.pull(statFile, pos);\r
 110                 assertNotNull(ch);\r
 111                 assertEquals(ch.getChunk().length(), 0);\r
 112                 // Output file size depends on the operation system fs!\r
 113                 // assertEquals(ch.getNextPosition(), 668);\r
 114 \r
 115                 ch = ProgressGetter.pull(statFile, pos);\r
 116                 assertNotNull(ch);\r
 117                 assertEquals(ch.getChunk().length(), 0);\r
 118                 // Output file size depends on the operation system and fs!\r
 119                 // assertEquals(ch.getNextPosition(), 668);\r
 120 \r
 121         }\r
 122 \r
 123         @Test(groups = { AllTestSuit.test_group_engine })\r
 124         public void testGetDelay() {\r
 125                 FilePuller fp = FilePuller.newFilePuller(Configurator\r
 126                                 .getWorkDirectory(jobId)\r
 127                                 + File.separator + "stat.log", 256);\r
 128                 // default delay is 5 minutes\r
 129                 assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 5 * 60);\r
 130                 long d = 1000 * 1000 * 1000L * 60; // 1m in nanoseconds\r
 131                 fp.setDelay(d, TimeUnit.NANOSECONDS);\r
 132                 assertEquals(fp.getDelayValue(TimeUnit.NANOSECONDS), d);\r
 133                 assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 60);\r
 134                 assertEquals(fp.getDelayValue(TimeUnit.MINUTES), 1);\r
 135         }\r
 136 \r
 137         @Test(groups = { AllTestSuit.test_group_engine }, dependsOnMethods = { "testPull" })\r
 138         public void testCache() {\r
 139                 assertNotNull(jobId, "init() method failed!");\r
 140                 assertNotNull(jobId2, "init() method failed!");\r
 141                 assertEquals(PulledFileCache.getSize(), 1); // One is from previous test\r
 142 \r
 143                 String statFile = Configurator.getWorkDirectory(jobId) + File.separator\r
 144                                 + ClustalW.getStatFile();\r
 145                 String statFile2 = Configurator.getWorkDirectory(jobId2)\r
 146                                 + File.separator + Muscle.getStatFile();\r
 147                 String statFile3 = Configurator.getWorkDirectory(jobId3)\r
 148                                 + File.separator + Muscle.getStatFile();\r
 149 \r
 150                 ChunkHolder ch = ProgressGetter.pull(statFile, 0);\r
 151                 assertEquals(PulledFileCache.getSize(), 1); // Still one as job has been\r
 152                 // retrieved from cache\r
 153                 ChunkHolder ch2 = ProgressGetter\r
 154                                 .pull(statFile2, 0, 5, TimeUnit.SECONDS); // 5\r
 155                 // second delay\r
 156                 assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
 157 \r
 158                 // Pull the first job completely\r
 159                 while (ch == null) {\r
 160                         ch = ProgressGetter.pull(statFile, 0);\r
 161                 }\r
 162                 String chunk = "";\r
 163                 long pos = 0;\r
 164                 do {\r
 165                         chunk = ch.getChunk();\r
 166                         assertNotNull(chunk);\r
 167                         pos = ch.getNextPosition();\r
 168                         ch = ProgressGetter.pull(statFile, pos);\r
 169                 } while (chunk.length() > 0);\r
 170 \r
 171                 try {\r
 172                         Thread.sleep(1000 * 6);\r
 173                 } catch (InterruptedException e) {\r
 174                         e.printStackTrace();\r
 175                         fail(e.getMessage());\r
 176                 }\r
 177                 // Elements are removed on put operation only\r
 178                 assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
 179                 ChunkHolder ch3 = ProgressGetter.pull(statFile3, 0);\r
 180                 // Now old element was removed, but new added, thus size remains\r
 181                 // constant\r
 182                 assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
 183 \r
 184         }\r
 185 \r
 186         @Test\r
 187         public void testGet() {\r
 188 \r
 189                 FilePuller pp = FilePuller\r
 190                                 .newProgressPuller(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
 191                                                 + "percentProgress.txt");\r
 192                 try {\r
 193                         assertEquals(pp.getProgress(), 12);\r
 194                         pp.disconnect();\r
 195                 } catch (NumberFormatException e) {\r
 196                         e.printStackTrace();\r
 197                         fail(e.getMessage());\r
 198                 } catch (IOException e) {\r
 199                         e.printStackTrace();\r
 200                         fail(e.getMessage());\r
 201                 }\r
 202         }\r
 203 }\r