class TestProxy(unittest.TestCase):
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
def testTaxoRooting(self):
ott = OTT()
phylo = self.np.get_tree(tree_id='tree324')
evaluate_tree_rooting(self.nexson, ott, phylo)
class TestProxy(unittest.TestCase):
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
def testTaxoRooting(self):
ott = OTT()
phylo = self.np.get_tree(tree_id='tree324')
evaluate_tree_rooting(self.nexson, ott, phylo)
class TestProxy(unittest.TestCase):
def setUp(self):
blob = pathmap.nexson_obj('9/v1.2.json')
self.np = NexsonProxy(nexson=blob)
def testGetters(self):
self.assertIs(self.np.get_tree('bogus'), None)
self.assertIsNot(self.np.get_tree('tree1'), None)
self.assertIs(self.np.get_tree('otu123'), None)
self.assertIs(self.np.get_otu('bogus'), None)
self.assertIs(self.np.get_otu('tree1'), None)
self.assertIsNot(self.np.get_otu('otu123'), None)
def testCaching(self):
f = self.np.get_tree('tree1')
s = self.np.get_tree('tree1')
self.assertIs(f, s)
fn = f.get_node('node247')
sn = s.get_node('node247')
self.assertIs(fn, sn)
fo = self.np.get_otu('otu123')
so = sn.otu
self.assertIs(fo, so)
def testTreeIter(self):
ntp = self.np.get_tree('tree1')
nbi = ntp['nodeById']
ebi = ntp['edgeBySourceId']
ks = set(nbi.keys())
its = set()
edge_less = None
for node in ntp:
its.add(node.node_id)
self.assertIs(node.node, nbi[node.node_id])
if node.edge is None:
self.assertIs(edge_less, None)
edge_less = node.node_id
else:
s = node.edge['@source']
ed = ebi[s]
self.assertIs(node.edge, ed[node.edge_id])
self.assertEqual(ntp['^ot:rootNodeId'], edge_less)
self.assertEqual(ks, its)
# looking for the tree properties: ot:unrootedTree, ot:inGroupClade
# and the study property ot:candidateTreeForSynthesis
print("studyid,treeid,preferred,ingroup,unrooted")
for d in included:
studyid = d['studyID']
treeid = d['treeID']
# expect these defaults for synthesis trees
unrootedTree = False
ingroupSpecified = True
preferredTree = True
check = True
nx = phy.get_study(studyid)['data']
np = NexsonProxy(nexson=nx)
candidateTreeList = np._nexml_el['^ot:candidateTreeForSynthesis']
if treeid not in candidateTreeList:
preferredTree = False
check = False
tree = np.get_tree(treeid)
if tree['^ot:inGroupClade'] == "":
ingroupSpecified = False
check = False
if tree['^ot:unrootedTree']:
unrootedTree = True
check = False
if not check:
print("{s},{t},{p},{i},{r}").format(
s=studyid,
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
def setUp(self):
blob = pathmap.nexson_obj('9/v1.2.json')
self.np = NexsonProxy(nexson=blob)
def setUp(self):
blob = pathmap.nexson_obj('9/v1.2.json')
self.np = NexsonProxy(nexson=blob)
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
