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 + "MafftParameters.xml";\r
  44 \r
  45         RunnerConfig<Mafft> rconfig = null;\r
  46 \r
  47         @BeforeMethod\r
  48         public void setup() {\r
  49                 try {\r
  50                         rconfig = new RunnerConfig<Mafft>();\r
  51                         rconfig.setRunnerClassName(Mafft.class.getName());\r
  52                         List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
  53 \r
  54                         RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class,\r
  55                                         Option.class, ValueConstrain.class);\r
  56                 } catch (JAXBException e) {\r
  57                         e.printStackTrace();\r
  58                         fail(e.getLocalizedMessage());\r
  59                 }\r
  60         }\r
  61 \r
  62         @Test\r
  63         public void testValidate() {\r
  64                 try {\r
  65                         rconfig.validate();\r
  66                 } catch (ValidationException e) {\r
  67                         e.printStackTrace();\r
  68                         fail(e.getLocalizedMessage());\r
  69                 } catch (IllegalStateException e) {\r
  70                         e.printStackTrace();\r
  71                         fail(e.getLocalizedMessage());\r
  72                 }\r
  73         }\r
  74 \r
  75         @Test(expectedExceptions = WrongParameterException.class)\r
  76         public void testCreateParameter() throws WrongParameterException {\r
  77                 Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
  78                 // TODO publish help on a compbio web site\r
  79                 p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
  80 \r
  81                 p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
  82                 // This attribute is required by strict schema\r
  83                 p3.setOptionName("--AAMATRIX");\r
  84                 p3.setRequired(true);\r
  85                 // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
  86                 // IN WITHIN POSSIBLE VALUES\r
  87                 p3.setDefaultValue("pam22");\r
  88                 String com = p3.toCommand(" ");\r
  89                 System.out.println("AAAAAAAAAAAAAA!" + com);\r
  90         }\r
  91 \r
  92         @Test()\r
  93         public void testParameterToCommand() throws WrongParameterException {\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                 // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 103                 // IN WITHIN POSSIBLE VALUES\r
 104                 p3.setDefaultValue("PAM");\r
 105                 String com = p3.toCommand("=");\r
 106                 assertTrue(com.startsWith("--AAMATRIX"));\r
 107                 assertTrue(com.endsWith("PAM"));\r
 108                 assertTrue(com.contains("="));\r
 109                 p3.setDefaultValue("ID");\r
 110                 com = p3.toCommand("=");\r
 111                 assertFalse(com.endsWith("PAM"));\r
 112                 assertFalse(com.contains("PAM"));\r
 113         }\r
 114 \r
 115         @Test(expectedExceptions = ValidationException.class)\r
 116         public void testOptionNoDefaultValidate() throws ValidationException {\r
 117                 Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
 118                 // TODO publish help on a compbio web site\r
 119                 p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 120 \r
 121                 p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
 122                 p3.setRequired(true);\r
 123                 // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 124                 // IN WITHIN POSSIBLE VALUES\r
 125                 p3.validate();\r
 126         }\r
 127 \r
 128         @Test(expectedExceptions = WrongParameterException.class)\r
 129         public void testOptionSetInvalidValue() throws WrongParameterException {\r
 130 \r
 131                 Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
 132                 // TODO publish help on a compbio web site\r
 133                 p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 134 \r
 135                 p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
 136                 p3.setRequired(true);\r
 137                 // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 138                 // IN WITHIN POSSIBLE VALUES\r
 139                 p3.setDefaultValue("AAA");\r
 140         }\r
 141 \r
 142         @Test()\r
 143         public void testOptionToCommand() {\r
 144                 try {\r
 145                         Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
 146                         // TODO publish help on a compbio web site\r
 147                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 148 \r
 149                         p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
 150                         p3.setRequired(true);\r
 151                         // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
 152                         // IN WITHIN POSSIBLE VALUES\r
 153                         p3.setDefaultValue("--BBBB");\r
 154                         p3.validate();\r
 155                         String com = p3.toCommand("=");\r
 156                         assertEquals("--BBBB", com);\r
 157                         p3.setDefaultValue("--ABMAT");\r
 158                         com = p3.toCommand("=");\r
 159                         assertEquals("--ABMAT", com);\r
