def test_synth_subtree(self):
def res_checker(test_case, results):
tree = results.tree
test_case.assertEqual(tree.seed_node.taxon.ott_id, 803675)
args = ['--ott-id=803675']
ex_runner(self, 'synth_subtree.py', args, res_checker)
def test_study_properties(self):
def res_checker(test_case, results):
rd = results.response_dict
test_case.assertTrue('tree_properties' in rd)
test_case.assertTrue('study_properties' in rd)
ex_runner(self, 'study_properties.py', [], res_checker)
def test_find_studies(self):
res = {"matched_studies": [{"ot:studyId": "pg_719"}]}
def res_checker(test_case, results):
test_case.assertEqual(res, results.response_dict)
args = ['--property=ot:studyId', 'pg_719']
ex_runner(self, 'find_studies.py', args, res_checker)
def test_synth_subtree(self):
def res_checker(test_case, results):
taxon = results.taxon
test_case.assertEqual(taxon.ott_id, 437610)
test_case.assertTrue(len(taxon.lineage) > 0)
args = ['--ott-id=437610']
ex_runner(self, 'taxon_info.py', args, res_checker)
def test_synth_node_info(self):
def res_checker(test_case, results):
nd_ref = results.node_ref
nd_id = nd_ref.node_id
# for n, ndf in enumerate(nd_ref.lineage):
# print('lineage_node_ref {} id={}'.format(n, ndf.node_id))
test_case.assertTrue(nd_id == 'ott189136' or nd_id.startswith('mrca'))
args = ['--ott-ids=189136', '--include-lineage']
ex_runner(self, 'synth_node_info.py', args, res_checker)
def test_synth_induced_subtree(self):
def res_checker(test_case, results):
tree = results.tree
tn = tree.taxon_namespace
for node in tree.leaf_node_iter():
taxon = node.taxon
if taxon.label != 'mrcaott246ott1566':
test_case.assertEqual(199350, taxon.ott_id)
args = ['--ott-ids=199350',
'--node-ids=mrcaott246ott1566'] # ott733093']
ex_runner(self, 'synth_induced_subtree.py', args, res_checker)
def test_tnrs_infer_contexts(self):
res = {
"ambiguous_names": [],
"context_name": "Mammals",
"context_ott_id": 244265,
}
def res_checker(test_case, results):
test_case.assertEqual(res, results.response_dict)
args = ['Pan', 'H**o']
ex_runner(self, 'tnrs_infer_contexts.py', args, res_checker)
def test_find_trees(self):
obj = {
"matched_trees": [
{"ot:studyId": "pg_719", "ot:treeId": "tree1294"},
{"ot:studyId": "pg_719", "ot:treeId": "tree1295"},
{"ot:studyId": "pg_719", "ot:treeId": "tree1296"}
],
"ot:studyId": "pg_719"
}
res = {"matched_studies": [obj]}
def res_checker(test_case, results):
test_case.assertEqual(res, results.response_dict)
args = ['--property=ot:studyId', 'pg_719']
ex_runner(self, 'find_trees.py', args, res_checker)
def test_get_tree(self):
obj = {
"matched_trees": [{
"ot:studyId": "pg_719",
"ot:treeId": "tree1294"
}, {
"ot:studyId": "pg_719",
"ot:treeId": "tree1295"
}, {
"ot:studyId": "pg_719",
"ot:treeId": "tree1296"
}],
"ot:studyId":
"pg_719"
}
res = {"matched_studies": [obj]}
def res_checker(test_case, results):
test_case.assertTrue(str(results.tree).startswith('('))
args = ['ot_1877', 'tree3', '--format=object']
ex_runner(self, 'get_tree.py', args, res_checker)
def test_tnrs_match_example(self):
args = ['Characidiopsis acuta']
ex_runner(self, 'tnrs_match_names.py', args)
def test_about_example(self):
ex_runner(self, 'about.py', None)