testsrc/compbio/metadata/OptionMarshallerTester.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.AssertJUnit.assertEquals;\r
  22 import static org.testng.AssertJUnit.assertFalse;\r
  23 import static org.testng.AssertJUnit.assertNotNull;\r
  24 import static org.testng.AssertJUnit.assertTrue;\r
  25 import static org.testng.AssertJUnit.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.FileOutputStream;\r
  31 import java.io.IOException;\r
  32 import java.net.MalformedURLException;\r
  33 import java.net.URL;\r
  34 import java.util.ArrayList;\r
  35 import java.util.List;\r
  36 \r
  37 import javax.xml.bind.JAXBContext;\r
  38 import javax.xml.bind.JAXBElement;\r
  39 import javax.xml.bind.JAXBException;\r
  40 import javax.xml.bind.Unmarshaller;\r
  41 import javax.xml.transform.stream.StreamSource;\r
  42 \r
  43 import org.testng.annotations.BeforeMethod;\r
  44 import org.testng.annotations.Test;\r
  45 import org.xml.sax.SAXException;\r
  46 \r
  47 import compbio.engine.conf.RunnerConfigMarshaller;\r
  48 import compbio.runner.msa.Mafft;\r
  49 \r
  50 public class OptionMarshallerTester {\r
  51 \r
  52     public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  53             + "MafftParameters.xml";\r
  54     public static String test_schema_output = "NextGenMafftOptionsSchema.xml";\r
  55     public static String test_output = "MafftOptions.xml.out";\r
  56     public static String reWrittenInput = AllTestSuit.OUTPUT_DIR_ABSOLUTE\r
  57             + "rewrittenMafftParams.xml";\r
  58 \r
  59     RunnerConfig<Mafft> rconfig = null;\r
  60     Option<Mafft> matrixParam = null;\r
  61 \r
  62     @BeforeMethod()\r
  63     public void setup() {\r
  64         // write some parameters programmatically\r
  65         try {\r
  66             rconfig = new RunnerConfig<Mafft>();\r
  67             rconfig.setRunnerClassName(Mafft.class.getName());\r
  68             List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
  69 \r
  70             Parameter<Mafft> p1 = new Parameter<Mafft>("Type",\r
  71                     "Type of the sequence (PROTEIN or DNA)");\r
  72             // TODO publish help on a compbio web site\r
  73 \r
  74             p1.setFurtherDetails(new URL("http",\r
  75                     "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
  76                     "Index.html"));\r
  77             p1.addPossibleValues("PROTEIN", "DNA");\r
  78             p1.setOptionName("-TYPE");\r
  79             p1.setRequired(false);\r
  80 \r
  81             /*\r
  82              * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
  83              * filename\r
  84              */\r
  85             Option<Mafft> p2 = new Option<Mafft>("MATRIX",\r
  86                     "Protein weight matrix");\r
  87             // TODO publish help on a compbio web site\r
  88 \r
  89             p2.setFurtherDetails(new URL("http",\r
  90                     "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
  91                     "Index.html"));\r
  92 \r
  93             p2.addOptionNames("-jtree");\r
  94             p2.addOptionNames("-jfasta");\r
  95             p2.setRequired(false);\r
  96 \r
  97             Parameter<Mafft> p3 = new Parameter<Mafft>("MATRIX2",\r
  98                     "Protein weight matrix");\r
  99             // TODO publish help on a compbio web site\r
 100             p3.setFurtherDetails(new URL("http",\r
 101                     "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 102                     "Index.html"));\r
 103 \r
 104             p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
 105             // This attribute is required by strict schema\r
 106             p3.setOptionName("-MATRIX");\r
 107             p3.setRequired(true);\r
 108             p3.setDefaultValue("id");\r
 109             ValueConstrain vc = new ValueConstrain();\r
 110             vc.setType(ValueConstrain.Type.Float);\r
 111             vc.setMin("-10.12");\r
 112             vc.setMax("0");\r
 113             p3.setValidValue(vc);\r
 114 \r
 115             prms.add(p1);\r
 116             prms.add(p2);\r
 117             prms.add(p3);\r
 118             matrixParam = p2;\r
 119             rconfig.setOptions(prms);\r
 120 \r
 121         } catch (MalformedURLException e) {\r
 122             e.printStackTrace();\r
