"""Comprehensive tests for gene CLI commands."""
import json
from unittest.mock import AsyncMock, patch
import pytest
from typer.testing import CliRunner
from biomcp.cli.main import app
from biomcp.integrations import GeneInfo
runner = CliRunner()
@pytest.fixture
def mock_gene_info():
"""Create a mock GeneInfo object."""
return GeneInfo(
gene_id="7157",
symbol="TP53",
name="tumor protein p53",
summary="This gene encodes a tumor suppressor protein containing "
"transcriptional activation, DNA binding, and oligomerization domains.",
alias=["p53", "LFS1", "TRP53"],
type_of_gene="protein-coding",
entrezgene=7157,
)
@pytest.fixture
def mock_gene_info_brca1():
"""Create a mock GeneInfo object for BRCA1."""
return GeneInfo(
gene_id="672",
symbol="BRCA1",
name="BRCA1 DNA repair associated",
summary="This gene encodes a nuclear phosphoprotein that plays a role "
"in maintaining genomic stability.",
alias=["BRCC1", "FANCS", "PNCA4"],
type_of_gene="protein-coding",
entrezgene=672,
)
class TestGeneGetCommand:
"""Test the 'gene get' command."""
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_by_symbol(self, mock_get_gene):
"""Test getting gene info by symbol."""
mock_get_gene.return_value = "# TP53\n\nTumor protein p53"
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_get_gene_by_id(self, mock_get_gene):
"""Test getting gene info by Entrez ID."""
mock_get_gene.return_value = "# TP53\n\nGene ID: 7157"
result = runner.invoke(app, ["gene", "get", "7157"])
assert result.exit_code == 0
assert "7157" in result.stdout
mock_get_gene.assert_called_once()
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_not_found(self, mock_get_gene):
"""Test handling of non-existent gene."""
error_msg = json.dumps(
{
"error": "Gene 'INVALID_GENE' not found",
"suggestion": "Please check the gene symbol or ID",
},
indent=2,
)
mock_get_gene.return_value = error_msg
result = runner.invoke(app, ["gene", "get", "INVALID_GENE"])
assert result.exit_code == 0
assert "not found" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_json_flag(self, mock_get_gene):
"""Test getting gene info with --json flag."""
json_output = json.dumps(
{
"gene_id": "7157",
"symbol": "TP53",
"name": "tumor protein p53",
"type_of_gene": "protein-coding",
},
indent=2,
)
mock_get_gene.return_value = json_output
result = runner.invoke(app, ["gene", "get", "TP53", "--json"])
assert result.exit_code == 0
assert "7157" in result.stdout
assert "tumor protein p53" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_json_short_flag(self, mock_get_gene):
"""Test getting gene info with -j short flag."""
json_output = json.dumps({"symbol": "TP53"}, indent=2)
mock_get_gene.return_value = json_output
result = runner.invoke(app, ["gene", "get", "TP53", "-j"])
assert result.exit_code == 0
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_pathway(self, mock_get_gene):
"""Test getting gene info with --enrich pathway flag."""
mock_get_gene.return_value = "# TP53\n\nTumor protein p53"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "pathway"]
)
assert result.exit_code == 0
assert "TP53" in result.stdout
assert "Enrichment Analysis" in result.stdout
assert "pathway" in result.stdout.lower()
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_ontology(self, mock_get_gene):
"""Test getting gene info with --enrich ontology flag."""
mock_get_gene.return_value = "# BRCA1\n\nBRCA1 DNA repair associated"
result = runner.invoke(
app, ["gene", "get", "BRCA1", "--enrich", "ontology"]
)
assert result.exit_code == 0
assert "BRCA1" in result.stdout
assert "Enrichment Analysis" in result.stdout
assert "ontology" in result.stdout.lower()
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_kegg(self, mock_get_gene):
"""Test getting gene info with --enrich kegg flag."""
