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", "Protein weight matrix");\r
  81                         // TODO publish help on a compbio web site\r
  82                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  83 \r
  84                         p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
  85                         // This attribute is required by strict schema\r
  86                         p3.setOptionName("--AAMATRIX");\r
  87                         p3.setRequired(true);\r
  88                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
  89                         // IN WITHIN POSSIBLE VALUES\r
  90                         p3.setDefaultValue("pam22");\r
  91                         String com = p3.toCommand(" ");\r
  92                         System.out.println("AAAAAAAAAAAAAA!" + com);\r
  93                 } catch (MalformedURLException e) {\r
  94                         e.printStackTrace();\r
  95                         fail(e.getMessage());\r
  96                 }\r
  97         }\r
  98 \r
  99         @Test()\r
 100         public void testParameterToCommand() throws WrongParameterException {\r
 101                 try {\r
 102                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 103                         // TODO publish help on a compbio web site\r
 104                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 105 \r
 106                         p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
 107                         // This attribute is required by strict schema\r
 108                         p3.setOptionName("--AAMATRIX");\r
 109                         p3.setRequired(true);\r
 110                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 111                         // IN WITHIN POSSIBLE VALUES\r
 112                         p3.setDefaultValue("PAM");\r
 113                         String com = p3.toCommand("=");\r
 114                         assertTrue(com.startsWith("--AAMATRIX"));\r
 115                         assertTrue(com.endsWith("PAM"));\r
 116                         assertTrue(com.contains("="));\r
 117                         p3.setDefaultValue("ID");\r
 118                         com = p3.toCommand("=");\r
 119                         assertFalse(com.endsWith("PAM"));\r
 120                         assertFalse(com.contains("PAM"));\r
 121                 } catch (MalformedURLException e) {\r
 122                         e.printStackTrace();\r
 123                         fail(e.getMessage());\r
 124                 }\r
 125         }\r
 126 \r
 127         @Test(expectedExceptions = ValidationException.class)\r
 128         public void testOptionNoDefaultValidate() throws ValidationException {\r
 129                 try {\r
 130                         Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
 131                         // TODO publish help on a compbio web site\r
 132                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 133 \r
 134                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
 135                         p3.setRequired(true);\r
 136                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 137                         // IN WITHIN POSSIBLE VALUES\r
 138                         p3.validate();\r
 139                 } catch (MalformedURLException e) {\r
 140                         e.printStackTrace();\r
 141                         fail(e.getMessage());\r
 142                 }\r
 143         }\r
 144 \r
 145         @Test(expectedExceptions = WrongParameterException.class)\r
 146         public void testOptionSetInvalidValue() throws WrongParameterException {\r
 147                 try {\r
 148                         Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
 149                         // TODO publish help on a compbio web site\r
 150                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 151 \r
 152                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
 153                         p3.setRequired(true);\r
 154                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 155                         // IN WITHIN POSSIBLE VALUES\r
 156                         p3.setDefaultValue("AAA");\r
 157                 } catch (MalformedURLException e) {\r
 158                         e.printStackTrace();\r
 159                         fail(e.getMessage());\r
 160                 }\r
 161         }\r
 162 \r
 163         @Test()\r
 164         public void testOptionToCommand() {\r
 165                 try {\r
 166                         Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
 167                         // TODO publish help on a compbio web site\r
 168                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 169 \r
 170                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
 171                         p3.setRequired(true);\r
 172                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 173                         // IN WITHIN POSSIBLE VALUES\r
 174                         p3.setDefaultValue("--BBBB");\r
 175                         p3.validate();\r
 176                         String com = p3.toCommand("=");\r
 177                         assertEquals("--BBBB", com);\r
 178                         p3.setDefaultValue("--ABMAT");\r
 179                         com = p3.toCommand("=");\r
 180                         assertEquals("--ABMAT", com);\r
 181                 } catch (MalformedURLException e) {\r
 182                         e.printStackTrace();\r
 183                         fail(e.getMessage());\r
 184                 } catch (ValidationException e) {\r
 185                         e.printStackTrace();\r
 186                         fail(e.getMessage());\r
 187                 } catch (WrongParameterException e) {\r
 188                         e.printStackTrace();\r
 189                         fail(e.getMessage());\r
