def test_query_different_sepchar(self):
"""
Test XpathExpressionEvaluator use with different sep char (.)
"""
xpath = XpathExpressionEvaluator(sep='.')
xpath.resolve('system.segid.residue', self.graph)
def test_query_wildcards(self):
"""
Test the use of wildcards in the search
"""
xpath = XpathExpressionEvaluator()
self.assertEqual(xpath.resolve('//*', self.graph).nodes.keys(), self.graph.nodes.keys())
self.assertEqual(set(xpath.resolve('/system/*/residue', self.graph).nodes.keys()), {3, 10, 21, 28})
def test_query_none_rootdesc(self):
"""
Test root down search using / from non-root position
"""
xpath = XpathExpressionEvaluator()
self.assertEqual(len(xpath.resolve('/segid', self.graph).nodes), 0)
self.assertEqual(len(xpath.resolve('/residue', self.graph).nodes), 0)
self.assertEqual(len(xpath.resolve('/segid/residue', self.graph).nodes), 0)
def test_query_rootdesc(self):
"""
Test root down search using /
"""
xpath = XpathExpressionEvaluator()
self.assertEqual(len(xpath.resolve('/', self.graph).nodes), 0)
self.assertEqual(
set(xpath.resolve('/system', self.graph).nodes.keys()), {1})
self.assertEqual(
set(xpath.resolve('/system/segid', self.graph).nodes.keys()),
{2, 20})
self.assertEqual(
set(
xpath.resolve('/system/segid/residue',
self.graph).nodes.keys()), {3, 10, 21, 28})
self.assertEqual(
set(xpath.resolve('/system//residue', self.graph).nodes.keys()),
{3, 10, 21, 28})
self.assertEqual(
set(
xpath.resolve('/system/segid/residue/atom',
self.graph).nodes.keys()),
{
4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23,
24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37
})
def xpath(self, expression, sep='/'):
"""
Evaluate XPath expression against graph
:param expression: XPath axpression
:type expression: :py:str
:param sep: XPath path location seperator
:type sep: :py:str
:rtype: :graphit:GraphAxis
"""
xpath = XpathExpressionEvaluator(sep=sep)
return xpath.resolve(expression, self)
def test_query_axis_filter(self):
"""
Test XPath axis based selection syntax
"""
xpath = XpathExpressionEvaluator()
self.assertEqual(
set(
xpath.resolve('//segid/child::residue',
self.graph).nodes.keys()), {3, 10, 21, 28})
self.assertEqual(
set(xpath.resolve('child::segid', self.graph).nodes.keys()),
{2, 20})
self.assertEqual(
set(
xpath.resolve('//residue[3]/following-sibling::residue',
self.graph).nodes.keys()), {21})
self.assertEqual(
set(
xpath.resolve('//atom/ancestor::segid',
self.graph).nodes.keys()), {2, 20})
self.assertEqual(
set(xpath.resolve('//residue/parent::*', self.graph).nodes.keys()),
{2, 20})
def test_query_indexselect(self):
"""
Test selection of nodes based on index
"""
xpath = XpathExpressionEvaluator()
self.assertEqual(set(xpath.resolve('//*[10]', self.graph).nodes.keys()), {11})
self.assertEqual(set(xpath.resolve('//residue[3]', self.graph).nodes.keys()), {28})
self.assertEqual(list(xpath.resolve('//residue[4]', self.graph).nodes.keys()), []) # Index out of range
self.assertEqual(set(xpath.resolve('//residue[3]/atom', self.graph).nodes.keys()), {29, 30, 31, 32, 33, 34,
35, 36, 37})
def test_query_selfdesc(self):
"""
Test basic path based query starting from current element (.)
"""
xpath = XpathExpressionEvaluator()
# By default we are at root
self.assertEqual(set(xpath.resolve('system', self.graph).nodes.keys()), {1})
self.assertEqual(set(xpath.resolve('system/segid/residue', self.graph).nodes.keys()), {3, 10, 21, 28})
# Start search from other node
sel = self.graph.getnodes(20)
self.assertEqual(len(xpath.resolve('system/segid/residue', sel).nodes), 0)
self.assertEqual(set(xpath.resolve('segid/residue', sel).nodes.keys()), {21, 28})
def test_query_attribute_filter(self):
"""
Test selection of nodes with filter on attributes
"""
xpath = XpathExpressionEvaluator()
self.assertEqual(
set(xpath.resolve('//segid[@value]', self.graph).nodes.keys()),
{2, 20})
self.assertEqual(
set(xpath.resolve('//residue[@extra]', self.graph).nodes.keys()),
{21, 28})
self.assertEqual(
set(
xpath.resolve('/system/segid/residue/atom[@elem="H"]',
self.graph).nodes.keys()), {9, 19, 27, 37})
self.assertEqual(
set(
xpath.resolve('//segid[@value="A"]/residue[@value=1]',
self.graph).nodes.keys()), {3})
self.assertEqual(
set(xpath.resolve('//atom[@value>620]', self.graph).nodes.keys()),
{
18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36,
37
})
self.assertEqual(
set(
xpath.resolve('//atom[@value>620][3]',
self.graph).nodes.keys()), {23})
self.assertEqual(
len(xpath.resolve('//atom[@value<608]', self.graph).nodes), 0)
self.assertEqual(
set(xpath.resolve('//atom[@value<=608]', self.graph).nodes.keys()),
{4})
# Select all nodes or all atom nodes with at least one attribute
sel = self.graph.getnodes(10)
self.assertEqual(set(xpath.resolve('//*[@*]', sel).nodes.keys()),
{10, 11, 12, 13, 14, 15, 16, 17, 18, 19})
self.assertEqual(set(xpath.resolve('//atom[@*]', sel).nodes.keys()),
{11, 12, 13, 14, 15, 16, 17, 18, 19})
