"""
Integration tests for Enrichr API.
These tests make real API calls to Enrichr and may fail due to network issues.
They are marked with @pytest.mark.integration and are allowed to fail in CI.
"""
import pytest
from biomcp.enrichr import EnrichrClient
@pytest.mark.integration
class TestEnrichrIntegration:
"""Integration tests for Enrichr API."""
@pytest.mark.asyncio
async def test_submit_and_retrieve_real_api(self):
"""Test real API call to submit gene list and retrieve enrichment."""
client = EnrichrClient()
# Submit a well-known gene list
genes = ["TP53", "BRCA1", "EGFR", "MYC", "KRAS"]
user_list_id = await client.submit_gene_list(
genes=genes, description="Integration test gene list"
)
assert user_list_id is not None
assert isinstance(user_list_id, str)
assert len(user_list_id) > 0
# Get enrichment results for GO Biological Process
results = await client.get_enrichment(
user_list_id=user_list_id, database="GO_Biological_Process_2021"
)
assert results is not None
assert isinstance(results, list)
# Should have some enrichment results for these cancer genes
assert len(results) > 0
# Check structure of first result
first_result = results[0]
assert hasattr(first_result, "rank")
assert hasattr(first_result, "path_name")
assert hasattr(first_result, "p_val")
assert hasattr(first_result, "z_score")
assert hasattr(first_result, "combined_score")
assert hasattr(first_result, "overlapping_genes")
assert hasattr(first_result, "adj_p_val")
assert hasattr(first_result, "database")
# Validate data types
assert isinstance(first_result.rank, int)
assert isinstance(first_result.path_name, str)
assert isinstance(first_result.p_val, int | float)
assert isinstance(first_result.overlapping_genes, list)
assert len(first_result.overlapping_genes) > 0
@pytest.mark.asyncio
async def test_enrich_kegg_pathway(self):
"""Test enrichment with KEGG pathway database."""
client = EnrichrClient()
# Use the convenience enrich() method
results = await client.enrich(
genes=["TP53", "BRCA1", "EGFR"],
database="pathway", # Friendly name
description="KEGG pathway test",
)
assert results is not None
assert isinstance(results, list)
assert len(results) > 0
# Should find cancer-related pathways
first_result = results[0]
assert first_result.database == "KEGG_2021_Human"
assert len(first_result.overlapping_genes) > 0
@pytest.mark.asyncio
async def test_enrich_go_molecular_function(self):
"""Test enrichment with GO Molecular Function database."""
client = EnrichrClient()
results = await client.enrich(
genes=["TP53", "MDM2", "ATM"],
database="go_molecular",
description="GO molecular function test",
)
assert results is not None
assert isinstance(results, list)
assert len(results) > 0
assert results[0].database == "GO_Molecular_Function_2021"
@pytest.mark.asyncio
async def test_enrich_with_full_database_name(self):
"""Test enrichment using full database name."""
client = EnrichrClient()
results = await client.enrich(
genes=["BRCA1", "BRCA2", "PALB2"],
database="Reactome_2022", # Full database name
description="Reactome test",
)
assert results is not None
assert isinstance(results, list)
# May have results depending on the gene set
# Just verify it doesn't error
@pytest.mark.asyncio
async def test_single_gene_enrichment(self):
"""Test enrichment with a single gene."""
client = EnrichrClient()
results = await client.enrich(
genes=["TP53"], database="ontology", description="Single gene test"
)
# Single gene should still work
assert results is not None
assert isinstance(results, list)
# TP53 is well-studied, should have enrichment terms
assert len(results) > 0
