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Viewing changes to source/TEST/SemanticValidator_test.C

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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source/TEST/SemanticValidator_test.C
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework 
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Andreas Bertsch $
 
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// $Authors: Marc Sturm, Andreas Bertsch $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/CONCEPT/ClassTest.h>
 
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#include <OpenMS/FORMAT/VALIDATORS/SemanticValidator.h>
 
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#include <OpenMS/DATASTRUCTURES/CVMappings.h>
 
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#include <OpenMS/FORMAT/CVMappingFile.h>
 
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#include <OpenMS/FORMAT/ControlledVocabulary.h>
 
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#include <OpenMS/SYSTEM/File.h>
 
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///////////////////////////
 
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START_TEST(SemanticValidator, "$Id: SemanticValidator_test.C 8210 2011-03-28 13:19:52Z aiche $")
 
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/////////////////////////////////////////////////////////////
 
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/////////////////////////////////////////////////////////////
 
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using namespace OpenMS;
 
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using namespace OpenMS::Internal;
 
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using namespace std;
 
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CVMappings mapping;
 
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CVMappingFile().load(OPENMS_GET_TEST_DATA_PATH("SemanticValidator_mapping.xml"),mapping);
 
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ControlledVocabulary cv;
 
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cv.loadFromOBO("PSI",OPENMS_GET_TEST_DATA_PATH("SemanticValidator_cv.obo"));
 
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cv.loadFromOBO("PATO",File::find("/CV/quality.obo"));
 
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cv.loadFromOBO("UO",File::find("/CV/unit.obo"));
 
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cv.loadFromOBO("brenda",File::find("/CV/brenda.obo"));
 
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cv.loadFromOBO("GO",File::find("/CV/goslim_goa.obo"));
 
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SemanticValidator* ptr = 0;
 
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SemanticValidator* nullPointer = 0;
 
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START_SECTION((SemanticValidator(const CVMappings& mapping, const ControlledVocabulary& cv)))
 
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        ptr = new SemanticValidator(mapping,cv);
 
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        TEST_NOT_EQUAL(ptr, nullPointer)
 
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END_SECTION
 
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START_SECTION((virtual ~SemanticValidator()))
 
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        delete ptr;
 
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END_SECTION
 
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START_SECTION((void setTag(const String& tag)))
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((void setAccessionAttribute(const String& accession)))
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((void setNameAttribute(const String& name)))
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((void setValueAttribute(const String& value)))
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((bool validate(const String &filename, StringList &errors, StringList &warnings)))
 
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        StringList errors, warnings;
 
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        //----------------------------------------------------------------------------------------
 
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        //test exceptions
 
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        SemanticValidator sv(mapping, cv);
 
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        TEST_EXCEPTION(Exception::FileNotFound, sv.validate("/does/not/exist", errors, warnings));
 
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        //----------------------------------------------------------------------------------------
 
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        //test of valid file
 
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        TEST_EQUAL(sv.validate(OPENMS_GET_TEST_DATA_PATH("SemanticValidator_valid.xml"), errors, warnings),true);
 
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        TEST_EQUAL(errors.size(),0)
 
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        TEST_EQUAL(warnings.size(),0)
 
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        //----------------------------------------------------------------------------------------
 
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        //test of corrupt file
 
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        TEST_EQUAL(sv.validate(OPENMS_GET_TEST_DATA_PATH("SemanticValidator_corrupt.xml"), errors, warnings),false);
 
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        TEST_EQUAL(errors.size(),5)
 
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        TEST_STRING_EQUAL(errors[0],"Violated mapping rule 'R3' at element '/mzML/fileDescription/sourceFileList/sourceFile', 2 should be present, 1 found!")
 
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        TEST_STRING_EQUAL(errors[1],"Name of CV term not correct: 'MS:1000554 - LCQ Deca2 - invalid repeat' should be 'LCQ Deca'")
 
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        TEST_STRING_EQUAL(errors[2],"CV term used in invalid element: 'MS:1000030 - vendor' at element '/mzML/instrumentConfigurationList/instrumentConfiguration'")
 
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        TEST_STRING_EQUAL(errors[3],"Violated mapping rule 'R6a' number of term repeats at element '/mzML/instrumentConfigurationList/instrumentConfiguration'")
 
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        TEST_STRING_EQUAL(errors[4],"Violated mapping rule 'R17a' at element '/mzML/run/spectrumList/spectrum/spectrumDescription', 1 should be present, 0 found!")
 
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        TEST_EQUAL(warnings.size(),4)
 
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        TEST_STRING_EQUAL(warnings[0],"Unknown CV term: 'MS:1111569 - SHA-1' at element '/mzML/fileDescription/sourceFileList/sourceFile'")
 
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        TEST_STRING_EQUAL(warnings[1],"Obsolete CV term: 'MS:1000030 - vendor' at element '/mzML/instrumentConfigurationList/instrumentConfiguration'")
 
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        TEST_STRING_EQUAL(warnings[2],"No mapping rule found for element '/mzML/acquisitionSettingsList/acquisitionSettings/targetList/target'")
 
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        TEST_STRING_EQUAL(warnings[3],"No mapping rule found for element '/mzML/acquisitionSettingsList/acquisitionSettings/targetList/target'")
 
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END_SECTION
 
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START_SECTION((void setCheckTermValueTypes(bool check)))
 
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        SemanticValidator sv(mapping, cv);
 
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        sv.setCheckTermValueTypes(true);
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((void setCheckUnits(bool check)))
 
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        SemanticValidator sv(mapping, cv);
 
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        sv.setCheckUnits(true);
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((void setUnitAccessionAttribute(const String &accession)))
 
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        SemanticValidator sv(mapping, cv);
 
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        sv.setUnitAccessionAttribute("unitAccession");
 
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        NOT_TESTABLE
 
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END_SECTION
 
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START_SECTION((void setUnitNameAttribute(const String &name)))
 
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        SemanticValidator sv(mapping, cv);
 
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        sv.setUnitNameAttribute("unit");
 
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        NOT_TESTABLE
 
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END_SECTION
 
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/////////////////////////////////////////////////////////////
 
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/////////////////////////////////////////////////////////////
 
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END_TEST