+++ /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
-\r
-package compbio.engine.conf;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.io.ByteArrayOutputStream;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
-import java.io.IOException;\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.validation.Schema;\r
-import javax.xml.validation.Validator;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-import org.xml.sax.SAXException;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.Option;\r
-import compbio.metadata.Parameter;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.metadata.ValueConstrain;\r
-import compbio.metadata.WrongParameterException;\r
-import compbio.runner.msa.Mafft;\r
-\r
-public class RunnerConfigMarshallerTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
- public static String test_schema_output = "RunnerConfigSchema.xml";\r
- public static String test_output = AllTestSuit.OUTPUT_DIR_ABSOLUTE + "MafftParameters.out.xml";\r
-\r
- public static String invalidDoc = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "InvalidMafftParameters.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
- Parameter<Mafft> matrixParam = null;\r
- RunnerConfigMarshaller<Mafft> pmarshaller = 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"); // "-retree"\r
- p2.setRequired(false);\r
-\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
- p3.setDefaultValue("pam");\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 = p3;\r
- rconfig.setOptions(prms);\r
-\r
- pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class, Option.class, ValueConstrain.class);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-\r
- @Test()\r
- public void testMarshalling() {\r
-\r
- File outfile = new File(this.test_output);\r
- try {\r
- pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- assertTrue("Output file expected, but nothing found!", outfile.exists());\r
- outfile.delete();\r
- }\r
-\r
- @Test()\r
- public void testUnMarshalling() {\r
-\r
- File outfile = new File(this.test_output);\r
- try {\r
- pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
-\r
- RunnerConfig<?> rconfig = pmarshaller.read(new FileInputStream(outfile), RunnerConfig.class, Parameter.class, Option.class,\r
- ValueConstrain.class);\r
- assertNotNull(rconfig);\r
- assertEquals(rconfig.getParameters().size(), this.rconfig.getParameters().size());\r
- assertEquals(rconfig.getRunnerClassName(), this.rconfig.getRunnerClassName());\r
- assertTrue(matrixParam.equals(rconfig.getArgument("MATRIX1")));\r
- assertFalse(matrixParam.equals(rconfig.getArgument("Type")));\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- // outfile.delete();\r
- }\r
-\r
- @Test()\r
- public void testValidation() {\r
- try {\r
- System.out.println("CCCC " + rconfig);\r
- // write schema\r
- pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
-\r
- File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
- assertTrue(schemafile.exists());\r
- // document is NOT valid even against a loose schema as elements in\r
- // java are annotated as required\r
- Validator looseValidator = RunnerConfigMarshaller.getValidator(schemafile.getAbsolutePath());\r
-\r
- // write output xml file\r
- File outfile = new File(this.test_output);\r
- pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
-\r
- assertTrue("Invalid output is NOT expected", RunnerConfigMarshaller.validate(looseValidator, test_output));\r
-\r
- Schema strictSchema = RunnerConfigMarshaller.getSchema(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
- + "RunnerConfigSchema.xsd");\r
-\r
- Validator strictVal = RunnerConfigMarshaller.getValidator(strictSchema);\r
-\r
- // document is invalid against strict schema\r
- assertFalse("Invalid output is expected", RunnerConfigMarshaller.validate(strictVal, invalidDoc));\r
-\r
- // schemafile.delete();\r
- // outfile.delete();\r
-\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\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.getMessage());\r
- }\r
-\r
- }\r
-\r
- @Test(expectedExceptions = JAXBException.class)\r
- public void testValidationOnMarshalling() throws SAXException, JAXBException, MalformedURLException {\r
- // This is not valid parameter\r
- Parameter<Mafft> p = new Parameter<Mafft>("MATRIXXX", "Protein weight matrix");\r
- // This attribute is required by strict schema\r
- // p.setOptionName("-M");\r
- p.setRequired(true);\r
- rconfig.addParameter(p);\r
- try {\r
-\r
- // strict schema invalidate this document and throw an exception\r
- // just discard the output\r
- pmarshaller.writeAndValidate(rconfig, AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator + "RunnerConfigSchema.xsd",\r
- new ByteArrayOutputStream());\r
-\r
- fail("Exception has been thrown before this place in unreachable");\r
-\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test()\r
- public void testSchemaFromCodeGeneration() {\r
- try {\r
-\r
- pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
- assertTrue("Schema file expected but not found", schemafile.exists());\r
- assertTrue("Schema file seems to be empty", schemafile.length() > 50);\r
- // schemafile.delete();\r
- }\r
-\r
-}\r
git://source.jalview.org / proteocache.git / blobdiff