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import json
from augur.__version__ import __version__
from augur.errors import AugurError
from augur.util_support.node_data_file import NodeDataFile
import pytest
@pytest.fixture()
def build_node_data_file(tmpdir):
def _build_node_data_file(contents):
with open(f"{tmpdir}/node.json", "w") as file:
file.write(contents)
return NodeDataFile(f"{tmpdir}/node.json")
return _build_node_data_file
class TestNodeDataFile:
def test_items(self, build_node_data_file):
node_data_file = build_node_data_file(
"""
{
"generated_by": "some app",
"nodes": { "a": 5 }
}
"""
)
items = node_data_file.items()
assert len(items) == 1
assert "generated_by" not in items
def test_validate_valid(self, build_node_data_file):
# Implied assertion that no exceptions are raised
build_node_data_file(
f"""
{{
"annotations": {{ "nuc": {{ "start": 1, "end": 100 }} }},
"generated_by": {{ "program": "augur", "version": "{__version__}" }},
"nodes": {{ "a": 5 }}
}}
"""
)
def test_validate_invalid_annotation(self, build_node_data_file):
with pytest.raises(AugurError, match="annotations.*invalid JSON format"):
build_node_data_file(
"""
{
"annotations": "hhhhh",
"nodes": { "a": 5 }
}
"""
)
def test_validate_nodes_not_dict(self, build_node_data_file):
with pytest.raises(AugurError, match="is not a dictionary"):
build_node_data_file('{ "nodes": "hhh" }')
def test_validate_incompatible_augur_version(self, build_node_data_file):
with pytest.raises(AugurError, match="incompatibility detected"):
build_node_data_file(
"""
{
"generated_by": { "program": "augur", "version": "0.1" },
"nodes": { "a": 5 }
}
"""
)
def test_validate_malformed_json(self, build_node_data_file):
with pytest.raises(json.decoder.JSONDecodeError):
build_node_data_file("hhhhhhhhhh")
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