class TestTreemachine(unittest.TestCase):
def setUp(self):
self.domains = get_test_ot_service_domains()
self.treemachine = Treemachine(self.domains)
def testSourceTree(self):
source_id_list = self.treemachine.synthetic_tree_id_list
self.assertTrue(isinstance(source_id_list, list))
# commented out due to https://github.com/OpenTreeOfLife/treemachine/issues/170
# f = source_id_list[0]
# r = self.treemachine.get_source_tree(**f)
# self.assertTrue(r['newick'].startswith('('))
def testSynthTree(self):
cdict = self.treemachine.synthetic_tree_info
if self.treemachine.use_v1:
for key in ['draftTreeName', 'startNodeTaxName', 'startNodeID', 'startNodeOTTId']:
self.assertTrue(key in cdict)
tree_id = cdict['draftTreeName']
node_id = str(cdict['startNodeID']) # Odd that this is a string
x = self.treemachine.get_synthetic_tree(tree_id,
format='newick',
node_id=node_id,
max_depth=2)
self.assertEqual(x['treeID'], tree_id)
self.assertTrue(x['newick'].startswith('('))
else:
tree_id, node_id = test_tol_about(self, cdict)
# This now exceed the limit for tips in a tree, so expect HTTPError (400 Client Error: Bad Request)
# instead of the previously expected ValueError
self.assertRaises(HTTPError,
self.treemachine.get_synthetic_tree,
tree_id,
format='newick',
node_id=node_id)
def testPrunedTree(self):
if self.treemachine.use_v1:
r = self.treemachine.get_synth_tree_pruned(ott_ids=example_ott_id_list)
self.assertEqual(len(example_ott_id_list), len(r['found_nodes']))
else:
r = self.treemachine.induced_subtree(ott_ids=example_ott_id_list)
for key in ['ott_ids_not_in_tree', u'node_ids_not_in_tree']:
self.assertEqual(r[key], [])
self.assertTrue(r['newick'].startswith('('))
def testMRCA(self):
if not self.treemachine.use_v1:
r = self.treemachine.mrca(ott_ids=example_ott_id_list)
self.assertTrue('mrca_node_id' in r)
# print('node_info is', self.treemachine.node_info(r['mrca_node_id']))
@unittest.skipIf(True, 'not sure whether this should be skipped...')
def testSearchForTaxon(self):
taxomachine = Taxomachine(self.domains)
anolis_taxon = taxomachine.autocomplete('Anolis')
ott_id = anolis_taxon[0]['ottId']
node_id = self.treemachine.get_node_id_for_ott_id(ott_id)
self.treemachine.get_synthetic_tree(format='newick', node_id=node_id, max_depth=12)
def setUp(self):
self.domains = get_test_ot_service_domains()
self.treemachine = Treemachine(self.domains)
class TestTreemachine(unittest.TestCase):
def setUp(self):
self.domains = get_test_ot_service_domains()
self.treemachine = Treemachine(self.domains)
def testSourceTree(self):
source_id_list = self.treemachine.synthetic_tree_id_list
self.assertTrue(isinstance(source_id_list, list))
f = source_id_list[0]
r = self.treemachine.get_source_tree(**f)
self.assertTrue(r['newick'].startswith('('))
def testSynthTree(self):
cdict = self.treemachine.synthetic_tree_info
if self.treemachine.use_v1:
for key in [
'draftTreeName', 'startNodeTaxName', 'startNodeID',
'startNodeOTTId'
]:
self.assertTrue(key in cdict)
tree_id = cdict['draftTreeName']
node_id = str(
cdict['startNodeID']) # Odd that this is a string
x = self.treemachine.get_synthetic_tree(tree_id,
format='newick',
node_id=node_id,
max_depth=2)
self.assertEqual(x['treeID'], tree_id)
self.assertTrue(x['newick'].startswith('('))
else:
for key in [
u'date', u'num_source_studies', u'root_taxon_name',
u'study_list', u'root_ott_id', u'root_node_id', u'tree_id',
u'taxonomy_version', u'num_tips'
]:
self.assertTrue(key in cdict)
tree_id = cdict['tree_id']
node_id = str(cdict['root_node_id']) # Odd that this is a string
self.assertRaises(ValueError,
self.treemachine.get_synthetic_tree,
tree_id,
format='newick',
node_id=node_id)
def testPrunedTree(self):
ott_ids = [
515698, 515712, 149491, 876340, 505091, 840022, 692350, 451182,
301424, 876348, 515698, 1045579, 267484, 128308, 380453, 678579,
883864, 863991, 3898562, 23821, 673540, 122251, 106729, 1084532,
541659
]
if self.treemachine.use_v1:
r = self.treemachine.get_synth_tree_pruned(ott_ids=ott_ids)
self.assertEqual(len(ott_ids), len(r['found_nodes']))
else:
r = self.treemachine.induced_subtree(ott_ids=ott_ids)
for key in ['ott_ids_not_in_tree', u'node_ids_not_in_tree']:
self.assertEqual(r[key], [])
self.assertTrue(r['subtree'].startswith('('))
def testMRCA(self):
ott_ids = [
515698, 515712, 149491, 876340, 505091, 840022, 692350, 451182,
301424, 876348, 515698, 1045579, 267484, 128308, 380453, 678579,
883864, 863991, 3898562, 23821, 673540, 122251, 106729, 1084532,
541659
]
if not self.treemachine.use_v1:
r = self.treemachine.mrca(ott_ids=ott_ids)
self.assertTrue('mrca_node_id' in r)
print('node_info is',
self.treemachine.node_info(r['mrca_node_id']))
@unittest.skipIf(True, 'not sure whether this should be skipped...')
