testsrc/compbio/engine/conf/RunnerConfigMarshallerTester.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.engine.conf;\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.ByteArrayOutputStream;\r
  28 import java.io.File;\r
  29 import java.io.FileInputStream;\r
  30 import java.io.FileNotFoundException;\r
  31 import java.io.FileOutputStream;\r
  32 import java.io.IOException;\r
  33 import java.net.MalformedURLException;\r
  34 import java.net.URL;\r
  35 import java.util.ArrayList;\r
  36 import java.util.List;\r
  37 \r
  38 import javax.xml.bind.JAXBException;\r
  39 import javax.xml.validation.Schema;\r
  40 import javax.xml.validation.Validator;\r
  41 \r
  42 import org.testng.annotations.BeforeMethod;\r
  43 import org.testng.annotations.Test;\r
  44 import org.xml.sax.SAXException;\r
  45 \r
  46 import compbio.metadata.AllTestSuit;\r
  47 import compbio.metadata.Option;\r
  48 import compbio.metadata.Parameter;\r
  49 import compbio.metadata.RunnerConfig;\r
  50 import compbio.metadata.ValueConstrain;\r
  51 import compbio.metadata.WrongParameterException;\r
  52 import compbio.runner.msa.Mafft;\r
  53 \r
  54 public class RunnerConfigMarshallerTester {\r
  55 \r
  56     public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  57             + "MafftParameters.xml";\r
  58     public static String test_schema_output = "RunnerConfigSchema.xml";\r
  59     public static String test_output = AllTestSuit.OUTPUT_DIR_ABSOLUTE\r
  60             + "MafftParameters.out.xml";\r
  61 \r
  62     public static String invalidDoc = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  63             + "InvalidMafftParameters.xml";\r
  64 \r
  65     RunnerConfig<Mafft> rconfig = null;\r
  66     Parameter<Mafft> matrixParam = null;\r
  67     RunnerConfigMarshaller<Mafft> pmarshaller = null;\r
  68 \r
  69     @BeforeMethod\r
  70     public void setup() {\r
  71         // write some parameters programmatically\r
  72         try {\r
  73             rconfig = new RunnerConfig<Mafft>();\r
  74             rconfig.setRunnerClassName(Mafft.class.getName());\r
  75             List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
  76 \r
  77             Parameter<Mafft> p1 = new Parameter<Mafft>("Type",\r
  78                     "Type of the sequence (PROTEIN or DNA)");\r
  79             // TODO publish help on a compbio web site\r
  80 \r
  81             p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  82             p1.addPossibleValues("PROTEIN", "DNA");\r
  83             p1.setOptionName("-TYPE");\r
  84             p1.setRequired(false);\r
  85 \r
  86             /*\r
  87              * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
  88              * filename\r
  89              */\r
  90             Option<Mafft> p2 = new Option<Mafft>("MATRIX",\r
  91                     "Protein weight matrix");\r
  92             // TODO publish help on a compbio web site\r
  93 \r
  94             p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  95 \r
  96             p2.addOptionNames("-jtree"); // "-retree"\r
  97             p2.setRequired(false);\r
  98 \r
  99             Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
 100                     "Protein weight matrix");\r
 101             // TODO publish help on a compbio web site\r
 102             p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/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("--AAMATRIX");\r
 107             p3.setRequired(true);\r
 108             p3.setDefaultValue("pam");\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 = p3;\r
 119             rconfig.setOptions(prms);\r
 120 \r
 121             pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class,\r
 122                     Parameter.class, Option.class, ValueConstrain.class);\r
 123         } catch (MalformedURLException e) {\r
 124             e.printStackTrace();\r
 125             fail(e.getLocalizedMessage());\r
 126         } catch (JAXBException e) {\r
 127             e.printStackTrace();\r
 128             fail(e.getLocalizedMessage());\r
 129         } catch (WrongParameterException e) {\r
 130             e.printStackTrace();\r
 131             fail(e.getLocalizedMessage());\r
 132         }\r
 133 \r
 134     }\r
 135 \r
 136     @Test()\r
 137     public void testMarshalling() {\r
 138 \r
 139         File outfile = new File(this.test_output);\r
 140         try {\r
 141             pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
 142         } catch (FileNotFoundException e) {\r
 143             e.printStackTrace();\r
 144             fail(e.getLocalizedMessage());\r
 145         } catch (JAXBException 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         }\r
 152         assertTrue("Output file expected, but nothing found!", outfile.exists());\r
 153         outfile.delete();\r
 154     }\r
 155 \r
 156     @Test()\r
 157     public void testUnMarshalling() {\r
 158 \r
 159         File outfile = new File(this.test_output);\r
 160         try {\r
 161             pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
 162 \r
 163             RunnerConfig<?> rconfig = pmarshaller.read(new FileInputStream(\r
 164                     outfile), RunnerConfig.class, Parameter.class,\r
 165                     Option.class, ValueConstrain.class);\r
 166             assertNotNull(rconfig);\r
