testsrc/compbio/metadata/RunnerConfigTester.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 package compbio.metadata;\r
  19 \r
  20 import static org.testng.AssertJUnit.assertEquals;\r
  21 import static org.testng.AssertJUnit.assertFalse;\r
  22 import static org.testng.AssertJUnit.assertTrue;\r
  23 import static org.testng.AssertJUnit.fail;\r
  24 \r
  25 import java.net.MalformedURLException;\r
  26 import java.net.URL;\r
  27 import java.util.ArrayList;\r
  28 import java.util.Arrays;\r
  29 import java.util.HashSet;\r
  30 import java.util.List;\r
  31 \r
  32 import javax.xml.bind.JAXBException;\r
  33 import javax.xml.bind.ValidationException;\r
  34 \r
  35 import org.testng.annotations.BeforeMethod;\r
  36 import org.testng.annotations.Test;\r
  37 \r
  38 import compbio.engine.conf.RunnerConfigMarshaller;\r
  39 import compbio.runner.msa.Mafft;\r
  40 \r
  41 public class RunnerConfigTester {\r
  42 \r
  43         public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  44                         + "MafftParameters.xml";\r
  45 \r
  46         RunnerConfig<Mafft> rconfig = null;\r
  47 \r
  48         @BeforeMethod\r
  49         public void setup() {\r
  50                 try {\r
  51                         rconfig = new RunnerConfig<Mafft>();\r
  52                         rconfig.setRunnerClassName(Mafft.class.getName());\r
  53                         List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
  54 \r
  55                         RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(\r
  56                                         RunnerConfig.class, Parameter.class, Option.class,\r
  57                                         ValueConstrain.class);\r
  58                 } catch (JAXBException e) {\r
  59                         e.printStackTrace();\r
  60                         fail(e.getLocalizedMessage());\r
  61                 }\r
  62         }\r
  63 \r
  64         @Test\r
  65         public void testValidate() {\r
  66                 try {\r
  67                         rconfig.validate();\r
  68                 } catch (ValidationException e) {\r
  69                         e.printStackTrace();\r
  70                         fail(e.getLocalizedMessage());\r
  71                 } catch (IllegalStateException e) {\r
  72                         e.printStackTrace();\r
  73                         fail(e.getLocalizedMessage());\r
  74                 }\r
  75         }\r
  76 \r
  77         @Test(expectedExceptions = WrongParameterException.class)\r
  78         public void testCreateParameter() throws WrongParameterException {\r
  79                 try {\r
  80                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
  81                                         "Protein weight matrix");\r
  82                         // TODO publish help on a compbio web site\r
  83                         p3.setFurtherDetails(new URL("http",\r
  84                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
  85                                         "Index.html"));\r
  86 \r
  87                         p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
  88                         // This attribute is required by strict schema\r
  89                         p3.setOptionName("--AAMATRIX");\r
  90                         p3.setRequired(true);\r
  91                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
  92                         // IN WITHIN POSSIBLE VALUES\r
  93                         p3.setDefaultValue("pam22");\r
  94                         String com = p3.toCommand(" ");\r
  95                         System.out.println("AAAAAAAAAAAAAA!" + com);\r
  96                 } catch (MalformedURLException e) {\r
  97                         e.printStackTrace();\r
  98                         fail(e.getMessage());\r
  99                 }\r
 100         }\r
 101 \r
 102         @Test()\r
 103         public void testParameterToCommand() throws WrongParameterException {\r
 104                 try {\r
 105                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
 106                                         "Protein weight matrix");\r
 107                         // TODO publish help on a compbio web site\r
 108                         p3.setFurtherDetails(new URL("http",\r
 109                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 110                                         "Index.html"));\r
 111 \r
 112                         p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
 113                         // This attribute is required by strict schema\r
 114                         p3.setOptionName("--AAMATRIX");\r
 115                         p3.setRequired(true);\r
 116                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 117                         // IN WITHIN POSSIBLE VALUES\r
 118                         p3.setDefaultValue("PAM");\r
 119                         String com = p3.toCommand("=");\r
 120                         assertTrue(com.startsWith("--AAMATRIX"));\r
 121                         assertTrue(com.endsWith("PAM"));\r
 122                         assertTrue(com.contains("="));\r
 123                         p3.setDefaultValue("ID");\r
 124                         com = p3.toCommand("=");\r
 125                         assertFalse(com.endsWith("PAM"));\r
 126                         assertFalse(com.contains("PAM"));\r
 127 \r
 128                 } catch (MalformedURLException e) {\r
 129                         e.printStackTrace();\r
