+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-package compbio.metadata;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.Arrays;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.ValidationException;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.runner.msa.Mafft;\r
-\r
-public class RunnerConfigTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
-\r
- @BeforeMethod\r
- public void setup() {\r
- try {\r
- rconfig = new RunnerConfig<Mafft>();\r
- rconfig.setRunnerClassName(Mafft.class.getName());\r
- List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
-\r
- RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class,\r
- Option.class, ValueConstrain.class);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void testValidate() {\r
- try {\r
- rconfig.validate();\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IllegalStateException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testCreateParameter() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("pam22");\r
- String com = p3.toCommand(" ");\r
- System.out.println("AAAAAAAAAAAAAA!" + com);\r
- }\r
-\r
- @Test()\r
- public void testParameterToCommand() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("PAM");\r
- String com = p3.toCommand("=");\r
- assertTrue(com.startsWith("--AAMATRIX"));\r
- assertTrue(com.endsWith("PAM"));\r
- assertTrue(com.contains("="));\r
- p3.setDefaultValue("ID");\r
- com = p3.toCommand("=");\r
- assertFalse(com.endsWith("PAM"));\r
- assertFalse(com.contains("PAM"));\r
- }\r
-\r
- @Test(expectedExceptions = ValidationException.class)\r
- public void testOptionNoDefaultValidate() throws ValidationException {\r
- Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.validate();\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testOptionSetInvalidValue() throws WrongParameterException {\r
-\r
- Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("AAA");\r
- }\r
-\r
- @Test()\r
- public void testOptionToCommand() {\r
- try {\r
- Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("--BBBB");\r
- p3.validate();\r
- String com = p3.toCommand("=");\r
- assertEquals("--BBBB", com);\r
- p3.setDefaultValue("--ABMAT");\r
- com = p3.toCommand("=");\r
- assertEquals("--ABMAT", com);\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = IllegalStateException.class)\r
- public void testCreateNumParameterWithoutValidValue() throws MalformedURLException {\r
- try {\r
- Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
- // This is causing exception is ValidValue constrain is not defined\r
- // for\r
- // numeric value\r
- p4.setDefaultValue("5");\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-\r
- @Test()\r
- public void testCreateParameterWithValidValueConstrain() throws MalformedURLException {\r
- Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("0");\r
- vc.setMax("10");\r
- p4.setValidValue(vc);\r
- try {\r
- p4.setDefaultValue("5");\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testValidateLowerBoundaryConstrainCheck() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
-\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
- // THIS IS CAUSING EXCEPTION\r
- p3.setDefaultValue("-11.0");\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testValidateUpperBoundaryConstrainCheck() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
-\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
- // THIS IS CAUSING EXCEPTION\r
- p3.setDefaultValue("1");\r
- }\r
-\r
- @Test()\r
- public void testValidateBoundaryConstrainCheck() {\r
- try {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
-\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- p3.setValidValue(vc);\r
- // Max value boundary is not defined so 1 is valid\r
- p3.setDefaultValue("1");\r
- p3.validate();\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = ValidationException.class)\r
- public void testValidateValueConstrain() throws ValidationException {\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- // NO BOUNDARIES DEFINED\r
- vc.validate();\r
- }\r
-}\r
git://source.jalview.org / proteocache.git / blobdiff