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(new URL("http",\r
  82                     "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
  83                     "Index.html"));\r
  84             p1.addPossibleValues("PROTEIN", "DNA");\r
  85             p1.setOptionName("-TYPE");\r
  86             p1.setRequired(false);\r
  87 \r
  88             /*\r
  89              * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
  90              * filename\r
  91              */\r
  92             Option<Mafft> p2 = new Option<Mafft>("MATRIX",\r
  93                     "Protein weight matrix");\r
  94             // TODO publish help on a compbio web site\r
  95 \r
  96             p2.setFurtherDetails(new URL("http",\r
  97                     "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
  98                     "Index.html"));\r
  99 \r
 100             p2.addOptionNames("-jtree"); // "-retree"\r
 101             p2.setRequired(false);\r
 102 \r
 103             Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
 104                     "Protein weight matrix");\r
 105             // TODO publish help on a compbio web site\r
 106             p3.setFurtherDetails(new URL("http",\r
 107                     "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 108                     "Index.html"));\r
 109 \r
 110             p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
 111             // This attribute is required by strict schema\r
 112             p3.setOptionName("--AAMATRIX");\r
 113             p3.setRequired(true);\r
 114             p3.setDefaultValue("pam");\r
 115             ValueConstrain vc = new ValueConstrain();\r
 116             vc.setType(ValueConstrain.Type.Float);\r
 117             vc.setMin("-10.12");\r
 118             vc.setMax("0");\r
 119             p3.setValidValue(vc);\r
 120 \r
 121             prms.add(p1);\r
 122             prms.add(p2);\r
 123             prms.add(p3);\r
 124             matrixParam = p3;\r
 125             rconfig.setOptions(prms);\r
 126 \r
 127             pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class,\r
 128                     Parameter.class, Option.class, ValueConstrain.class);\r
 129         } catch (MalformedURLException e) {\r
 130             e.printStackTrace();\r
 131             fail(e.getLocalizedMessage());\r
 132         } catch (JAXBException e) {\r
 133             e.printStackTrace();\r
 134             fail(e.getLocalizedMessage());\r
 135         } catch (WrongParameterException e) {\r
 136             e.printStackTrace();\r
 137             fail(e.getLocalizedMessage());\r
 138         }\r
 139 \r
 140     }\r
 141 \r
 142     @Test()\r
 143     public void testMarshalling() {\r
 144 \r
 145         File outfile = new File(this.test_output);\r
 146         try {\r
 147             pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
 148         } catch (FileNotFoundException e) {\r
 149             e.printStackTrace();\r
 150             fail(e.getLocalizedMessage());\r
 151         } catch (JAXBException e) {\r
 152             e.printStackTrace();\r
 153             fail(e.getLocalizedMessage());\r
 154         } catch (IOException e) {\r
 155             e.printStackTrace();\r
 156             fail(e.getLocalizedMessage());\r
 157         }\r
 158         assertTrue("Output file expected, but nothing found!", outfile.exists());\r
 159         outfile.delete();\r
 160     }\r
 161 \r
 162     @Test()\r
 163     public void testUnMarshalling() {\r
 164 \r
 165         File outfile = new File(this.test_output);\r
 166         try {\r
 167             pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
 168 \r
 169             RunnerConfig<?> rconfig = pmarshaller.read(new FileInputStream(\r
 170                     outfile), RunnerConfig.class, Parameter.class,\r
 171                     Option.class, ValueConstrain.class);\r
 172             assertNotNull(rconfig);\r
 173             assertEquals(rconfig.getParameters().size(), this.rconfig\r
 174                     .getParameters().size());\r
 175             assertEquals(rconfig.getRunnerClassName(), this.rconfig\r
 176                     .getRunnerClassName());\r
 177             assertTrue(matrixParam.equals(rconfig.getArgument("MATRIX1")));\r
 178             assertFalse(matrixParam.equals(rconfig.getArgument("Type")));\r
 179         } catch (FileNotFoundException e) {\r
 180             e.printStackTrace();\r
 181             fail(e.getLocalizedMessage());\r
 182         } catch (JAXBException e) {\r
 183             e.printStackTrace();\r
 184             fail(e.getLocalizedMessage());\r
 185         } catch (IOException e) {\r
