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from augur.util_support.node_data_reader import NodeDataReader
import pytest
@pytest.fixture()
def prepare_file(tmpdir):
def _prepare_file(name, contents):
with open(f"{tmpdir}/{name}", "w") as file:
file.write(contents)
return _prepare_file
class TestNodeDataFile:
def test_read(self, tmpdir, prepare_file):
prepare_file(
"file1.json",
"""
{
"a": 5,
"nodes": {
"NODE_1": { "x": 5 },
"NODE_2": { "x": 6 },
"NODE_3": { "x": 7 }
}
}
""",
)
prepare_file(
"file2.json",
"""
{
"nodes": {
"NODE_3": { "y": 8 },
"NODE_4": { "x": 9 }
}
}
""",
)
node_data = NodeDataReader(
[f"{tmpdir}/file1.json", f"{tmpdir}/file2.json"]
).read()
assert node_data == {
"a": 5,
"nodes": {
"NODE_1": {"x": 5},
"NODE_2": {"x": 6},
"NODE_3": {"x": 7, "y": 8},
"NODE_4": {"x": 9},
},
}
def test_read_bad_file(self):
NodeDataReader(["/does/not/exist.json"])
def test_read_dict_nonuniformity(self, tmpdir, prepare_file):
prepare_file(
"file1.json",
"""
{
"nodes": {"node_name": "some_value"},
"a": {}
}
""",
)
prepare_file(
"file2.json",
"""
{
"nodes": {"node_name": "some_other_value"},
"a": "nah"
}
""",
)
with pytest.raises(SystemExit):
NodeDataReader([f"{tmpdir}/file1.json", f"{tmpdir}/file2.json"]).read()
def test_read_check_against_tree(self, tmpdir, prepare_file):
prepare_file(
"file1.json",
"""
{
"a": 5,
"nodes": {
"NODE_1": { "x": 5 },
"NODE_2": { "x": 6 },
"NODE_3": { "x": 7 }
}
}
""",
)
prepare_file("tree.newick", "(NODE_1, NODE_2) NODE_3")
NodeDataReader([f"{tmpdir}/file1.json"], f"{tmpdir}/tree.newick").read()
def test_read_check_against_tree_bad(self, tmpdir, prepare_file):
prepare_file(
"file1.json",
"""
{
"a": 5,
"nodes": {
"NODE_1": { "x": 5 },
"NODE_2": { "x": 6 },
"NODE_3": { "x": 7 }
}
}
""",
)
prepare_file("tree.newick", "Noooooooooope")
with pytest.raises(SystemExit):
NodeDataReader([f"{tmpdir}/file1.json"], f"{tmpdir}/tree.newick").read()
def test_read_check_against_missing_tree(self, tmpdir):
with pytest.raises(SystemExit):
node_names_from_tree = NodeDataReader(
[f"{tmpdir}/file1.json"],
f"{tmpdir}/missing_file.txt"
).node_names_from_tree_file
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