# @file TestSyncAnnotation.rb
# @brief tests for improved syncAnnotation functions
#
# @author Akiya Jouraku (Ruby conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# src/sbml/test/TestSyncAnnotation.cpp
# using the conversion program dev/utilities/translateTests/translateTests.pl.
# Any changes made here will be lost the next time the file is regenerated.
#
# -----------------------------------------------------------------------------
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
# Copyright 2005-2010 California Institute of Technology.
# Copyright 2002-2005 California Institute of Technology and
# Japan Science and Technology Corporation.
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation. A copy of the license agreement is provided
# in the file named "LICENSE.txt" included with this software distribution
# and also available online as http://sbml.org/software/libsbml/license.html
# -----------------------------------------------------------------------------
require 'test/unit'
require 'libSBML'
class TestSyncAnnotation < Test::Unit::TestCase
def equals(*x)
case x.size
when 2
e, s = x
return e == s
when 1
e, = x
return e == @@oss.str()
end
end
def setup
filename = "../../sbml/annotation/test/test-data/annotationL3_2.xml"
@@d = LibSBML::readSBML(filename)
@@m = @@d.getModel()
end
def teardown
@@d = nil
end
def test_SyncAnnotation_deleteCVTerms
c = @@m.getCompartment(1)
xml = LibSBML::RDFAnnotationParser.deleteRDFCVTermAnnotation(c.getAnnotation())
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,xml.toXMLString())
end
def test_SyncAnnotation_deleteModelOnly
c = @@m.getCompartment(1)
xml = LibSBML::RDFAnnotationParser.deleteRDFHistoryAnnotation(c.getAnnotation())
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,xml.toXMLString())
end
def test_SyncAnnotation_deleteModelOnly_1
c = @@m.getCompartment(7)
xml = LibSBML::RDFAnnotationParser.deleteRDFHistoryAnnotation(c.getAnnotation())
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,xml.toXMLString())
xml = LibSBML::RDFAnnotationParser.deleteRDFHistoryAnnotation(nil)
assert( xml == nil )
xml = LibSBML::RDFAnnotationParser.deleteRDFHistoryAnnotation(LibSBML::XMLNode.convertStringToXMLNode(""))
assert( xml == nil )
end
def test_SyncAnnotation_modifyBoth_1
c = @@m.getCompartment(0)
mh = @@m.getModelHistory().clone()
cv = @@m.getCVTerm(0).clone()
c.setModelHistory(mh)
c.addCVTerm(cv)
c.unsetCVTerms()
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
c.unsetModelHistory()
c.addCVTerm(cv)
expected1 = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected1,c.toSBML())
c.setModelHistory(mh)
c.unsetCVTerms()
c.addCVTerm(cv)
expected2 = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected2,c.toSBML())
end
def test_SyncAnnotation_modifyBoth_2
c = @@m.getCompartment(0)
mh = @@m.getModelHistory().clone()
cv = @@m.getCVTerm(0).clone()
c.setModelHistory(mh)
c.unsetModelHistory()
c.addCVTerm(cv)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyBoth_3
c = @@m.getCompartment(0)
mh = @@m.getModelHistory().clone()
cv = @@m.getCVTerm(0).clone()
c.setModelHistory(mh)
c.addCVTerm(cv)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyBoth_4
c = @@m.getCompartment(1)
mh = c.getModelHistory().clone()
cv = c.getCVTerm(0).clone()
c.unsetModelHistory()
c.unsetCVTerms()
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
c.setModelHistory(mh)
c.addCVTerm(cv)
c.unsetCVTerms()
expected1 = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected1,c.toSBML())
c.unsetModelHistory()
c.unsetCVTerms()
c.addCVTerm(cv)
expected2 = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected2,c.toSBML())
c.unsetModelHistory()
c.unsetCVTerms()
c.addCVTerm(cv)
c.setModelHistory(mh)
expected3 = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected3,c.toSBML())
end
def test_SyncAnnotation_modifyCVTerms_1
c = @@m.getCompartment(4)
cv = c.getCVTerm(0).clone()
c.unsetCVTerms()
c.addCVTerm(cv)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyCVTerms_2
@@m.unsetCVTerms()
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,@@m.getAnnotation().toXMLString())
end
def test_SyncAnnotation_modifyCVTerms_3
cv = @@m.getCVTerm(0).clone()
@@m.unsetCVTerms()
@@m.addCVTerm(cv)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,@@m.getAnnotation().toXMLString())
end
def test_SyncAnnotation_modifyCVTerms_4
cv = @@m.getCVTerm(0).clone()
c = @@m.getCompartment(0)
c.addCVTerm(cv)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyCVTerms_5
c = @@m.getCompartment(6)
cv = c.getCVTerm(0).clone()
c.unsetCVTerms()
c.addCVTerm(cv)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyHistory_1
c = @@m.getCompartment(3)
mh = c.getModelHistory().clone()
c.unsetModelHistory()
c.setModelHistory(mh)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyHistory_2
@@m.unsetModelHistory()
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,@@m.getAnnotation().toXMLString())
end
def test_SyncAnnotation_modifyHistory_3
mh = @@m.getModelHistory().clone()
@@m.unsetModelHistory()
@@m.setModelHistory(mh)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,@@m.getAnnotation().toXMLString())
end
def test_SyncAnnotation_modifyHistory_4
c = @@m.getCompartment(0)
mh = @@m.getModelHistory().clone()
c.setModelHistory(mh)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_modifyHistory_5
c = @@m.getCompartment(5)
mh = c.getModelHistory().clone()
c.unsetModelHistory()
c.setModelHistory(mh)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_noChanges_1
c = @@m.getCompartment(1)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_noChanges_2
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,@@m.getAnnotation().toXMLString())
end
def test_SyncAnnotation_stringChangesMetaid
c = LibSBML::Compartment.new(3,1)
c.setMetaId("_000005")
c.setId("A")
addedAnn = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
c.setAnnotation(addedAnn)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_stringChangesMetaid_1
c = LibSBML::Model.new(2,3)
c.setMetaId("_000005")
c.setId("A")
addedAnn = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
c.setAnnotation(addedAnn)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_stringChangesMetaid_2
c = LibSBML::Compartment.new(2,3)
c.setMetaId("_000005")
c.setId("A")
addedAnn = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
c.setAnnotation(addedAnn)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_stringChangesMetaid_3
c = LibSBML::Model.new(3,1)
c.setMetaId("_000005")
c.setId("A")
addedAnn = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
c.setAnnotation(addedAnn)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
def test_SyncAnnotation_stringHistoryWhenNotValid
c = LibSBML::Compartment.new(2,4)
c.setMetaId("_000003")
c.setId("A")
addedAnn = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
c.setAnnotation(addedAnn)
expected = "\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" Le Novere\n" +
" Nicolas\n" +
" \n" +
" lenov@ebi.ac.uk\n" +
" \n" +
" EMBL-EBI\n" +
" \n" +
" \n" +
" \n" +
" \n" +
" \n" +
" 2005-02-02T14:56:11Z\n" +
" \n" +
" \n" +
" 2006-05-30T10:46:02Z\n" +
" \n" +
" \n" +
" \n" +
" \n" +
""
assert_equal true, equals(expected,c.toSBML())
end
end