 130                         fail(e.getMessage());\r
 131                 }\r
 132         }\r
 133 \r
 134         @Test(expectedExceptions = ValidationException.class)\r
 135         public void testOptionNoDefaultValidate() throws ValidationException {\r
 136                 try {\r
 137                         Option<Mafft> p3 = new Option<Mafft>("Matrix1",\r
 138                                         "Protein weight matrix");\r
 139                         // TODO publish help on a compbio web site\r
 140                         p3.setFurtherDetails(new URL("http",\r
 141                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 142                                         "Index.html"));\r
 143 \r
 144                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX",\r
 145                                         "--ABMAT", "--BBBB")));\r
 146                         p3.setRequired(true);\r
 147                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 148                         // IN WITHIN POSSIBLE VALUES\r
 149                         p3.validate();\r
 150 \r
 151                 } catch (MalformedURLException e) {\r
 152                         e.printStackTrace();\r
 153                         fail(e.getMessage());\r
 154                 }\r
 155         }\r
 156 \r
 157         @Test(expectedExceptions = WrongParameterException.class)\r
 158         public void testOptionSetInvalidValue() throws WrongParameterException {\r
 159                 try {\r
 160                         Option<Mafft> p3 = new Option<Mafft>("Matrix1",\r
 161                                         "Protein weight matrix");\r
 162                         // TODO publish help on a compbio web site\r
 163                         p3.setFurtherDetails(new URL("http",\r
 164                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 165                                         "Index.html"));\r
 166 \r
 167                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX",\r
 168                                         "--ABMAT", "--BBBB")));\r
 169                         p3.setRequired(true);\r
 170                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 171                         // IN WITHIN POSSIBLE VALUES\r
 172                         p3.setDefaultValue("AAA");\r
 173 \r
 174                 } catch (MalformedURLException e) {\r
 175                         e.printStackTrace();\r
 176                         fail(e.getMessage());\r
 177                 }\r
 178         }\r
 179 \r
 180         @Test()\r
 181         public void testOptionToCommand() {\r
 182                 try {\r
 183                         Option<Mafft> p3 = new Option<Mafft>("Matrix1",\r
 184                                         "Protein weight matrix");\r
 185                         // TODO publish help on a compbio web site\r
 186                         p3.setFurtherDetails(new URL("http",\r
 187                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 188                                         "Index.html"));\r
 189 \r
 190                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX",\r
 191                                         "--ABMAT", "--BBBB")));\r
 192                         p3.setRequired(true);\r
 193                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 194                         // IN WITHIN POSSIBLE VALUES\r
 195                         p3.setDefaultValue("--BBBB");\r
 196                         p3.validate();\r
 197                         String com = p3.toCommand("=");\r
 198                         assertEquals("--BBBB", com);\r
 199                         p3.setDefaultValue("--ABMAT");\r
 200                         com = p3.toCommand("=");\r
 201                         assertEquals("--ABMAT", com);\r
 202                 } catch (MalformedURLException e) {\r
 203                         e.printStackTrace();\r
 204                         fail(e.getMessage());\r
 205                 } catch (ValidationException e) {\r
 206                         e.printStackTrace();\r
 207                         fail(e.getMessage());\r
 208                 } catch (WrongParameterException e) {\r
 209                         e.printStackTrace();\r
 210                         fail(e.getMessage());\r
 211                 }\r
 212         }\r
 213 \r
 214         @Test(expectedExceptions = IllegalStateException.class)\r
 215         public void testCreateNumParameterWithoutValidValue() {\r
 216                 try {\r
 217                         Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix",\r
 218                                         "DNA weight matrix");\r
 219                         // This is causing exception is ValidValue constrain is not defined\r
 220                         // for\r
 221                         // numeric value\r
 222                         p4.setDefaultValue("5");\r
 223                 } catch (WrongParameterException e) {\r
 224                         e.printStackTrace();\r
 225                         fail(e.getLocalizedMessage());\r
 226                 }\r
 227 \r
 228         }\r
 229 \r
 230         @Test()\r
 231         public void testCreateParameterWithValidValueConstrain() {\r
 232 \r
 233                 Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix",\r
 234                                 "DNA weight matrix");\r
 235                 ValueConstrain vc = new ValueConstrain();\r
 236                 vc.setType(ValueConstrain.Type.Float);\r
