testsrc/compbio/engine/client/CommandBuilderTester.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.client;\r
  20 \r
  21 import static org.testng.Assert.assertEquals;\r
  22 import static org.testng.Assert.assertFalse;\r
  23 import static org.testng.Assert.assertNotSame;\r
  24 import static org.testng.Assert.assertTrue;\r
  25 import static org.testng.Assert.fail;\r
  26 \r
  27 import java.io.FileNotFoundException;\r
  28 import java.io.IOException;\r
  29 import java.util.Arrays;\r
  30 import java.util.List;\r
  31 \r
  32 import org.testng.annotations.Test;\r
  33 \r
  34 import compbio.metadata.RunnerConfig;\r
  35 import compbio.runner.msa.ClustalW;\r
  36 import compbio.runner.msa.Mafft;\r
  37 import compbio.runner.msa.Muscle;\r
  38 \r
  39 public class CommandBuilderTester {\r
  40 \r
  41         @Test()\r
  42         public void testCommandBuilding() {\r
  43                 CommandBuilder<ClustalW> builder = new CommandBuilder<ClustalW>("=");\r
  44                 builder.setParam("-MATRIX", "blosum65");\r
  45                 assertTrue(builder.getCommands().size() == 1);\r
  46                 String p = builder.getParamValue("-MATRIX");\r
  47                 builder.setParam("-clustalw");\r
  48                 builder.setParam("-in", "\\gile\\path\\abs.txt");\r
  49                 System.out.println(builder.getCommands());\r
  50                 assertTrue(builder.getCommands().size() == 3);\r
  51                 builder.setParam("-stat=/test.log");\r
  52                 assertTrue(builder.getCommands().size() == 4);\r
  53                 System.out.println("CP:" + builder.getCommands());\r
  54                 assertTrue(builder.setParam("-stat=/newtest.log"));\r
  55 \r
  56                 List<String> clist = Arrays.asList("-prop", "-tree=treefile.txt",\r
  57                                 "-clustalw");\r
  58                 builder.addParams(clist);\r
  59                 assertTrue(builder.size() == 6);\r
  60                 builder.setParams(clist);\r
  61                 assertTrue(builder.size() == 3);\r
  62                 System.out.println("CP:" + builder.getCommands());\r
  63                 String option = "-log=error.txt";\r
  64                 builder.setFirst(option);\r
  65                 assertEquals(builder.getCommands().get(0), option);\r
  66                 builder.setParam("-newParam2");\r
  67                 assertEquals(builder.getCommands().get(0), option);\r
  68                 builder.setLast(option);\r
  69                 assertNotSame(builder.getCommands().get(0), option);\r
  70                 assertEquals(builder.getCommands().get(builder.size() - 1), option);\r
  71                 builder.setParam("-newParam3");\r
  72                 assertEquals(builder.getCommands().get(builder.size() - 1), option);\r
  73                 builder.setParam("-prm5", "prm5Value");\r
  74                 assertTrue(builder.hasParam("-prm5"));\r
  75         }\r
  76 \r
  77         @Test\r
  78         public void testSpaceDelimiterExecutable() {\r
  79                 CommandBuilder<Muscle> cbuilder = new CommandBuilder<Muscle>(" ");\r
  80                 cbuilder.addParams(Arrays.asList("-clwstrict", "-quiet", "-verbose",\r
  81                                 "-log", "EXEC_STAT_FILE"));\r
  82         }\r
  83 \r
  84         @Test\r
  85         public void testOptionsToCommand() {\r
  86                 try {\r
  87                         RunnerConfig<Mafft> rconf = ConfExecutable\r
  88                                         .getRunnerOptions(Mafft.class);\r
  89                         CommandBuilder<Mafft> cbuilder = CommandBuilder.newCommandBuilder(\r
  90                                         rconf.getArguments(), Mafft.KEY_VALUE_SEPARATOR);\r
  91                         String comm = "";\r
  92                         for (String val : cbuilder.getCommands()) {\r
  93                                 assertFalse(val.contains(cbuilder.nameValueSeparator));\r
  94                                 comm += val + cbuilder.nameValueSeparator;\r
  95                         }\r
  96                         assertEquals(cbuilder.getCommandString(), comm);\r
  97                 } catch (FileNotFoundException e) {\r
  98                         e.printStackTrace();\r
  99                         fail(e.getLocalizedMessage());\r
 100                 } catch (IOException e) {\r
 101                         e.printStackTrace();\r
 102                         fail(e.getLocalizedMessage());\r
 103                 }\r
 104 \r
 105         }\r
 106 }\r