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Fix problems with tests
[jabaws.git] / testsrc / compbio / metadata / RunnerConfigTester.java
diff --git a/testsrc/compbio/metadata/RunnerConfigTester.java b/testsrc/compbio/metadata/RunnerConfigTester.java
index 3bf2368..99549e1 100644 (file)
--- a/testsrc/compbio/metadata/RunnerConfigTester.java
+++ b/testsrc/compbio/metadata/RunnerConfigTester.java
@@ -40,8 +40,7 @@ import compbio.runner.msa.Mafft;
 \r
 public class RunnerConfigTester {\r
 \r
-       public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
-                       + "MafftParameters.xml";\r
+       public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
 \r
        RunnerConfig<Mafft> rconfig = null;\r
 \r
@@ -52,9 +51,8 @@ public class RunnerConfigTester {
                        rconfig.setRunnerClassName(Mafft.class.getName());\r
                        List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
 \r
-                       RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(\r
-                                       RunnerConfig.class, Parameter.class, Option.class,\r
-                                       ValueConstrain.class);\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
@@ -76,88 +74,69 @@ public class RunnerConfigTester {
 \r
        @Test(expectedExceptions = WrongParameterException.class)\r
        public void testCreateParameter() throws WrongParameterException {\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
+               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
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\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
-               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
+               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
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\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
-               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
+               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
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\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
-               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("AAA");\r
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\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
@@ -178,9 +157,6 @@ public class RunnerConfigTester {
                        p3.setDefaultValue("--ABMAT");\r
                        com = p3.toCommand("=");\r
                        assertEquals("--ABMAT", com);\r
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
                } catch (ValidationException e) {\r
                        e.printStackTrace();\r
                        fail(e.getMessage());\r
@@ -222,51 +198,39 @@ public class RunnerConfigTester {
        }\r
 \r
        @Test(expectedExceptions = WrongParameterException.class)\r
-       public void testValidateLowerBoundaryConstrainCheck()\r
-                       throws WrongParameterException {\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
+       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
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\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()\r
-                       throws WrongParameterException {\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
+       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
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\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
@@ -286,9 +250,6 @@ public class RunnerConfigTester {
                        // Max value boundary is not defined so 1 is valid\r
                        p3.setDefaultValue("1");\r
                        p3.validate();\r
-               } catch (MalformedURLException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
                } catch (WrongParameterException e) {\r
                        e.printStackTrace();\r
                        fail(e.getMessage());\r