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