 167             assertEquals(rconfig.getParameters().size(), this.rconfig\r
 168                     .getParameters().size());\r
 169             assertEquals(rconfig.getRunnerClassName(), this.rconfig\r
 170                     .getRunnerClassName());\r
 171             assertTrue(matrixParam.equals(rconfig.getArgument("MATRIX1")));\r
 172             assertFalse(matrixParam.equals(rconfig.getArgument("Type")));\r
 173         } catch (FileNotFoundException e) {\r
 174             e.printStackTrace();\r
 175             fail(e.getLocalizedMessage());\r
 176         } catch (JAXBException e) {\r
 177             e.printStackTrace();\r
 178             fail(e.getLocalizedMessage());\r
 179         } catch (IOException e) {\r
 180             e.printStackTrace();\r
 181             fail(e.getLocalizedMessage());\r
 182         }\r
 183         // outfile.delete();\r
 184     }\r
 185 \r
 186     @Test()\r
 187     public void testValidation() {\r
 188         try {\r
 189             System.out.println("CCCC " + rconfig);\r
 190             // write schema\r
 191             pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 192                     test_schema_output);\r
 193 \r
 194             File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 195                     test_schema_output);\r
 196             assertTrue(schemafile.exists());\r
 197             // document is NOT valid even against a loose schema as elements in\r
 198             // java are annotated as required\r
 199             Validator looseValidator = RunnerConfigMarshaller\r
 200                     .getValidator(schemafile.getAbsolutePath());\r
 201 \r
 202             // write output xml file\r
 203             File outfile = new File(this.test_output);\r
 204             pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
 205 \r
 206             assertTrue("Invalid output is NOT expected", RunnerConfigMarshaller\r
 207                     .validate(looseValidator, test_output));\r
 208 \r
 209             Schema strictSchema = RunnerConfigMarshaller\r
 210                     .getSchema(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
 211                             + File.separator + "RunnerConfigSchema.xsd");\r
 212 \r
 213             Validator strictVal = RunnerConfigMarshaller\r
 214                     .getValidator(strictSchema);\r
 215 \r
 216             // document is invalid against strict schema\r
 217             assertFalse("Invalid output is expected", RunnerConfigMarshaller\r
 218                     .validate(strictVal, invalidDoc));\r
 219 \r
 220             // schemafile.delete();\r
 221             // outfile.delete();\r
 222 \r
 223         } catch (MalformedURLException e) {\r
 224             e.printStackTrace();\r
 225             fail(e.getLocalizedMessage());\r
 226         } catch (JAXBException e) {\r
 227             e.printStackTrace();\r
 228             fail(e.getLocalizedMessage());\r
 229         } catch (IOException e) {\r
 230             e.printStackTrace();\r
 231             fail(e.getLocalizedMessage());\r
 232         } catch (SAXException e) {\r
 233             e.printStackTrace();\r
 234             fail(e.getMessage());\r
 235         }\r
 236 \r
 237     }\r
 238 \r
 239     @Test(expectedExceptions = JAXBException.class)\r
 240     public void testValidationOnMarshalling() throws SAXException,\r
 241             JAXBException, MalformedURLException {\r
 242         // This is not valid parameter\r
 243         Parameter<Mafft> p = new Parameter<Mafft>("MATRIXXX", "Protein weight matrix");\r
 244         // This attribute is required by strict schema\r
 245         // p.setOptionName("-M");\r
 246         p.setRequired(true);\r
 247         rconfig.addParameter(p);\r
 248         try {\r
 249 \r
 250             // strict schema invalidate this document and throw an exception\r
 251             // just discard the output\r
 252             pmarshaller.writeAndValidate(rconfig,\r
 253                     AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
 254                             + "RunnerConfigSchema.xsd",\r
 255                     new ByteArrayOutputStream());\r
 256 \r
 257             fail("Exception has been thrown before this place in unreachable");\r
 258 \r
 259         } catch (MalformedURLException e) {\r
 260             e.printStackTrace();\r
 261             fail(e.getLocalizedMessage());\r
 262         } catch (IOException e) {\r
 263             e.printStackTrace();\r
 264             fail(e.getLocalizedMessage());\r
 265         }\r
 266     }\r
 267 \r
 268     @Test()\r
 269     public void testSchemaFromCodeGeneration() {\r
 270         try {\r
 271 \r
 272             pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 273                     test_schema_output);\r
 274         } catch (JAXBException e) {\r
 275             e.printStackTrace();\r
 276             fail(e.getLocalizedMessage());\r
 277         } catch (IOException e) {\r
 278             e.printStackTrace();\r
 279             fail(e.getLocalizedMessage());\r
 280         }\r
 281         File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 282                 test_schema_output);\r
 283         assertTrue("Schema file expected but not found", schemafile.exists());\r
 284         assertTrue("Schema file seems to be empty", schemafile.length() > 50);\r
 285         // schemafile.delete();\r
 286     }\r
 287 \r
 288 }\r