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         private static PresetManager<Mafft> getPresets() {\r
 146                 Preset<Mafft> preset1 = new Preset<Mafft>();\r
 147                 preset1.name = "L-INS-i (Accuracy-oriented)";\r
 148                 preset1.description = "dsfjkg fdjksghkjsgdfh jksdfg sdfgkjhsdfgk kjsdfg ";\r
 149 \r
 150                 List<String> optionNames = new ArrayList<String>();\r
 151                 optionNames.add("--localpair");\r
 152                 optionNames.add("--maxiterate 1000");\r
 153                 preset1.option = optionNames;\r
 154                 PresetManager<Mafft> prman = new PresetManager<Mafft>();\r
 155                 prman.preset = Collections.singletonList(preset1);\r
 156                 prman.runnerClassName = Mafft.class.getCanonicalName();\r
 157 \r
 158                 return prman;\r
 159         }\r
 160 }\r