\r
public class OptionMarshallerTester {\r
\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "MafftParameters.xml";\r
- public static String test_schema_output = "NextGenMafftOptionsSchema.xml";\r
- public static String test_output = "MafftOptions.xml.out";\r
- public static String reWrittenInput = AllTestSuit.OUTPUT_DIR_ABSOLUTE\r
- + "rewrittenMafftParams.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
- Option<Mafft> matrixParam = null;\r
-\r
- @BeforeMethod()\r
- public void setup() {\r
- // write some parameters programmatically\r
- try {\r
- rconfig = new RunnerConfig<Mafft>();\r
- rconfig.setRunnerClassName(Mafft.class.getName());\r
- List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
-\r
- Parameter<Mafft> p1 = new Parameter<Mafft>("Type",\r
- "Type of the sequence (PROTEIN or DNA)");\r
- // TODO publish help on a compbio web site\r
-\r
- p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- p1.addPossibleValues("PROTEIN", "DNA");\r
- p1.setOptionName("-TYPE");\r
- p1.setRequired(false);\r
-\r
- /*\r
- * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
- * filename\r
- */\r
- Option<Mafft> p2 = new Option<Mafft>("MATRIX",\r
- "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
-\r
- p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p2.addOptionNames("-jtree");\r
- p2.addOptionNames("-jfasta");\r
- p2.setRequired(false);\r
-\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("MATRIX2",\r
- "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("-MATRIX");\r
- p3.setRequired(true);\r
- p3.setDefaultValue("id");\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
-\r
- prms.add(p1);\r
- prms.add(p2);\r
- prms.add(p3);\r
- matrixParam = p2;\r
- rconfig.setOptions(prms);\r
-\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
+ public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
+ public static String test_schema_output = "NextGenMafftOptionsSchema.xml";\r
+ public static String test_output = "MafftOptions.xml.out";\r
+ public static String reWrittenInput = AllTestSuit.OUTPUT_DIR_ABSOLUTE + "rewrittenMafftParams.xml";\r
+\r
+ RunnerConfig<Mafft> rconfig = null;\r
+ Option<Mafft> matrixParam = null;\r
+\r
+ @BeforeMethod()\r
+ public void setup() {\r
+ // write some parameters programmatically\r
+ try {\r
+ rconfig = new RunnerConfig<Mafft>();\r
+ rconfig.setRunnerClassName(Mafft.class.getName());\r
+ List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
+\r
+ Parameter<Mafft> p1 = new Parameter<Mafft>("Type", "Type of the sequence (PROTEIN or DNA)");\r
+ // TODO publish help on a compbio web site\r
+\r
+ p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
+ p1.addPossibleValues("PROTEIN", "DNA");\r
+ p1.setOptionName("-TYPE");\r
+ p1.setRequired(false);\r
+\r
+ /*\r
+ * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
+ * filename\r
+ */\r
+ Option<Mafft> p2 = new Option<Mafft>("MATRIX", "Protein weight matrix");\r
+ // TODO publish help on a compbio web site\r
+\r
+ p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
+\r
+ p2.addOptionNames("-jtree");\r
+ p2.addOptionNames("-jfasta");\r
+ p2.setRequired(false);\r
+\r
+ Parameter<Mafft> p3 = new Parameter<Mafft>("MATRIX2", "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("-MATRIX");\r
+ p3.setRequired(true);\r
+ p3.setDefaultValue("id");\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
+\r
+ prms.add(p1);\r
+ prms.add(p2);\r
+ prms.add(p3);\r
+ matrixParam = p2;\r
+ rconfig.setOptions(prms);\r
+\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
}\r
- }\r
-\r
- @Test(expectedExceptions = { javax.xml.bind.MarshalException.class })\r
- public void testMarshalling() throws JAXBException {\r
-\r
- File outfile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_output);\r
- try {\r
- RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(\r
- RunnerConfig.class);\r
-\r
- // This throws an exception\r
- // I am not sure why\r
- rmarsh.writeAndValidate(rconfig,\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
- + "RunnerConfigSchema.xsd", new FileOutputStream(\r
- outfile));\r
-\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (SAXException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
+\r
+ @Test(expectedExceptions = { javax.xml.bind.MarshalException.class })\r
+ public void testMarshalling() throws JAXBException {\r
+\r
+ File outfile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_output);\r
+ try {\r
+ RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class);\r
+\r
+ // This throws an exception\r
+ // I am not sure why\r
+ rmarsh.writeAndValidate(rconfig, AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator + "RunnerConfigSchema.xsd",\r
+ new FileOutputStream(outfile));\r
+\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (SAXException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ assertTrue("Output file expected, but nothing found!", outfile.exists());\r
+ // outfile.delete();\r
}\r
- assertTrue("Output file expected, but nothing found!", outfile.exists());\r
- // outfile.delete();\r
- }\r
-\r
- @Test()\r
- public void testUnMarshalling() {\r
- try {\r
- File input = new File(this.test_input);\r
- assertTrue(input.exists());\r
- JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
- Unmarshaller um = ctx.createUnmarshaller();\r
- JAXBElement<RunnerConfig> rconfig = um.unmarshal(new StreamSource(input), RunnerConfig.class);\r
- RunnerConfig<Mafft> runner = rconfig.getValue();\r
- assertNotNull(runner);\r
- System.out.println(runner);\r
- assertFalse(runner.options.isEmpty());\r
- assertFalse(runner.parameters.isEmpty());\r
- assertEquals(7, runner.options.size());\r
- assertEquals(8, runner.parameters.size());\r
- Option<Mafft> stypeOption = runner.getArgument("Sequence type");\r
- System.out.println(stypeOption);\r
- assertNotNull(stypeOption);\r
- assertFalse(stypeOption.isRequired);\r
- assertEquals("--auto", stypeOption.defaultValue);\r
- assertEquals(2, stypeOption.optionNames.size());\r
-\r
- assertEquals(" ", runner.getPrmSeparator());\r
- Option<Mafft> guidetrOption = runner.getArgument("Guide tree rebuild");\r
- Parameter<Mafft> guidetr = (Parameter<Mafft>) guidetrOption;\r
- ValueConstrain constraint = guidetr.getValidValue();\r
- assertEquals("Integer", constraint.type.toString());\r
- assertEquals(1, constraint.getMin());\r
- assertEquals(100, constraint.getMax());\r
-\r
- RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class);\r
- // Now see if we can write a valid document back discard the actual\r
- // output only validation is important here\r
- rmarsh.write(rconfig, new FileOutputStream(new File(reWrittenInput)));\r
- RunnerConfig<Mafft> rc = rmarsh.readAndValidate(new FileInputStream(new File(reWrittenInput)), RunnerConfig.class);\r
- assertEquals(runner, rc);\r
-\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (SAXException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
+\r
+ @Test()\r
+ public void testUnMarshalling() {\r
+ try {\r
+ File input = new File(this.test_input);\r
+ assertTrue(input.exists());\r
+ JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
+ Unmarshaller um = ctx.createUnmarshaller();\r
+ JAXBElement<RunnerConfig> rconfig = um.unmarshal(new StreamSource(input), RunnerConfig.class);\r
+ RunnerConfig<Mafft> runner = rconfig.getValue();\r
+ assertNotNull(runner);\r
+ System.out.println(runner);\r
+ assertFalse(runner.options.isEmpty());\r
+ assertFalse(runner.parameters.isEmpty());\r
+ assertEquals(7, runner.options.size());\r
+ assertEquals(8, runner.parameters.size());\r
+ Option<Mafft> stypeOption = runner.getArgument("Sequence type");\r
+ System.out.println(stypeOption);\r
+ assertNotNull(stypeOption);\r
+ assertFalse(stypeOption.isRequired);\r
+ assertEquals("--auto", stypeOption.defaultValue);\r
+ assertEquals(2, stypeOption.optionNames.size());\r
+\r
+ assertEquals(" ", runner.getPrmSeparator());\r
+ Option<Mafft> guidetrOption = runner.getArgument("Guide tree rebuild");\r
+ Parameter<Mafft> guidetr = (Parameter<Mafft>) guidetrOption;\r
+ ValueConstrain constraint = guidetr.getValidValue();\r
+ assertEquals("Integer", constraint.type.toString());\r
+ assertEquals(1, constraint.getMin());\r
+ assertEquals(100, constraint.getMax());\r
+\r
+ RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class);\r
+ // Now see if we can write a valid document back discard the actual\r
+ // output only validation is important here\r
+ rmarsh.write(rconfig, new FileOutputStream(new File(reWrittenInput)));\r
+ RunnerConfig<Mafft> rc = rmarsh.readAndValidate(new FileInputStream(new File(reWrittenInput)), RunnerConfig.class);\r
+ assertEquals(runner, rc);\r
+\r
+ } catch (JAXBException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (SAXException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
}\r
- }\r
}\r
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