def test_singlular(self):
"""Clade, Phylogeny: Singular properties for plural attributes."""
conf = PX.Confidence(0.9, "bootstrap")
taxo = PX.Taxonomy(rank="genus")
# Clade.taxonomy, Clade.confidence
clade = PX.Clade(confidences=[conf], taxonomies=[taxo])
self.assertEqual(clade.confidence.type, "bootstrap")
self.assertEqual(clade.taxonomy.rank, "genus")
# raise if len > 1
clade.confidences.append(conf)
self.assertRaises(AttributeError, getattr, clade, "confidence")
clade.taxonomies.append(taxo)
self.assertRaises(AttributeError, getattr, clade, "taxonomy")
# None if []
clade.confidences = []
self.assertEqual(clade.confidence, None)
clade.taxonomies = []
self.assertEqual(clade.taxonomy, None)
# Phylogeny.confidence
tree = PX.Phylogeny(True, confidences=[conf])
self.assertEqual(tree.confidence.type, "bootstrap")
tree.confidences.append(conf)
self.assertRaises(AttributeError, getattr, tree, "confidence")
tree.confidences = []
self.assertEqual(tree.confidence, None)
def _parse_phylogeny(self, parent):
"""Parse a single phylogeny within the phyloXML tree (PRIVATE).
Recursively builds a phylogenetic tree with help from parse_clade, then
clears the XML event history for the phylogeny element and returns
control to the top-level parsing function.
"""
phylogeny = PX.Phylogeny(
**_dict_str2bool(parent.attrib, ["rooted", "rerootable"]))
list_types = {
# XML tag, plural attribute
"confidence": "confidences",
"property": "properties",
"clade_relation": "clade_relations",
"sequence_relation": "sequence_relations",
}
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == "start" and tag == "clade":
if phylogeny.root is not None:
raise ValueError(
"Phylogeny object should only have 1 clade")
phylogeny.root = self._parse_clade(elem)
continue
if event == "end":
if tag == "phylogeny":
parent.clear()
break
# Handle the other non-recursive children
if tag in list_types:
getattr(phylogeny,
list_types[tag]).append(getattr(self, tag)(elem))
# Complex types
elif tag in ("date", "id"):
setattr(phylogeny, tag, getattr(self, tag)(elem))
# Simple types
elif tag in ("name", "description"):
setattr(phylogeny, tag, _collapse_wspace(elem.text))
# Unknown tags
elif namespace != NAMESPACES["phy"]:
phylogeny.other.append(self.other(elem, namespace, tag))
parent.clear()
else:
# NB: This shouldn't happen in valid files
raise PhyloXMLError("Misidentified tag: " + tag)
return phylogeny
def _parse_phylogeny(self, parent):
"""Parse a single phylogeny within the phyloXML tree (PRIVATE).
Recursively builds a phylogenetic tree with help from parse_clade, then
clears the XML event history for the phylogeny element and returns
control to the top-level parsing function.
"""
phylogeny = PX.Phylogeny(**_dict_str2bool(parent.attrib,
['rooted', 'rerootable']))
list_types = {
# XML tag, plural attribute
'confidence': 'confidences',
'property': 'properties',
'clade_relation': 'clade_relations',
'sequence_relation': 'sequence_relations',
}
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == 'start' and tag == 'clade':
assert phylogeny.root is None, \
"Phylogeny object should only have 1 clade"
phylogeny.root = self._parse_clade(elem)
continue
if event == 'end':
if tag == 'phylogeny':
parent.clear()
break
# Handle the other non-recursive children
if tag in list_types:
getattr(phylogeny, list_types[tag]).append(
getattr(self, tag)(elem))
# Complex types
elif tag in ('date', 'id'):
setattr(phylogeny, tag, getattr(self, tag)(elem))
# Simple types
elif tag in ('name', 'description'):
setattr(phylogeny, tag, _collapse_wspace(elem.text))
# Unknown tags
elif namespace != NAMESPACES['phy']:
phylogeny.other.append(self.other(elem, namespace, tag))
parent.clear()
else:
# NB: This shouldn't happen in valid files
raise PhyloXMLError('Misidentified tag: ' + tag)
return phylogeny