mock_get_gene.return_value = (
"# EGFR\n\nEpidermal growth factor receptor"
)
result = runner.invoke(
app, ["gene", "get", "EGFR", "--enrich", "kegg"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_reactome(self, mock_get_gene):
"""Test getting gene info with --enrich reactome flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "reactome"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_wikipathways(self, mock_get_gene):
"""Test getting gene info with --enrich wikipathways flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "wikipathways"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_go_process(self, mock_get_gene):
"""Test getting gene info with --enrich go_process flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "go_process"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_go_molecular(self, mock_get_gene):
"""Test getting gene info with --enrich go_molecular flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "go_molecular"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_go_cellular(self, mock_get_gene):
"""Test getting gene info with --enrich go_cellular flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "go_cellular"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_celltypes(self, mock_get_gene):
"""Test getting gene info with --enrich celltypes flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "celltypes"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_tissues(self, mock_get_gene):
"""Test getting gene info with --enrich tissues flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "tissues"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_diseases(self, mock_get_gene):
"""Test getting gene info with --enrich diseases flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "diseases"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_gwas(self, mock_get_gene):
"""Test getting gene info with --enrich gwas flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "gwas"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_transcription_factors(self, mock_get_gene):
"""Test getting gene info with --enrich transcription_factors flag."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "transcription_factors"]
)
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_with_enrich_tf(self, mock_get_gene):
"""Test getting gene info with --enrich tf flag (alias for transcription_factors)."""
mock_get_gene.return_value = "# TP53\n\nGene info"
result = runner.invoke(app, ["gene", "get", "TP53", "--enrich", "tf"])
assert result.exit_code == 0
assert "Enrichment Analysis" in result.stdout
def test_get_gene_with_invalid_enrich_type(self):
"""Test getting gene info with invalid enrichment type."""
result = runner.invoke(
app, ["gene", "get", "TP53", "--enrich", "invalid_type"]
)
assert result.exit_code == 1
assert "Invalid enrichment type" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_get_gene_combined_json_and_enrich(self, mock_get_gene):
"""Test getting gene info with both --json and --enrich flags."""
json_output = json.dumps({"symbol": "TP53"}, indent=2)
mock_get_gene.return_value = json_output
result = runner.invoke(
app, ["gene", "get", "TP53", "--json", "--enrich", "pathway"]
)
assert result.exit_code == 0
assert "TP53" in result.stdout
assert "Enrichment Analysis" in result.stdout
class TestGeneSearchCommand:
"""Test the 'gene search' command."""
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_basic(self, mock_get_gene):
"""Test basic gene search."""
mock_get_gene.return_value = "# TP53\n\nTumor protein p53"
result = runner.invoke(app, ["gene", "search", "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_search_genes_with_page(self, mock_get_gene):
"""Test gene search with page parameter."""
mock_get_gene.return_value = "# kinase\n\nResults"
result = runner.invoke(
app, ["gene", "search", "kinase", "--page", "2"]
)
assert result.exit_code == 0
assert (
"pagination" in result.stdout.lower()
or "development" in result.stdout
)
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_with_page_short_flag(self, mock_get_gene):
"""Test gene search with -p short flag for page."""
mock_get_gene.return_value = "# kinase\n\nResults"
result = runner.invoke(app, ["gene", "search", "kinase", "-p", "2"])
assert result.exit_code == 0
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_with_page_size(self, mock_get_gene):
"""Test gene search with page_size parameter."""
mock_get_gene.return_value = "# kinase\n\nResults"
result = runner.invoke(
app, ["gene", "search", "kinase", "--page-size", "20"]
)
assert result.exit_code == 0
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_with_pagination(self, mock_get_gene):
"""Test gene search with full pagination parameters."""
mock_get_gene.return_value = "# kinase\n\nResults"
result = runner.invoke(
app,
["gene", "search", "kinase", "--page", "2", "--page-size", "20"],
)
assert result.exit_code == 0
# Should show development note when pagination is used
assert "development" in result.stdout.lower()
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_with_json_output(self, mock_get_gene):
"""Test gene search with JSON output."""
json_output = json.dumps(
{"symbol": "BRCA1", "name": "BRCA1 DNA repair associated"},
indent=2,
)
mock_get_gene.return_value = json_output
result = runner.invoke(app, ["gene", "search", "BRCA", "--json"])
assert result.exit_code == 0
assert "BRCA" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_with_json_short_flag(self, mock_get_gene):
"""Test gene search with -j short flag."""
json_output = json.dumps({"symbol": "BRCA1"}, indent=2)
mock_get_gene.return_value = json_output
result = runner.invoke(app, ["gene", "search", "BRCA", "-j"])
assert result.exit_code == 0
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_quoted_query(self, mock_get_gene):
"""Test gene search with quoted multi-word query."""