 160                 } catch (ValidationException e) {\r
 161                         e.printStackTrace();\r
 162                         fail(e.getMessage());\r
 163                 } catch (WrongParameterException e) {\r
 164                         e.printStackTrace();\r
 165                         fail(e.getMessage());\r
 166                 }\r
 167         }\r
 168 \r
 169         @Test(expectedExceptions = IllegalStateException.class)\r
 170         public void testCreateNumParameterWithoutValidValue() throws MalformedURLException {\r
 171                 try {\r
 172                         Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
 173                         // This is causing exception is ValidValue constrain is not defined\r
 174                         // for\r
 175                         // numeric value\r
 176                         p4.setDefaultValue("5");\r
 177                 } catch (WrongParameterException e) {\r
 178                         e.printStackTrace();\r
 179                         fail(e.getLocalizedMessage());\r
 180                 }\r
 181 \r
 182         }\r
 183 \r
 184         @Test()\r
 185         public void testCreateParameterWithValidValueConstrain() throws MalformedURLException {\r
 186                 Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
 187                 ValueConstrain vc = new ValueConstrain();\r
 188                 vc.setType(ValueConstrain.Type.Float);\r
 189                 vc.setMin("0");\r
 190                 vc.setMax("10");\r
 191                 p4.setValidValue(vc);\r
 192                 try {\r
 193                         p4.setDefaultValue("5");\r
 194                 } catch (WrongParameterException e) {\r
 195                         e.printStackTrace();\r
 196                         fail(e.getLocalizedMessage());\r
 197                 }\r
 198         }\r
 199 \r
 200         @Test(expectedExceptions = WrongParameterException.class)\r
 201         public void testValidateLowerBoundaryConstrainCheck() throws WrongParameterException {\r
 202                 Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 203                 // TODO publish help on a compbio web site\r
 204                 p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 205                 // This attribute is required by strict schema\r
 206                 p3.setOptionName("--AAMATRIX");\r
 207                 p3.setRequired(true);\r
 208 \r
 209                 ValueConstrain vc = new ValueConstrain();\r
 210                 vc.setType(ValueConstrain.Type.Float);\r
 211                 vc.setMin("-10.12");\r
 212                 vc.setMax("0");\r
 213                 p3.setValidValue(vc);\r
 214                 // THIS IS CAUSING EXCEPTION\r
 215                 p3.setDefaultValue("-11.0");\r
 216         }\r
 217 \r
 218         @Test(expectedExceptions = WrongParameterException.class)\r
 219         public void testValidateUpperBoundaryConstrainCheck() throws WrongParameterException {\r
 220                 Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 221                 // TODO publish help on a compbio web site\r
 222                 p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 223                 // This attribute is required by strict schema\r
 224                 p3.setOptionName("--AAMATRIX");\r
 225                 p3.setRequired(true);\r
 226 \r
 227                 ValueConstrain vc = new ValueConstrain();\r
 228                 vc.setType(ValueConstrain.Type.Float);\r
 229                 vc.setMin("-10.12");\r
 230                 vc.setMax("0");\r
 231                 p3.setValidValue(vc);\r
 232                 // THIS IS CAUSING EXCEPTION\r
 233                 p3.setDefaultValue("1");\r
 234         }\r
 235 \r
 236         @Test()\r
 237         public void testValidateBoundaryConstrainCheck() {\r
 238                 try {\r
 239                         Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
 240                         // TODO publish help on a compbio web site\r
 241                         p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
 242                         // This attribute is required by strict schema\r
 243                         p3.setOptionName("--AAMATRIX");\r
 244                         p3.setRequired(true);\r
 245 \r
 246                         ValueConstrain vc = new ValueConstrain();\r
 247                         vc.setType(ValueConstrain.Type.Float);\r
 248                         vc.setMin("-10.12");\r
 249                         p3.setValidValue(vc);\r
 250                         // Max value boundary is not defined so 1 is valid\r
 251                         p3.setDefaultValue("1");\r
 252                         p3.validate();\r
 253                 } catch (WrongParameterException e) {\r
 254                         e.printStackTrace();\r
 255                         fail(e.getMessage());\r
 256                 } catch (ValidationException e) {\r
 257                         e.printStackTrace();\r
 258                         fail(e.getMessage());\r
 259                 }\r
 260         }\r
 261 \r
 262         @Test(expectedExceptions = ValidationException.class)\r
 263         public void testValidateValueConstrain() throws ValidationException {\r
 264                 ValueConstrain vc = new ValueConstrain();\r
 265                 vc.setType(ValueConstrain.Type.Float);\r
 266                 // NO BOUNDARIES DEFINED\r
 267                 vc.validate();\r
 268         }\r
 269 }\r