--- /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