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_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_dict_nonuniformity(self, tmpdir, prepare_file):
prepare_file(
"file1.json",
"""
{
"nodes": {},
"a": {}
}
""",
)
prepare_file(
"file2.json",
"""
{
"nodes": {},
"a": "nah"
}
""",
)
with pytest.raises(SystemExit):
NodeDataReader([f"{tmpdir}/file1.json",
f"{tmpdir}/file2.json"]).read()
def test_read_bad_file(self):
NodeDataReader(["/does/not/exist.json"])
def read_node_data(fnames, tree=None):
return NodeDataReader(fnames, tree).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