 190                 }\r
 191         }\r
 192 \r
 193         @Test(expectedExceptions = IllegalStateException.class)\r
 194         public void testCreateNumParameterWithoutValidValue() throws MalformedURLException {\r
 195                 try {\r
 196                         Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
 197                         // This is causing exception is ValidValue constrain is not defined\r
 198                         // for\r
 199                         // numeric value\r
 200                         p4.setDefaultValue("5");\r
 201                 } catch (WrongParameterException e) {\r
 202                         e.printStackTrace();\r
 203                         fail(e.getLocalizedMessage());\r
 204                 }\r
 205 \r
 206         }\r
 207 \r
 208         @Test()\r
 209         public void testCreateParameterWithValidValueConstrain() throws MalformedURLException {\r
 210                 Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
 211                 ValueConstrain vc = new ValueConstrain();\r
 212                 vc.setType(ValueConstrain.Type.Float);\r
 213                 vc.setMin("0");\r
 214                 vc.setMax("10");\r
 215                 p4.setValidValue(vc);\r
 216                 try {\r
 217                         p4.setDefaultValue("5");\r
 218                 } catch (WrongParameterException e) {\r
 219                         e.printStackTrace();\r
 220                         fail(e.getLocalizedMessage());\r
 221                 }\r
 222         }\r
 223 \r
 224         @Test(expectedExceptions = WrongParameterException.class)\r
 225         public void testValidateLowerBoundaryConstrainCheck()\r
 226                         throws WrongParameterException {\r
 227                 try {\r
 228                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 229                         // TODO publish help on a compbio web site\r
 230                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 231                         // This attribute is required by strict schema\r
 232                         p3.setOptionName("--AAMATRIX");\r
 233                         p3.setRequired(true);\r
 234 \r
 235                         ValueConstrain vc = new ValueConstrain();\r
 236                         vc.setType(ValueConstrain.Type.Float);\r
 237                         vc.setMin("-10.12");\r
 238                         vc.setMax("0");\r
 239                         p3.setValidValue(vc);\r
 240                         // THIS IS CAUSING EXCEPTION\r
 241                         p3.setDefaultValue("-11.0");\r
 242                 } catch (MalformedURLException e) {\r
 243                         e.printStackTrace();\r
 244                         fail(e.getMessage());\r
 245                 }\r
 246         }\r
 247 \r
 248         @Test(expectedExceptions = WrongParameterException.class)\r
 249         public void testValidateUpperBoundaryConstrainCheck()\r
 250                         throws WrongParameterException {\r
 251                 try {\r
 252                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 253                         // TODO publish help on a compbio web site\r
 254                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 255                         // This attribute is required by strict schema\r
 256                         p3.setOptionName("--AAMATRIX");\r
 257                         p3.setRequired(true);\r
 258 \r
 259                         ValueConstrain vc = new ValueConstrain();\r
 260                         vc.setType(ValueConstrain.Type.Float);\r
 261                         vc.setMin("-10.12");\r
 262                         vc.setMax("0");\r
 263                         p3.setValidValue(vc);\r
 264                         // THIS IS CAUSING EXCEPTION\r
 265                         p3.setDefaultValue("1");\r
 266                 } catch (MalformedURLException e) {\r
 267                         e.printStackTrace();\r
 268                         fail(e.getMessage());\r
 269                 }\r
 270         }\r
 271 \r
 272         @Test()\r
 273         public void testValidateBoundaryConstrainCheck() {\r
 274                 try {\r
 275                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 276                         // TODO publish help on a compbio web site\r
 277                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 278                         // This attribute is required by strict schema\r
 279                         p3.setOptionName("--AAMATRIX");\r
 280                         p3.setRequired(true);\r
 281 \r
 282                         ValueConstrain vc = new ValueConstrain();\r
 283                         vc.setType(ValueConstrain.Type.Float);\r
 284                         vc.setMin("-10.12");\r
 285                         p3.setValidValue(vc);\r
 286                         // Max value boundary is not defined so 1 is valid\r
 287                         p3.setDefaultValue("1");\r
 288                         p3.validate();\r
 289                 } catch (MalformedURLException e) {\r
 290                         e.printStackTrace();\r
 291                         fail(e.getMessage());\r
 292                 } catch (WrongParameterException e) {\r
 293                         e.printStackTrace();\r
 294                         fail(e.getMessage());\r
 295                 } catch (ValidationException e) {\r
 296                         e.printStackTrace();\r
 297                         fail(e.getMessage());\r
 298                 }\r
 299         }\r
 300 \r
 301         @Test(expectedExceptions = ValidationException.class)\r
 302         public void testValidateValueConstrain() throws ValidationException {\r
 303                 ValueConstrain vc = new ValueConstrain();\r
 304                 vc.setType(ValueConstrain.Type.Float);\r
 305                 // NO BOUNDARIES DEFINED\r
 306                 vc.validate();\r
 307         }\r
 308 }\r