def testSearchForTaxon(self):
taxomachine = Taxomachine(self.domains)
anolis_taxon = taxomachine.autocomplete('Anolis')
ottId = anolis_taxon[0]['ottId']
node_id = self.treemachine.get_node_id_for_ott_id(ottId)
self.treemachine.get_synthetic_tree(format='newick',
node_id=node_id,
max_depth=12)
def setUp(self):
self.domains = get_test_ot_service_domains()
self.treemachine = Treemachine(self.domains)
class TestTreemachine(unittest.TestCase):
def setUp(self):
self.domains = get_test_ot_service_domains()
self.treemachine = Treemachine(self.domains)
def testSourceTree(self):
source_id_list = self.treemachine.synthetic_tree_id_list
self.assertTrue(isinstance(source_id_list, list))
f = source_id_list[0]
r = self.treemachine.get_source_tree(**f)
self.assertTrue(r['newick'].startswith('('))
def testSynthTree(self):
cdict = self.treemachine.synthetic_tree_info
if self.treemachine.use_v1:
for key in ['draftTreeName', 'startNodeTaxName', 'startNodeID', 'startNodeOTTId']:
self.assertTrue(key in cdict)
tree_id = cdict['draftTreeName']
node_id = str(cdict['startNodeID']) # Odd that this is a string
x = self.treemachine.get_synthetic_tree(tree_id,
format='newick',
node_id=node_id,
max_depth=2)
self.assertEqual(x['treeID'], tree_id)
self.assertTrue(x['newick'].startswith('('))
else:
for key in [u'date',
u'num_source_studies',
u'root_taxon_name',
u'study_list',
u'root_ott_id',
u'root_node_id',
u'tree_id',
u'taxonomy_version',
u'num_tips']:
self.assertTrue(key in cdict)
tree_id = cdict['tree_id']
node_id = str(cdict['root_node_id']) # Odd that this is a string
self.assertRaises(ValueError,
self.treemachine.get_synthetic_tree,
tree_id,
format='newick',
node_id=node_id)
def testPrunedTree(self):
ott_ids = [515698, 515712, 149491, 876340, 505091, 840022, 692350, 451182, 301424, 876348, 515698, 1045579,
267484, 128308, 380453, 678579, 883864, 863991,
3898562, 23821, 673540, 122251, 106729, 1084532, 541659]
if self.treemachine.use_v1:
r = self.treemachine.get_synth_tree_pruned(ott_ids=ott_ids)
self.assertEqual(len(ott_ids), len(r['found_nodes']))
else:
r = self.treemachine.induced_subtree(ott_ids=ott_ids)
for key in ['ott_ids_not_in_tree', u'node_ids_not_in_tree']:
self.assertEqual(r[key], [])
self.assertTrue(r['subtree'].startswith('('))
def testMRCA(self):
ott_ids = [515698, 515712, 149491, 876340, 505091, 840022, 692350, 451182,
301424, 876348, 515698, 1045579, 267484,
128308, 380453, 678579, 883864, 863991, 3898562, 23821, 673540, 122251, 106729, 1084532, 541659]
if not self.treemachine.use_v1:
r = self.treemachine.mrca(ott_ids=ott_ids)
self.assertTrue('mrca_node_id' in r)
print('node_info is', self.treemachine.node_info(r['mrca_node_id']))
@unittest.skipIf(True, 'not sure whether this should be skipped...')
def testSearchForTaxon(self):
taxomachine = Taxomachine(self.domains)
anolis_taxon = taxomachine.autocomplete('Anolis')
ottId = anolis_taxon[0]['ottId']
node_id = self.treemachine.get_node_id_for_ott_id(ottId)
self.treemachine.get_synthetic_tree(format='newick', node_id=node_id, max_depth=12)