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