"""Unit tests for identifier mapping (no network required)."""
import pytest
from mcp_proto_okn.identifier_mapping import (
IDENTIFIER_BRIDGES,
find_common_identifiers,
get_graphs_for_identifier,
suggest_join_strategy,
build_gene_lookup_query,
build_gene_bridge_query,
)
def test_find_common_cas():
"""biobricks-tox21 and biobricks-ice share CAS."""
common = find_common_identifiers("biobricks-tox21", "biobricks-ice")
assert "CAS" in common
def test_find_common_none():
"""dreamkg and scales share nothing."""
common = find_common_identifiers("dreamkg", "scales")
assert len(common) == 0
def test_get_graphs_for_identifier_cas():
"""CAS found in multiple graphs."""
graphs = get_graphs_for_identifier("CAS")
assert "biobricks-tox21" in graphs
assert "biobricks-ice" in graphs
assert "sawgraph" in graphs
assert len(graphs) >= 4
def test_get_graphs_for_identifier_unknown():
"""Unknown identifier type returns empty list."""
graphs = get_graphs_for_identifier("UNKNOWN_ID_TYPE")
assert len(graphs) == 0
def test_suggest_join_joinable():
"""Returns strategy with common identifiers."""
result = suggest_join_strategy("biobricks-tox21", "biobricks-ice")
assert result["can_join"] is True
assert "CAS" in result["common_identifiers"]
assert len(result["strategy"]) > 0
def test_suggest_join_not_joinable():
"""Returns can_join: false when no shared identifiers."""
result = suggest_join_strategy("dreamkg", "scales")
assert result["can_join"] is False
assert len(result["common_identifiers"]) == 0
def test_gene_bridges_ncbi_to_ensembl():
"""spoke-genelab (NCBI) and spoke-okn (Ensembl) can join via bridge."""
result = suggest_join_strategy("spoke-genelab", "spoke-okn")
assert result["can_join"] is True
# They might have direct overlap or need bridge
if not result["common_identifiers"]:
assert "bridge_graph" in result
assert result["bridge_graph"] == "gene-expression-atlas-okn"
def test_gene_bridges_symbol():
"""spoke-genelab and gene-expression-atlas-okn share GeneSymbol."""
common = find_common_identifiers("spoke-genelab", "gene-expression-atlas-okn")
assert "GeneSymbol" in common
def test_gene_bridges_ncbi():
"""spoke-genelab and gene-expression-atlas-okn share NCBI_Gene."""
common = find_common_identifiers("spoke-genelab", "gene-expression-atlas-okn")
assert "NCBI_Gene" in common
def test_build_gene_lookup_query_spoke_okn():
"""Generates SPARQL using ensembl property for spoke-okn."""
query = build_gene_lookup_query("spoke-okn", "FOS")
assert query is not None
assert "ensembl" in query
assert "FOS" in query
def test_build_gene_lookup_query_spoke_genelab():
"""Generates SPARQL using symbol property for spoke-genelab."""
query = build_gene_lookup_query("spoke-genelab", "Fos")
assert query is not None
assert "symbol" in query
assert "Fos" in query
def test_build_gene_lookup_query_gene_expression_atlas():
"""Generates SPARQL with both NCBI and Ensembl for gene-expression-atlas-okn."""
query = build_gene_lookup_query("gene-expression-atlas-okn", "BRCA1")
assert query is not None
assert "ncbi_gene_id" in query
assert "ensembl_id" in query
assert "BRCA1" in query
def test_build_gene_lookup_query_biobricks_ice():
"""Generates SPARQL for biobricks-ice Entrez gene lookup."""
query = build_gene_lookup_query("biobricks-ice", "672")
assert query is not None
assert "entrez_gene_id" in query
def test_build_gene_lookup_query_unknown_graph():
"""Returns None for unsupported graph."""
query = build_gene_lookup_query("dreamkg", "BRCA1")
assert query is None
def test_build_gene_bridge_query():
"""Generates bridge query via gene-expression-atlas-okn."""
query = build_gene_bridge_query(
"spoke-genelab",
"spoke-okn",
["14281", "2353"],
)
assert query is not None
assert "14281" in query
assert "2353" in query
def test_build_gene_bridge_query_empty_ids():
"""Returns None when no gene IDs provided."""
query = build_gene_bridge_query("spoke-genelab", "spoke-okn", [])
assert query is None
def test_identifier_bridges_structure():
"""IDENTIFIER_BRIDGES has expected structure."""
assert "CAS" in IDENTIFIER_BRIDGES
assert "Ensembl" in IDENTIFIER_BRIDGES
assert "NCBI_Gene" in IDENTIFIER_BRIDGES
assert "MONDO" in IDENTIFIER_BRIDGES
assert "FIPS" in IDENTIFIER_BRIDGES
# Each entry should have description
for id_type, graphs in IDENTIFIER_BRIDGES.items():
for graph_name, info in graphs.items():
assert "description" in info, f"Missing description for {id_type}/{graph_name}"
