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("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  75             p1.addPossibleValues("PROTEIN", "DNA");\r
  76             p1.setOptionName("-TYPE");\r
  77             p1.setRequired(false);\r
  78 \r
  79             /*\r
  80              * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
  81              * filename\r
  82              */\r
  83             Option<Mafft> p2 = new Option<Mafft>("MATRIX",\r
  84                     "Protein weight matrix");\r
  85             // TODO publish help on a compbio web site\r
  86 \r
  87             p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  88 \r
  89             p2.addOptionNames("-jtree");\r
  90             p2.addOptionNames("-jfasta");\r
  91             p2.setRequired(false);\r
  92 \r
  93             Parameter<Mafft> p3 = new Parameter<Mafft>("MATRIX2",\r
  94                     "Protein weight matrix");\r
  95             // TODO publish help on a compbio web site\r
  96             p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  97 \r
  98             p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
  99             // This attribute is required by strict schema\r
 100             p3.setOptionName("-MATRIX");\r
 101             p3.setRequired(true);\r
 102             p3.setDefaultValue("id");\r
 103             ValueConstrain vc = new ValueConstrain();\r
 104             vc.setType(ValueConstrain.Type.Float);\r
 105             vc.setMin("-10.12");\r
 106             vc.setMax("0");\r
 107             p3.setValidValue(vc);\r
 108 \r
 109             prms.add(p1);\r
 110             prms.add(p2);\r
 111             prms.add(p3);\r
 112             matrixParam = p2;\r
 113             rconfig.setOptions(prms);\r
 114 \r
 115         } catch (MalformedURLException e) {\r
 116             e.printStackTrace();\r
 117             fail(e.getLocalizedMessage());\r
 118         } catch (WrongParameterException e) {\r
 119             e.printStackTrace();\r
 120             fail(e.getLocalizedMessage());\r
 121         }\r
 122     }\r
 123 \r
 124     @Test(expectedExceptions = { javax.xml.bind.MarshalException.class })\r
 125     public void testMarshalling() throws JAXBException {\r
 126 \r
 127         File outfile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_output);\r
 128         try {\r
 129             RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(\r
 130                     RunnerConfig.class);\r
 131 \r
 132             // This throws an exception\r
 133             // I am not sure why\r
 134             rmarsh.writeAndValidate(rconfig,\r
 135                     AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
 136                             + "RunnerConfigSchema.xsd", new FileOutputStream(\r
 137                             outfile));\r
 138 \r
 139         } catch (FileNotFoundException e) {\r
 140             e.printStackTrace();\r
 141             fail(e.getLocalizedMessage());\r
 142         } catch (IOException e) {\r
 143             e.printStackTrace();\r
 144             fail(e.getLocalizedMessage());\r
 145         } catch (SAXException e) {\r
 146             e.printStackTrace();\r
 147             fail(e.getLocalizedMessage());\r
 148         }\r
 149         assertTrue("Output file expected, but nothing found!", outfile.exists());\r
 150         // outfile.delete();\r
 151     }\r
 152 \r
 153     @Test()\r
 154     public void testUnMarshalling() {\r
 155         try {\r
 156                 File input = new File(this.test_input);\r
 157                 assertTrue(input.exists());\r
 158                 JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
 159                 Unmarshaller um = ctx.createUnmarshaller();\r
 160                 JAXBElement<RunnerConfig> rconfig = um.unmarshal(new StreamSource(input), RunnerConfig.class);\r
 161                 RunnerConfig<Mafft> runner = rconfig.getValue();\r
 162                 assertNotNull(runner);\r
 163                 System.out.println(runner);\r
 164                 assertFalse(runner.options.isEmpty());\r
 165                 assertFalse(runner.parameters.isEmpty());\r
 166                 assertEquals(7, runner.options.size());\r
 167                 assertEquals(8, runner.parameters.size());\r
 168                 Option<Mafft> stypeOption = runner.getArgument("Sequence type");\r
 169                 System.out.println(stypeOption);\r
 170                 assertNotNull(stypeOption);\r
 171                 assertFalse(stypeOption.isRequired);\r
 172                 assertEquals("--auto", stypeOption.defaultValue);\r
 173                 assertEquals(2, stypeOption.optionNames.size());\r
 174 \r
 175                 assertEquals(" ", runner.getPrmSeparator());\r
 176                 Option<Mafft> guidetrOption = runner.getArgument("Guide tree rebuild");\r
 177                 Parameter<Mafft> guidetr = (Parameter<Mafft>) guidetrOption;\r
 178                 ValueConstrain constraint = guidetr.getValidValue();\r
 179                 assertEquals("Integer", constraint.type.toString());\r
 180                 assertEquals(1, constraint.getMin());\r
 181                 assertEquals(100, constraint.getMax());\r
 182 \r
 183                 RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class);\r
 184                 // Now see if we can write a valid document back discard the actual\r
 185                 // output only validation is important here\r
 186                 rmarsh.write(rconfig, new FileOutputStream(new File(reWrittenInput)));\r
 187                 RunnerConfig<Mafft> rc = rmarsh.readAndValidate(new FileInputStream(new File(reWrittenInput)), RunnerConfig.class);\r
 188                 assertEquals(runner, rc);\r
 189 \r
 190         } catch (JAXBException e) {\r
 191                 e.printStackTrace();\r
 192                 fail(e.getLocalizedMessage());\r
 193         } catch (IOException e) {\r
 194                 e.printStackTrace();\r
 195                 fail(e.getLocalizedMessage());\r
 196         } catch (SAXException e) {\r
 197                 e.printStackTrace();\r
 198                 fail(e.getLocalizedMessage());\r
 199         }\r
 200     }\r
 201 }\r