def test_RDFAnnotation_testMissingAbout(self):
withAbout = wrapString(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description rdf:about=\"#_000004\">\n" +
" <bqbiol:is>\n" + " <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:is>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" +
" </annotation>")
emptyAbout = wrapString(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description rdf:about=\"\">\n" +
" <bqbiol:is>\n" + " <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:is>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" +
" </annotation>")
noAbout = wrapString(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description>\n" + " <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:is>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" +
" </annotation>")
cvTerms = libsbml.CVTermList()
stream = libsbml.XMLInputStream(withAbout, False)
node = libsbml.XMLNode(stream)
libsbml.RDFAnnotationParser.parseRDFAnnotation(node, cvTerms)
self.assert_(cvTerms.getSize() == 1)
cvTerms = None
cvTerms = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(node, cvTerms)
self.assert_(cvTerms.getSize() == 1)
cvTerms = None
cvTerms = None
cvTerms = libsbml.CVTermList()
stream1 = libsbml.XMLInputStream(emptyAbout, False)
node1 = libsbml.XMLNode(stream1)
libsbml.RDFAnnotationParser.parseRDFAnnotation(node1, cvTerms)
self.assert_(cvTerms.getSize() == 0)
cvTerms = None
cvTerms = None
cvTerms = libsbml.CVTermList()
stream2 = libsbml.XMLInputStream(noAbout, False)
node2 = libsbml.XMLNode(stream2)
libsbml.RDFAnnotationParser.parseRDFAnnotation(node2, cvTerms)
self.assert_(cvTerms.getSize() == 0)
cvTerms = None
cvTerms = None
pass
def test_sbase_has_read(self):
compartment = libsbml.Compartment(3, 1)
assert compartment is not None
stream = libsbml.XMLInputStream(
"""<?xml version="1.0" encoding="utf-8"?>
<compartment id="vol1" name="compartment 1" size="2.0" />""", False)
compartment.read(stream)
assert compartment.id == 'vol1'
assert compartment.name == 'compartment 1'
assert compartment.volume == 2.0
def test_read_stylesheet_24(self):
info = libsbml.LocalRenderInformation(2, 4)
stream = libsbml.XMLInputStream(STYLE_SHEET, True)
info.read(stream)
assert info.id == 'SBGN_default'
line = info.getLineEnding('inhibitor')
assert isinstance(line, libsbml.LineEnding)
assert line.id == 'inhibitor'
group = line.getGroup()
assert isinstance(group, libsbml.RenderGroup)
assert group.stroke == 'black'
assert group.fill == 'black'
assert group.stroke_width == 0.1
assert group.getNumElements() > 0
p = group.getElement(0)
assert isinstance(p, libsbml.Polygon)
for elt in p.getListOfElements():
assert (isinstance(elt, libsbml.RenderPoint))
def test_downcast_polygon(self):
group = libsbml.RenderGroup(3, 1)
stream = libsbml.XMLInputStream(
"""<?xml version="1.0" encoding="utf-8"?>
<g stroke="black" stroke-width="0.1" fill="black">
<polygon>
<listOfElements>
<element xsi:type="RenderPoint" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" x="0.0" y="0.0"/>
<element xsi:type="RenderPoint" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" x="0.3" y="0.0"/>
<element xsi:type="RenderPoint" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" x="0.3" y="8.0"/>
<element xsi:type="RenderPoint" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" x="0.0" y="8.0"/>
</listOfElements>
</polygon>
</g> """, False)
group.read(stream)
assert group.stroke == 'black'
assert group.fill == 'black'
assert group.stroke_width == 0.1
assert group.getNumElements() > 0
p = group.getElement(0)
assert isinstance(p, libsbml.Polygon)
for elt in p.getListOfElements():
assert (isinstance(elt, libsbml.RenderPoint))
import libsbml
info = libsbml.LocalRenderInformation()
#stream = libsbml.XMLInputStream("/Development/sbwBuild/source/SBMLLayout/SBMLExtension/SBGNstyles.xml")
stream = libsbml.XMLInputStream("SBGNstyles.xml")
info.read(stream)
print("lri: ", info.getLevel(), info.getVersion())
les = info.getListOfLineEndings()
print("les: ", type(les), len(les))
for le in les:
if le.getId() == "product":
element = le.getGroup().getElement(0)
if element.getElementName() == "polygon":
print("list of elements: ", len(element.getListOfElements()))