testsrc/compbio/metadata/PresetTester.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.metadata;\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.assertNotNull;\r
  24 import static org.testng.Assert.assertTrue;\r
  25 import static org.testng.Assert.fail;\r
  26 \r
  27 import java.io.File;\r
  28 import java.io.FileInputStream;\r
  29 import java.io.FileNotFoundException;\r
  30 import java.io.IOException;\r
  31 import java.util.ArrayList;\r
  32 import java.util.Collections;\r
  33 import java.util.List;\r
  34 \r
  35 import javax.xml.bind.JAXBContext;\r
  36 import javax.xml.bind.JAXBElement;\r
  37 import javax.xml.bind.JAXBException;\r
  38 import javax.xml.bind.Unmarshaller;\r
  39 import javax.xml.transform.stream.StreamSource;\r
  40 \r
  41 import org.testng.annotations.BeforeTest;\r
  42 import org.testng.annotations.Test;\r
  43 import org.xml.sax.SAXException;\r
  44 \r
  45 import compbio.engine.conf.RunnerConfigMarshaller;\r
  46 import compbio.runner.msa.Mafft;\r
  47 \r
  48 public class PresetTester {\r
  49 \r
  50     public static final String input = AllTestSuit.TEST_DATA_PATH\r
  51             + "MafftPresets.xml";\r
  52     public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  53             + "MafftParameters.xml";\r
  54 \r
  55     PresetManager<Mafft> presets = null;\r
  56     RunnerConfig<Mafft> rconfParams = null;\r
  57 \r
  58     @BeforeTest(enabled = true)\r
  59     public void loadPresets() {\r
  60         try {\r
  61             // Load Preset definitions\r
  62             RunnerConfigMarshaller<Mafft> rconfigPresets = new RunnerConfigMarshaller<Mafft>(\r
  63                     PresetManager.class);\r
  64             File infile = new File(input);\r
  65             assertTrue(infile.exists());\r
  66             presets = rconfigPresets.read(new FileInputStream(infile),\r
  67                     PresetManager.class);\r
  68             assertNotNull(presets);\r
  69             assertFalse(presets.preset.isEmpty());\r
  70 \r
  71             // Load Parameters definitions\r
  72             File input = new File(this.test_input);\r
  73             assertTrue(input.exists());\r
  74             JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
  75             Unmarshaller um = ctx.createUnmarshaller();\r
  76             JAXBElement<RunnerConfig> rconfigParams = um.unmarshal(\r
  77                     new StreamSource(input), RunnerConfig.class);\r
  78             rconfParams = rconfigParams.getValue();\r
  79             assertNotNull(rconfParams);\r
  80 \r
  81         } catch (JAXBException e) {\r
  82             e.printStackTrace();\r
  83             fail(e.getMessage());\r
  84         } catch (FileNotFoundException e) {\r
  85             e.printStackTrace();\r
  86             fail(e.getMessage());\r
  87         }\r
  88     }\r
  89 \r
  90     @Test\r
  91     public void marshallPreset() {\r
  92         try {\r
  93             RunnerConfigMarshaller<Mafft> rconfig = new RunnerConfigMarshaller<Mafft>(\r
  94                     PresetManager.class);\r
  95             PresetManager<Mafft> pman = getPresets();\r
  96             assertNotNull(pman);\r
  97             rconfig.readAndValidate(new FileInputStream(new File(input)),\r
  98                     PresetManager.class);\r
  99         } catch (JAXBException e) {\r
 100             e.printStackTrace();\r
 101             fail(e.getMessage());\r
 102         } catch (IOException e) {\r
 103             e.printStackTrace();\r
 104             fail(e.getMessage());\r
 105         } catch (SAXException e) {\r
 106             e.printStackTrace();\r
 107             fail(e.getMessage());\r
 108         }\r
 109     }\r
 110 \r
 111     @Test\r
 112     public void validatePresets() {\r
 113         assertNotNull(presets);\r
 114         assertEquals(presets.getPresets().size(), 6);\r
 115         try {\r
 116             for (Preset<Mafft> pr : presets.getPresets()) {\r
 117                 List<Option<Mafft>> options;\r
 118                 options = pr.getArguments(rconfParams);\r
 119                 assertFalse(options.isEmpty());\r
 120                 if (pr.name.equals("L-INS-i (Accuracy-oriented)")) {\r
 121                     assertEquals(options.size(), 2);\r
 122                     Option<Mafft> o = options.get(0);\r
 123                     if (o.name.equals("Pairwise alignment computation method")) {\r
 124                         List<String> onames = o.getOptionNames();\r
 125                         boolean match = false;\r
 126                         for (String oname : onames) {\r
 127                             if (oname.equals("--localpair")) {\r
 128                                 match = true;\r
 129                                 break;\r
 130                             }\r
 131                         }\r
 132                         assertTrue(match);\r
 133                     }\r
 134                 }\r
 135                 if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {\r
 136                     assertEquals(options.size(), 4);\r
 137                 }\r
 138             }\r
 139         } catch (WrongParameterException e) {\r
 140             e.printStackTrace();\r
 141             fail(e.getMessage());\r
 142         }\r
 143     }\r
 144 \r
 145     @Test\r
 146     public void testPresetWithMuptiOptions() {\r
 147         assertNotNull(presets);\r
 148         assertEquals(presets.getPresets().size(), 6);\r
 149         try {\r
 150             for (Preset<Mafft> pr : presets.getPresets()) {\r
 151                 List<Option<Mafft>> options;\r
 152                 options = pr.getArguments(rconfParams);\r
 153                 assertFalse(options.isEmpty());\r
 154                 if (pr.name.equals("E-INS-i (Accuracy-oriented)")) {\r
 155                     assertEquals(options.size(), 3);\r
 156                     Option<Mafft> o = options.get(0);\r
 157                     if (o.name.equals("Pairwise alignment computation method")) {\r
 158                         List<String> onames = o.getOptionNames();\r
 159                         boolean match = false;\r
 160                         for (String oname : onames) {\r
 161                             if (oname.equals("--genafpair")) {\r
 162                                 match = true;\r
 163                                 break;\r
 164                             }\r
 165                         }\r
 166                         assertTrue(match);\r
 167                     }\r
 168                 }\r
 169                 if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {\r
 170                     assertEquals(options.size(), 4);\r
 171                 }\r
 172             }\r
 173         } catch (WrongParameterException e) {\r
 174             e.printStackTrace();\r
 175             fail(e.getMessage());\r
 176         }\r
 177     }\r
 178 \r
 179     private static PresetManager<Mafft> getPresets() {\r
 180         Preset<Mafft> preset1 = new Preset<Mafft>();\r
 181         preset1.name = "L-INS-i (Accuracy-oriented)";\r
 182         preset1.description = "dsfjkg fdjksghkjsgdfh jksdfg sdfgkjhsdfgk kjsdfg ";\r
 183 \r
 184         List<String> optionNames = new ArrayList<String>();\r
 185         optionNames.add("--localpair");\r
 186         optionNames.add("--maxiterate 1000");\r
 187         preset1.option = optionNames;\r
 188         PresetManager<Mafft> prman = new PresetManager<Mafft>();\r
 189         prman.preset = Collections.singletonList(preset1);\r
 190         prman.runnerClassName = Mafft.class.getCanonicalName();\r
 191 \r
 192         return prman;\r
 193     }\r
 194 }\r