def test_good_gbif_ids(self):
"""Tests that tree can be retrieved when input is set of GBIF ids
"""
gbif_ids = GBIF_ID_MAP.keys()
id_map = open_tree.get_ottids_from_gbifids(gbif_ids)
# Make sure we haven't lost any ids
assert len(gbif_ids) == len(id_map.keys())
resp = open_tree.induced_subtree(
id_map.keys(), label_format=open_tree.LABEL_FORMAT.ID)
newick = resp['newick']
tree = dendropy.Tree.get(data=newick, schema='newick')
# Number of labels in the tree plus the number of unmatched should
# be less than or equal the number of keys in id_map. Less than if
# one of the ids matches somewhere other than a tiop
assert len(tree.taxon_namespace) + len(
resp['unmatched_ott_ids']) <= len(id_map.keys())
for taxon in tree.taxon_namespace:
# Id map contains integers as of now, check to make sure each tip
# is in mapping
# Taxon labels look like 'ott{ottid}'
search_label = taxon.label.strip('ott')
assert search_label in id_map.keys()
# Make sure any unmatched ids are in mapping
for unmatched in resp['unmatched_ott_ids']:
assert str(unmatched) in id_map.keys()
def test_all_good_ottids(self):
"""Test that the service responds correctly when only good ids are used
"""
resp = open_tree.induced_subtree(
GOOD_OTT_IDS, label_format=open_tree.LABEL_FORMAT.ID)
newick = resp['newick']
# Should fail if bad newick
tree = dendropy.Tree.get(data=newick, schema='newick')
# Make sure tree is not None
assert tree is not None
def test_all_bad_ottids(self):
"""Test that the service responds appropriately when given bad data
"""
resp = open_tree.induced_subtree(
BAD_OTT_IDS, label_format=open_tree.LABEL_FORMAT.ID)
newick = resp['newick']
# Should fail if bad newick
tree = dendropy.Tree.get(data=newick, schema='newick')
# Make sure tree is not None
assert tree is not None
def test_some_bad_ottids(self):
"""Test that the service handles a mix of good and bad ott ids
"""
test_ids = GOOD_OTT_IDS
test_ids.extend(BAD_OTT_IDS)
resp = open_tree.induced_subtree(
test_ids, label_format=open_tree.LABEL_FORMAT.ID)
newick = resp['newick']
# Should fail if bad newick
tree = dendropy.Tree.get(data=newick, schema='newick')
# Make sure tree is not None
assert tree is not None
def test_good_taxa(self):
"""Tests that a tree can be retrieved starting with good taxon names."""
taxa_info, unmatched_names = open_tree.get_info_for_names(TAXON_NAMES)
assert len(unmatched_names) == 0
ott_ids = [tax['ott_id'] for tax in taxa_info.values()]
assert len(ott_ids) == len(TAXON_NAMES)
resp = open_tree.induced_subtree(
ott_ids, label_format=open_tree.LABEL_FORMAT.ID
)
newick = resp['newick']
tree = dendropy.Tree.get(data=newick, schema='newick')
assert len(tree.taxon_namespace) == len(ott_ids)
for taxon in tree.taxon_namespace:
# Id map contains integers as of now, check to make sure each tip
# is in mapping
# Taxon labels look like 'ott{ottid}'
search_label = taxon.label.replace('ott', '')
assert int(search_label) in ott_ids