"""Tests for database operations."""
import os
import pytest
from biopython_mcp.database import (
clinvar_variant_lookup,
entrez_fetch,
entrez_info,
entrez_search,
entrez_summary,
fetch_genbank,
fetch_sequence_by_id,
fetch_uniprot,
gene_info_fetch,
pubmed_search,
search_pubmed,
variant_literature_link,
)
class TestFetchGenBank:
"""Tests for fetch_genbank function."""
@pytest.mark.entrez
def test_fetch_genbank_valid(self) -> None:
"""Test fetching valid GenBank record."""
result = fetch_genbank("NM_000207", email=os.environ["NCBI_EMAIL"])
assert result["success"] is True
assert result["accession"] == "NM_000207"
assert "data" in result
assert result["length"] > 0
def test_fetch_genbank_invalid(self) -> None:
"""Test fetching invalid GenBank record."""
result = fetch_genbank("INVALID_ID", email="test@example.com")
assert result["success"] is False
assert "error" in result
class TestFetchUniProt:
"""Tests for fetch_uniprot function."""
@pytest.mark.network
def test_fetch_uniprot_valid(self) -> None:
"""Test fetching valid UniProt record."""
# Use a well-known stable UniProt accession.
result = fetch_uniprot("P69905")
assert result["success"] is True
assert result["uniprot_id"] == "P69905"
assert "data" in result
assert result["length"] > 0
def test_fetch_uniprot_formats(self) -> None:
"""Test different UniProt formats."""
for fmt in ["fasta", "txt", "xml"]:
result = fetch_uniprot("INVALID", format=fmt)
assert "format" in result or "error" in result
class TestSearchPubMed:
"""Tests for search_pubmed function."""
@pytest.mark.entrez
def test_search_pubmed_valid(self) -> None:
"""Test searching PubMed."""
result = search_pubmed("cancer", max_results=3, email=os.environ["NCBI_EMAIL"])
assert result["success"] is True
assert "results" in result
assert result["count"] <= 3
def test_search_pubmed_parameters(self) -> None:
"""Test PubMed search parameters."""
result = search_pubmed("test", max_results=1, email="test@example.com")
assert "query" in result
class TestFetchSequenceById:
"""Tests for fetch_sequence_by_id function."""
@pytest.mark.entrez
def test_fetch_sequence_valid(self) -> None:
"""Test fetching valid sequence."""
result = fetch_sequence_by_id("nucleotide", "NM_000207", email=os.environ["NCBI_EMAIL"])
assert result["success"] is True
assert result["database"] == "nucleotide"
assert result["length"] > 0
def test_fetch_sequence_invalid_db(self) -> None:
"""Test fetching from invalid database."""
result = fetch_sequence_by_id("invalid_db", "test", email="test@example.com")
assert result["success"] is False
# Tests for new Entrez tools
class TestEntrezInfo:
"""Tests for entrez_info function."""
@pytest.mark.entrez
def test_entrez_info_all_databases(self) -> None:
"""Test listing all databases."""
result = entrez_info()
assert result["success"] is True
assert "databases" in result
assert "pubmed" in result["databases"]
assert result["count"] > 0
@pytest.mark.entrez
def test_entrez_info_specific_database(self) -> None:
"""Test getting info for specific database."""
result = entrez_info("pubmed")
assert result["success"] is True
assert result["database"] == "pubmed"
assert "description" in result
assert "fields" in result
class TestEntrezSearch:
"""Tests for entrez_search function."""
@pytest.mark.entrez
def test_entrez_search_pubmed(self) -> None:
"""Test searching PubMed."""
result = entrez_search("pubmed", "cancer", max_results=5)
assert result["success"] is True
assert len(result["ids"]) <= 5
assert result["total_found"] > 0
assert result["database"] == "pubmed"
@pytest.mark.entrez
def test_entrez_search_gene(self) -> None:
"""Test searching gene database."""
result = entrez_search("gene", "BRCA1[Gene] AND Homo sapiens[Organism]", max_results=1)
assert result["success"] is True
assert "ids" in result
def test_entrez_search_invalid_db(self) -> None:
"""Test searching invalid database."""
result = entrez_search("invalid_db", "test")
assert result["success"] is False
assert "error" in result
class TestEntrezFetch:
"""Tests for entrez_fetch function."""
