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import unittest
import tempfile
import os
from tests.common import createTestFile, readTestDbTable
from tol_data.gen_otol_data import genData
def runGenData(treeFileContents: str, annFileContents: str, pickedFileContents: str):
""" Sets up files to be read by genData(), runs it, reads the output database, and returns node+edge info """
with tempfile.TemporaryDirectory() as tempDir:
# Create temp tree file
treeFile = os.path.join(tempDir, 'tree.tre')
createTestFile(treeFile, treeFileContents)
# Create temp annotations file
annFile = os.path.join(tempDir, 'ann.json')
createTestFile(annFile, annFileContents)
# Create temp picked names file
pickedFile = os.path.join(tempDir, 'pn.txt')
createTestFile(pickedFile, pickedFileContents)
# Run genData()
dbFile = os.path.join(tempDir, 'data.db')
genData(treeFile, annFile, pickedFile, dbFile)
# Read database
nodes = readTestDbTable(dbFile, 'SELECT name, id, tips FROM nodes')
edges = readTestDbTable(dbFile, 'SELECT parent, child, p_support FROM edges')
return nodes, edges
class TestGenData(unittest.TestCase):
def setUp(self):
self.maxDiff = None # Remove output-diff size limit
def test_newick(self):
treeFileContents = """
(
'land plants ott2',
(
'TRAVELLER''s tree ott100',
(domestic_banana_ott4, (lemon_ott6, orange_ott7)citrus_ott5)mrcaott4ott5
) mrcaott100ott4,
'Highly Unu2u8| name!! ott999',
'citrus ott230'
)cellular_organisms_ott1;"""
annFileContents = '{"nodes": {}}'
pickedFileContents = ''
nodes, edges = runGenData(treeFileContents, annFileContents, pickedFileContents)
self.assertEqual(nodes, {
('land plants', 'ott2', 1),
('traveller\'s tree', 'ott100', 1),
('domestic banana', 'ott4', 1),
('lemon', 'ott6', 1),
('orange', 'ott7', 1),
('citrus', 'ott5', 2),
('[citrus + domestic banana]', 'mrcaott4ott5', 3),
('[citrus + traveller\'s tree]', 'mrcaott100ott4', 4),
('highly unu2u8| name!! ', 'ott999', 1),
('citrus [2]', 'ott230', 1),
('cellular organisms', 'ott1', 7),
})
self.assertEqual(edges, {
('cellular organisms', 'land plants', 0),
('cellular organisms', '[citrus + traveller\'s tree]', 0),
('cellular organisms', 'highly unu2u8| name!! ', 0),
('cellular organisms', 'citrus [2]', 0),
('[citrus + traveller\'s tree]', 'traveller\'s tree', 0),
('[citrus + traveller\'s tree]', '[citrus + domestic banana]', 0),
('[citrus + domestic banana]', 'domestic banana', 0),
('[citrus + domestic banana]', 'citrus', 0),
('citrus', 'lemon', 0),
('citrus', 'orange', 0),
})
def test_newick_invalid(self):
with self.assertRaises(Exception):
runGenData('(A,B,(C,D));', '{"nodes": {}}', '')
def test_annotations(self):
treeFileContents = '(two_ott2, three_ott3, four_ott4)one_ott1;'
annFileContents = """
{
"date_completed": "xxx",
"nodes": {
"ott3": {
"supported_by": {
"tree1": "node1"
}
},
"ott4": {
"supported_by": {
"tree1": "node2",
"tree2": "node100"
},
"conflicts_with": {
"tree3": ["x", "y"]
}
}
}
}"""
nodes, edges = runGenData(treeFileContents, annFileContents, '')
self.assertEqual(nodes, {
('one', 'ott1', 3),
('two', 'ott2', 1),
('three', 'ott3', 1),
('four', 'ott4', 1),
})
self.assertEqual(edges, {
('one', 'two', 0),
('one', 'three', 1),
('one', 'four', 0),
})
def test_picked_names_file(self):
treeFileContents = '(one_ott2, two_ott3)one_ott1;'
pickedFileContents = 'one|ott2'
nodes, edges = runGenData(treeFileContents, '{"nodes": {}}', pickedFileContents)
self.assertEqual(nodes, {
('one [2]', 'ott1', 2),
('one', 'ott2', 1),
('two', 'ott3', 1),
})
self.assertEqual(edges, {
('one [2]', 'one', 0),
('one [2]', 'two', 0),
})
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