 186             e.printStackTrace();\r
 187             fail(e.getLocalizedMessage());\r
 188         }\r
 189         // outfile.delete();\r
 190     }\r
 191 \r
 192     @Test()\r
 193     public void testValidation() {\r
 194         try {\r
 195             System.out.println("CCCC " + rconfig);\r
 196             // write schema\r
 197             pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 198                     test_schema_output);\r
 199 \r
 200             File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 201                     test_schema_output);\r
 202             assertTrue(schemafile.exists());\r
 203             // document is NOT valid even against a loose schema as elements in\r
 204             // java are annotated as required\r
 205             Validator looseValidator = RunnerConfigMarshaller\r
 206                     .getValidator(schemafile.getAbsolutePath());\r
 207 \r
 208             // write output xml file\r
 209             File outfile = new File(this.test_output);\r
 210             pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
 211 \r
 212             assertTrue("Invalid output is NOT expected", RunnerConfigMarshaller\r
 213                     .validate(looseValidator, test_output));\r
 214 \r
 215             Schema strictSchema = RunnerConfigMarshaller\r
 216                     .getSchema(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
 217                             + File.separator + "RunnerConfigSchema.xsd");\r
 218 \r
 219             Validator strictVal = RunnerConfigMarshaller\r
 220                     .getValidator(strictSchema);\r
 221 \r
 222             // document is invalid against strict schema\r
 223             assertFalse("Invalid output is expected", RunnerConfigMarshaller\r
 224                     .validate(strictVal, invalidDoc));\r
 225 \r
 226             // schemafile.delete();\r
 227             // outfile.delete();\r
 228 \r
 229         } catch (MalformedURLException e) {\r
 230             e.printStackTrace();\r
 231             fail(e.getLocalizedMessage());\r
 232         } catch (JAXBException e) {\r
 233             e.printStackTrace();\r
 234             fail(e.getLocalizedMessage());\r
 235         } catch (IOException e) {\r
 236             e.printStackTrace();\r
 237             fail(e.getLocalizedMessage());\r
 238         } catch (SAXException e) {\r
 239             e.printStackTrace();\r
 240             fail(e.getMessage());\r
 241         }\r
 242 \r
 243     }\r
 244 \r
 245     @Test(expectedExceptions = JAXBException.class)\r
 246     public void testValidationOnMarshalling() throws SAXException,\r
 247             JAXBException {\r
 248         // This is not valid parameter\r
 249         Parameter<Mafft> p = new Parameter<Mafft>("MATRIXXX",\r
 250                 "Protein weight matrix");\r
 251         // This attribute is required by strict schema\r
 252         // p.setOptionName("-M");\r
 253         p.setRequired(true);\r
 254         rconfig.addParameter(p);\r
 255         try {\r
 256 \r
 257             // strict schema invalidate this document and throw an exception\r
 258             // just discard the output\r
 259             pmarshaller.writeAndValidate(rconfig,\r
 260                     AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
 261                             + "RunnerConfigSchema.xsd",\r
 262                     new ByteArrayOutputStream());\r
 263 \r
 264             fail("Exception has been thrown before this place in unreachable");\r
 265 \r
 266         } catch (MalformedURLException e) {\r
 267             e.printStackTrace();\r
 268             fail(e.getLocalizedMessage());\r
 269         } catch (IOException e) {\r
 270             e.printStackTrace();\r
 271             fail(e.getLocalizedMessage());\r
 272         }\r
 273     }\r
 274 \r
 275     @Test()\r
 276     public void testSchemaFromCodeGeneration() {\r
 277         try {\r
 278 \r
 279             pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 280                     test_schema_output);\r
 281         } catch (JAXBException e) {\r
 282             e.printStackTrace();\r
 283             fail(e.getLocalizedMessage());\r
 284         } catch (IOException e) {\r
 285             e.printStackTrace();\r
 286             fail(e.getLocalizedMessage());\r
 287         }\r
 288         File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE,\r
 289                 test_schema_output);\r
 290         assertTrue("Schema file expected but not found", schemafile.exists());\r
 291         assertTrue("Schema file seems to be empty", schemafile.length() > 50);\r
 292         // schemafile.delete();\r
 293     }\r
 294 \r
 295 }\r