@pytest.mark.entrez
def test_entrez_fetch_single_id(self) -> None:
"""Test fetching single record."""
result = entrez_fetch("nucleotide", "NM_000207", rettype="fasta", retmode="text")
assert result["success"] is True
assert result["count"] == 1
assert "NM_000207" in result["ids"]
@pytest.mark.entrez
def test_entrez_fetch_multiple_ids_string(self) -> None:
"""Test fetching multiple IDs as comma-separated string."""
result = entrez_fetch("gene", "672,7157", rettype="xml")
assert result["success"] is True
assert result["count"] == 2
@pytest.mark.entrez
def test_entrez_fetch_multiple_ids_list(self) -> None:
"""Test fetching multiple IDs as list."""
result = entrez_fetch("gene", ["672", "7157"], rettype="xml")
assert result["success"] is True
assert result["count"] == 2
def test_entrez_fetch_no_ids(self) -> None:
"""Test fetching with empty IDs."""
result = entrez_fetch("pubmed", "")
assert result["success"] is False
assert "No valid IDs" in result["error"]
class TestEntrezSummary:
"""Tests for entrez_summary function."""
@pytest.mark.entrez
def test_entrez_summary_gene(self) -> None:
"""Test getting gene summary."""
result = entrez_summary("gene", "672") # BRCA1
assert result["success"] is True
assert result["count"] > 0
assert "summaries" in result
@pytest.mark.entrez
def test_entrez_summary_multiple(self) -> None:
"""Test getting summaries for multiple IDs."""
result = entrez_summary("gene", ["672", "7157"])
assert result["success"] is True
assert result["count"] == 2
def test_entrez_summary_empty(self) -> None:
"""Test summary with empty IDs."""
result = entrez_summary("pubmed", "")
assert result["success"] is False
class TestClinvarVariantLookup:
"""Tests for clinvar_variant_lookup function."""
@pytest.mark.entrez
def test_clinvar_lookup_by_gene(self) -> None:
"""Test ClinVar lookup by gene."""
result = clinvar_variant_lookup(gene="BRCA1", significance="pathogenic", max_results=3)
assert result["success"] is True
assert result["count"] <= 3
assert "query_terms" in result
@pytest.mark.entrez
def test_clinvar_lookup_by_gene_only(self) -> None:
"""Test ClinVar lookup with gene only."""
result = clinvar_variant_lookup(gene="BRCA2", max_results=2)
assert result["success"] is True
assert result["query_terms"]["gene"] == "BRCA2"
def test_clinvar_lookup_no_params(self) -> None:
"""Test ClinVar lookup with no parameters."""
result = clinvar_variant_lookup()
assert result["success"] is False
assert "At least one" in result["error"]
class TestGeneInfoFetch:
"""Tests for gene_info_fetch function."""
@pytest.mark.entrez
def test_gene_fetch_by_symbol(self) -> None:
"""Test fetching gene by symbol."""
result = gene_info_fetch(gene_symbol="BRCA1")
assert result["success"] is True
assert result["symbol"] == "BRCA1"
assert "summary" in result
@pytest.mark.entrez
def test_gene_fetch_by_id(self) -> None:
"""Test fetching gene by ID."""
result = gene_info_fetch(gene_id="672") # BRCA1
assert result["success"] is True
assert result["gene_id"] == "672"
def test_gene_fetch_no_params(self) -> None:
"""Test gene fetch with no parameters."""
result = gene_info_fetch()
assert result["success"] is False
assert "required" in result["error"].lower()
class TestPubmedSearch:
"""Tests for pubmed_search function."""
@pytest.mark.entrez
def test_pubmed_search_basic(self) -> None:
"""Test basic PubMed search."""
result = pubmed_search("BRCA1", max_results=3)
assert result["success"] is True
assert len(result["articles"]) <= 3
assert all("pmid" in article for article in result["articles"])
assert all("abstract" in article for article in result["articles"])
@pytest.mark.entrez
def test_pubmed_search_year_filter(self) -> None:
"""Test PubMed search with year filter."""
result = pubmed_search("cancer", year_start=2023, year_end=2024, max_results=2)
assert result["success"] is True
assert "articles" in result
@pytest.mark.entrez
def test_pubmed_search_no_results(self) -> None:
"""Test PubMed search with no results."""
result = pubmed_search("zzzzzzznonexistent12345", max_results=1)
assert result["success"] is True
assert result["count"] == 0
assert result["articles"] == []
class TestVariantLiteratureLink:
"""Tests for variant_literature_link function."""
@pytest.mark.entrez
def test_variant_link_clinvar(self) -> None:
"""Test linking ClinVar variant to literature."""
# Use a real ClinVar ID that has literature
result = variant_literature_link("12345", source_db="clinvar", max_results=5)
assert result["success"] is True
assert "linked_pmids" in result
assert "articles" in result
def test_variant_link_invalid_db(self) -> None:
"""Test with invalid source database."""
result = variant_literature_link("12345", source_db="invalid")
assert result["success"] is False
assert "invalid" in result["error"].lower()
