"""Unit tests for gene and drug CLI commands."""
import re
from unittest.mock import patch
from typer.testing import CliRunner
from biomcp.cli.main import app
runner = CliRunner()
def strip_ansi(text: str) -> str:
"""Remove ANSI escape codes from text."""
ansi_escape = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])")
return ansi_escape.sub("", text)
class TestGeneCLI:
"""Test gene CLI commands."""
def test_gene_help(self):
"""Test gene command shows help."""
result = runner.invoke(app, ["gene", "--help"])
assert result.exit_code == 0
assert "gene" in result.stdout.lower()
assert "get" in result.stdout.lower()
def test_gene_get_help(self):
"""Test gene get command shows help."""
result = runner.invoke(app, ["gene", "get", "--help"])
assert result.exit_code == 0
output = strip_ansi(result.stdout)
assert "gene" in output.lower()
assert "--json" in output
@patch("biomcp.cli.genes.get_gene")
def test_gene_get_success(self, mock_get_gene):
"""Test successful gene retrieval."""
mock_get_gene.return_value = "## Gene: TP53\n- **Symbol**: TP53"
result = runner.invoke(app, ["gene", "get", "TP53"])
assert result.exit_code == 0
assert "TP53" in result.stdout
mock_get_gene.assert_called_once()
@patch("biomcp.cli.genes.get_gene")
def test_gene_get_json_output(self, mock_get_gene):
"""Test gene retrieval with JSON output."""
mock_get_gene.return_value = (
'{"symbol": "TP53", "name": "tumor protein p53"}'
)
result = runner.invoke(app, ["gene", "get", "TP53", "--json"])
assert result.exit_code == 0
mock_get_gene.assert_called_once()
call_args = mock_get_gene.call_args
# Check kwargs since the function is called with keyword arguments
assert call_args.kwargs.get("gene_id_or_symbol") == "TP53"
assert call_args.kwargs.get("output_json") is True
@patch("biomcp.cli.genes.get_gene")
def test_gene_get_not_found(self, mock_get_gene):
"""Test gene not found response."""
mock_get_gene.return_value = '{"error": "Gene \'INVALID\' not found"}'
result = runner.invoke(app, ["gene", "get", "INVALID"])
assert result.exit_code == 0
assert (
"error" in result.stdout.lower()
or "not found" in result.stdout.lower()
)
def test_gene_no_args_shows_help(self):
"""Test that running gene without subcommand shows help."""
result = runner.invoke(app, ["gene"])
assert result.exit_code == 0
assert "get" in result.stdout.lower()
class TestDrugCLI:
"""Test drug CLI commands."""
def test_drug_help(self):
"""Test drug command shows help."""
result = runner.invoke(app, ["drug", "--help"])
assert result.exit_code == 0
assert "drug" in result.stdout.lower()
assert "get" in result.stdout.lower()
def test_drug_get_help(self):
"""Test drug get command shows help."""
result = runner.invoke(app, ["drug", "get", "--help"])
assert result.exit_code == 0
output = strip_ansi(result.stdout)
assert "drug" in output.lower()
assert "--json" in output
@patch("biomcp.cli.drugs.get_drug")
def test_drug_get_success(self, mock_get_drug):
"""Test successful drug retrieval."""
mock_get_drug.return_value = (
"## Drug: Imatinib\n- **DrugBank ID**: DB00619"
)
result = runner.invoke(app, ["drug", "get", "imatinib"])
assert result.exit_code == 0
assert (
"Imatinib" in result.stdout or "imatinib" in result.stdout.lower()
)
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_drug_get_json_output(self, mock_get_drug):
"""Test drug retrieval with JSON output."""
mock_get_drug.return_value = (
'{"name": "imatinib", "drugbank_id": "DB00619"}'
)
result = runner.invoke(app, ["drug", "get", "imatinib", "--json"])
assert result.exit_code == 0
mock_get_drug.assert_called_once()
call_args = mock_get_drug.call_args
assert call_args[0][0] == "imatinib"
assert call_args[1]["output_json"] is True
@patch("biomcp.cli.drugs.get_drug")
def test_drug_get_by_drugbank_id(self, mock_get_drug):
"""Test drug retrieval by DrugBank ID."""
mock_get_drug.return_value = (
"## Drug: Imatinib\n- **DrugBank ID**: DB00619"
)
result = runner.invoke(app, ["drug", "get", "DB00619"])
assert result.exit_code == 0
mock_get_drug.assert_called_once_with("DB00619", output_json=False)
@patch("biomcp.cli.drugs.get_drug")
def test_drug_get_not_found(self, mock_get_drug):
"""Test drug not found response."""
mock_get_drug.return_value = "Drug 'INVALID' not found in MyChem.info"
result = runner.invoke(app, ["drug", "get", "INVALID"])
assert result.exit_code == 0
assert "not found" in result.stdout.lower()
def test_drug_no_args_shows_help(self):
"""Test that running drug without subcommand shows help."""
result = runner.invoke(app, ["drug"])
assert result.exit_code == 0
assert "get" in result.stdout.lower()
class TestCLIRegistration:
"""Test that gene and drug commands are registered in main CLI."""
def test_main_help_shows_gene(self):
"""Test that main help includes gene command."""
result = runner.invoke(app, ["--help"])
assert result.exit_code == 0
assert "gene" in result.stdout.lower()
def test_main_help_shows_drug(self):
"""Test that main help includes drug command."""
result = runner.invoke(app, ["--help"])
assert result.exit_code == 0
assert "drug" in result.stdout.lower()