mock_get_gene.return_value = "# tumor protein\n\nResults"
result = runner.invoke(app, ["gene", "search", "tumor protein"])
assert result.exit_code == 0
assert "tumor protein" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_not_found(self, mock_get_gene):
"""Test gene search with no results."""
error_msg = json.dumps(
{
"error": "Gene 'INVALID_QUERY' not found",
"suggestion": "Please check the gene symbol or ID",
},
indent=2,
)
mock_get_gene.return_value = error_msg
result = runner.invoke(app, ["gene", "search", "INVALID_QUERY"])
assert result.exit_code == 0
assert "not found" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_search_genes_with_all_options(self, mock_get_gene):
"""Test gene search with all available options."""
json_output = json.dumps({"symbol": "kinase"}, indent=2)
mock_get_gene.return_value = json_output
result = runner.invoke(
app,
[
"gene",
"search",
"kinase",
"--page",
"2",
"--page-size",
"20",
"--json",
],
)
assert result.exit_code == 0
class TestGeneCliIntegration:
"""Integration-style tests for gene CLI (still using mocks)."""
@patch("biomcp.integrations.biothings_client.http_client")
def test_get_gene_full_flow(self, mock_http_client):
"""Test full gene get flow with mocked HTTP client."""
# Mock the API response
mock_http_client.request_api = AsyncMock(
return_value=(
{
"_id": "7157",
"symbol": "TP53",
"name": "tumor protein p53",
"summary": "This gene encodes a tumor suppressor protein...",
"alias": ["p53", "LFS1"],
"type_of_gene": "protein-coding",
"entrezgene": 7157,
},
None,
)
)
result = runner.invoke(app, ["gene", "get", "7157"])
assert result.exit_code == 0
assert "TP53" in result.stdout
assert "tumor protein p53" in result.stdout
@patch("biomcp.integrations.biothings_client.http_client")
def test_get_gene_with_aliases(self, mock_http_client):
"""Test gene with multiple aliases."""
# Mock both the query (to find BRCA1) and the get (to retrieve details)
mock_http_client.request_api = AsyncMock(
side_effect=[
# First call: query for BRCA1
(
{
"hits": [
{
"_id": "672",
"symbol": "BRCA1",
"name": "BRCA1 DNA repair associated",
"taxid": 9606,
}
]
},
None,
),
# Second call: get full details
(
{
"_id": "672",
"symbol": "BRCA1",
"name": "BRCA1 DNA repair associated",
"alias": [
"BRCC1",
"FANCS",
"PNCA4",
"RNF53",
"BRCAI",
"BRCA1/BRCA2-containing complex, subunit 1",
"breast cancer 1",
"breast cancer 1, early onset",
"breast cancer type 1 susceptibility protein",
"RING finger protein 53",
"PPP1R53",
],
"type_of_gene": "protein-coding",
"entrezgene": 672,
},
None,
),
]
)
result = runner.invoke(app, ["gene", "get", "BRCA1"])
assert result.exit_code == 0
assert "BRCA1" in result.stdout
# Should show limited aliases with "and X more" message
assert "alias" in result.stdout.lower() or "BRCC1" in result.stdout
@patch("biomcp.cli.genes.get_gene")
def test_gene_command_error_handling(self, mock_get_gene):
"""Test error handling in gene commands."""
# Simulate an error response from the API
error_msg = json.dumps(
{
"error": "Failed to retrieve gene information",
"details": "API connection error",
},
indent=2,
)
mock_get_gene.return_value = error_msg
result = runner.invoke(app, ["gene", "get", "TP53"])
# Should exit successfully but show error message
assert result.exit_code == 0
assert "error" in result.stdout.lower()
def test_gene_help_command(self):
"""Test gene command help text."""
result = runner.invoke(app, ["gene", "--help"])
assert result.exit_code == 0
assert "gene" in result.stdout.lower()
assert "get" in result.stdout.lower()
assert "search" in result.stdout.lower()
def test_gene_get_help_command(self):
"""Test gene get command help text."""
result = runner.invoke(app, ["gene", "get", "--help"])
assert result.exit_code == 0
assert "TP53" in result.stdout
assert "enrich" in result.stdout.lower()
assert "json" in result.stdout.lower()
def test_gene_search_help_command(self):
"""Test gene search command help text."""
result = runner.invoke(app, ["gene", "search", "--help"])
assert result.exit_code == 0
assert "search" in result.stdout.lower()
assert "page" in result.stdout.lower()
assert "json" in result.stdout.lower()