 237                 vc.setMin("0");\r
 238                 vc.setMax("10");\r
 239                 p4.setValidValue(vc);\r
 240                 try {\r
 241                         p4.setDefaultValue("5");\r
 242                 } catch (WrongParameterException e) {\r
 243                         e.printStackTrace();\r
 244                         fail(e.getLocalizedMessage());\r
 245                 }\r
 246         }\r
 247 \r
 248         @Test(expectedExceptions = WrongParameterException.class)\r
 249         public void testValidateLowerBoundaryConstrainCheck()\r
 250                         throws WrongParameterException {\r
 251                 try {\r
 252                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
 253                                         "Protein weight matrix");\r
 254                         // TODO publish help on a compbio web site\r
 255                         p3.setFurtherDetails(new URL("http",\r
 256                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 257                                         "Index.html"));\r
 258                         // This attribute is required by strict schema\r
 259                         p3.setOptionName("--AAMATRIX");\r
 260                         p3.setRequired(true);\r
 261 \r
 262                         ValueConstrain vc = new ValueConstrain();\r
 263                         vc.setType(ValueConstrain.Type.Float);\r
 264                         vc.setMin("-10.12");\r
 265                         vc.setMax("0");\r
 266                         p3.setValidValue(vc);\r
 267                         // THIS IS CAUSING EXCEPTION\r
 268                         p3.setDefaultValue("-11.0");\r
 269 \r
 270                 } catch (MalformedURLException e) {\r
 271                         e.printStackTrace();\r
 272                         fail(e.getMessage());\r
 273                 }\r
 274         }\r
 275 \r
 276         @Test(expectedExceptions = WrongParameterException.class)\r
 277         public void testValidateUpperBoundaryConstrainCheck()\r
 278                         throws WrongParameterException {\r
 279                 try {\r
 280                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
 281                                         "Protein weight matrix");\r
 282                         // TODO publish help on a compbio web site\r
 283                         p3.setFurtherDetails(new URL("http",\r
 284                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 285                                         "Index.html"));\r
 286                         // This attribute is required by strict schema\r
 287                         p3.setOptionName("--AAMATRIX");\r
 288                         p3.setRequired(true);\r
 289 \r
 290                         ValueConstrain vc = new ValueConstrain();\r
 291                         vc.setType(ValueConstrain.Type.Float);\r
 292                         vc.setMin("-10.12");\r
 293                         vc.setMax("0");\r
 294                         p3.setValidValue(vc);\r
 295                         // THIS IS CAUSING EXCEPTION\r
 296                         p3.setDefaultValue("1");\r
 297 \r
 298                 } catch (MalformedURLException e) {\r
 299                         e.printStackTrace();\r
 300                         fail(e.getMessage());\r
 301                 }\r
 302         }\r
 303 \r
 304         @Test()\r
 305         public void testValidateBoundaryConstrainCheck() {\r
 306                 try {\r
 307                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
 308                                         "Protein weight matrix");\r
 309                         // TODO publish help on a compbio web site\r
 310                         p3.setFurtherDetails(new URL("http",\r
 311                                         "www.compbio.dundee.ac.uk/users/pvtroshin/ws/",\r
 312                                         "Index.html"));\r
 313                         // This attribute is required by strict schema\r
 314                         p3.setOptionName("--AAMATRIX");\r
 315                         p3.setRequired(true);\r
 316 \r
 317                         ValueConstrain vc = new ValueConstrain();\r
 318                         vc.setType(ValueConstrain.Type.Float);\r
 319                         vc.setMin("-10.12");\r
 320                         p3.setValidValue(vc);\r
 321                         // Max value boundary is not defined so 1 is valid\r
 322                         p3.setDefaultValue("1");\r
 323                         p3.validate();\r
 324                 } catch (MalformedURLException e) {\r
 325                         e.printStackTrace();\r
 326                         fail(e.getMessage());\r
 327                 } catch (WrongParameterException e) {\r
 328                         e.printStackTrace();\r
 329                         fail(e.getMessage());\r
 330                 } catch (ValidationException e) {\r
 331                         e.printStackTrace();\r
 332                         fail(e.getMessage());\r
 333                 }\r
 334         }\r
 335 \r
 336         @Test(expectedExceptions = ValidationException.class)\r
 337         public void testValidateValueConstrain() throws ValidationException {\r
 338                 ValueConstrain vc = new ValueConstrain();\r
 339                 vc.setType(ValueConstrain.Type.Float);\r
 340                 // NO BOUNDARIES DEFINED\r
 341                 vc.validate();\r
 342         }\r
 343 }\r