 123             fail(e.getLocalizedMessage());\r
 124         } catch (WrongParameterException e) {\r
 125             e.printStackTrace();\r
 126             fail(e.getLocalizedMessage());\r
 127         }\r
 128     }\r
 129 \r
 130     @Test(expectedExceptions = { javax.xml.bind.MarshalException.class })\r
 131     public void testMarshalling() throws JAXBException {\r
 132 \r
 133         File outfile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_output);\r
 134         try {\r
 135             RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(\r
 136                     RunnerConfig.class);\r
 137 \r
 138             // This throws an exception\r
 139             // I am not sure why\r
 140             rmarsh.writeAndValidate(rconfig,\r
 141                     AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
 142                             + "RunnerConfigSchema.xsd", new FileOutputStream(\r
 143                             outfile));\r
 144 \r
 145         } catch (FileNotFoundException e) {\r
 146             e.printStackTrace();\r
 147             fail(e.getLocalizedMessage());\r
 148         } catch (IOException e) {\r
 149             e.printStackTrace();\r
 150             fail(e.getLocalizedMessage());\r
 151         } catch (SAXException e) {\r
 152             e.printStackTrace();\r
 153             fail(e.getLocalizedMessage());\r
 154         }\r
 155         assertTrue("Output file expected, but nothing found!", outfile.exists());\r
 156         // outfile.delete();\r
 157     }\r
 158 \r
 159     @Test()\r
 160     public void testUnMarshalling() {\r
 161         try {\r
 162             File input = new File(this.test_input);\r
 163             assertTrue(input.exists());\r
 164             JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
 165             Unmarshaller um = ctx.createUnmarshaller();\r
 166             JAXBElement<RunnerConfig> rconfig = um.unmarshal(new StreamSource(\r
 167                     input), RunnerConfig.class);\r
 168             RunnerConfig<Mafft> runner = rconfig.getValue();\r
 169             assertNotNull(runner);\r
 170             System.out.println(runner);\r
 171             assertFalse(runner.options.isEmpty());\r
 172             assertFalse(runner.parameters.isEmpty());\r
 173             assertEquals(7, runner.options.size());\r
 174             assertEquals(8, runner.parameters.size());\r
 175             Option<Mafft> stypeOption = runner.getArgument("Sequence type");\r
 176             System.out.println(stypeOption);\r
 177             assertNotNull(stypeOption);\r
 178             assertFalse(stypeOption.isRequired);\r
 179             assertEquals("--auto", stypeOption.defaultValue);\r
 180             assertEquals(2, stypeOption.optionNames.size());\r
 181 \r
 182             assertEquals(" ", runner.getPrmSeparator());\r
 183             Option<Mafft> guidetrOption = runner\r
 184                     .getArgument("Guide tree rebuild");\r
 185             Parameter<Mafft> guidetr = (Parameter<Mafft>) guidetrOption;\r
 186             ValueConstrain constraint = guidetr.getValidValue();\r
 187             assertEquals("Integer", constraint.type.toString());\r
 188             assertEquals(1, constraint.getMin());\r
 189             assertEquals(100, constraint.getMax());\r
 190 \r
 191             RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(\r
 192                     RunnerConfig.class);\r
 193             // Now see if we can write a valid document back discard the actual\r
 194             // output only validation is important here\r
 195             rmarsh.write(rconfig,\r
 196                     new FileOutputStream(new File(reWrittenInput)));\r
 197 \r
 198             RunnerConfig<Mafft> rc = rmarsh.readAndValidate(\r
 199                     new FileInputStream(new File(reWrittenInput)),\r
 200                     RunnerConfig.class);\r
 201             assertEquals(runner, rc);\r
 202 \r
 203         } catch (JAXBException e) {\r
 204             e.printStackTrace();\r
 205             fail(e.getLocalizedMessage());\r
 206         } catch (IOException e) {\r
 207             e.printStackTrace();\r
 208             fail(e.getLocalizedMessage());\r
 209         } catch (SAXException e) {\r
 210             e.printStackTrace();\r
 211             fail(e.getLocalizedMessage());\r
 212         }\r
 213     }\r
 214 }\r