@biothings-explorer/query_graph_handler/__test__/integration/QueryEdge.test.js

A nodejs module to query TRAPI Query Graph

const QNode = require("../../src/query_node");
const QEdge = require("../../src/query_edge");

describe("Testing QueryEdge Module", () => {
    const gene_node1 = new QNode("n1", { categories: "Gene", ids: "NCBIGene:1017" });
    const type_node = new QNode("n2", { categories: "SmallMolecule" });
    const disease1_node = new QNode("n1", { categories: "Disease", ids: "MONDO:000123" });
    const node1_equivalent_ids = {
        "NCBIGene:1017": {
            db_ids: {
                NCBIGene: ["1017"],
                SYMBOL: ['CDK2']
            }
        }
    }
    //gene_node1.setEquivalentIDs(node1_equivalent_ids);
    const node2_equivalent_ids = {
        "NCBIGene:1017": {
            db_ids: {
                NCBIGene: ["1017"],
                SYMBOL: ['CDK2']
            }
        },
        "NCBIGene:1018": {
            db_ids: {
                NCBIGene: ["1018"],
                SYMBOL: ['CDK3']
            }
        }
    }
    const gene_node2 = new QNode("n2", { categories: "Gene", ids: ["NCBIGene:1017", "NCBIGene:1018"] });
    const gene_node1_with_id_annotated = new QNode("n1", { categories: "Gene", ids: "NCBIGene:1017" });
    gene_node1_with_id_annotated.setEquivalentIDs(node1_equivalent_ids);
    //gene_node2.setEquivalentIDs(node2_equivalent_ids);
    const invalid_node = new QNode("n3", { categories: "INVALID", curie: ["NCBIGene:1017", "NCBIGene:1018"] })
    const chemical_node1 = new QNode("n3", { categories: "SmallMolecule" });
    const chemical_node2 = new QNode("n4", { categories: "SmallMolecule", curie: "CHEMBL.COMPUND:CHEMBL744" });
    const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 });
    const edge2 = new QEdge("e02", { subject: gene_node1_with_id_annotated, object: chemical_node1 });
    const edge3 = new QEdge('e04', { subject: gene_node2, object: chemical_node1 });
    const edge4 = new QEdge('e05', { object: gene_node2, subject: chemical_node1 });
    const edge5 = new QEdge('e06', { object: gene_node1_with_id_annotated, subject: chemical_node1 });
    const invalid_edge = new QEdge("e03", { subject: invalid_node, object: chemical_node1 })

    describe("Testing isReversed function", () => {
        test("test if only the object of the edge has curie defined, should return true", () => {
            const res = edge4.isReversed();
            expect(res).toBeTruthy();
        });

        test("test if the subject of the edge has curie defined, should return false", () => {
            const res = edge1.isReversed();
            expect(res).toBeFalsy();
        });

        test("test if both subject and object curie not defined, should return false", () => {
            const node1 = new QNode("n1", { categories: "Gene" });
            const node2 = new QNode("n2", { categories: "SmallMolecule" });
            const edge = new QEdge("e01", { subject: node1, object: node2 });
            expect(edge.isReversed()).toBeFalsy();
        });

    })

    describe("Testing getInputCurie function", () => {
        test("test return an array of one curie if subject has only one curie specified", () => {
            const res = edge1.getInputCurie();
            expect(res).toEqual(['NCBIGene:1017']);
        });

        test("test return an array of two curie if subject has only an array of two curies specified", () => {
            const res = edge3.getInputCurie();
            expect(res).toEqual(['NCBIGene:1017', 'NCBIGene:1018']);
        });

        test("test return an array of two curies if edge is reversed and object has two curies specified", () => {
            const res = edge4.getInputCurie();
            expect(res).toEqual(['NCBIGene:1017', 'NCBIGene:1018']);
        });

    })

    describe("Testing hasInput function", () => {
        test("test return true if subject has only one curie specified", () => {
            const res = edge1.hasInput();
            expect(res).toBeTruthy();
        });

        test("test return true if subject has only an array of two curies specified", () => {
            const res = edge3.hasInput();
            expect(res).toBeTruthy();
        });

        test("test return true if subject has no curies specified but object does", () => {
            const res = edge4.hasInput();
            expect(res).toBeTruthy();
        });

        test("test return false if both subject and object has no curies specified", () => {
            const node1 = new QNode("n1", { categories: "Gene" });
            const node2 = new QNode("n2", { categories: "SmallMolecule" });
            const edge = new QEdge("e01", { subject: node1, object: node2 });
            expect(edge.hasInput()).toBeFalsy();
        });

    })

    describe("Testing hasInputResolved function", () => {
        test("test return true if subject has input resolved", () => {
            const res = edge2.hasInputResolved();
            expect(res).toBeTruthy();
        });

        test("test return false if both subject and object do not have input resolved", () => {
            const res = edge1.hasInputResolved();
            expect(res).toBeFalsy();
        });

        test("test return true if subject doesn't have input resolved, but object does", () => {
            const res = edge5.hasInputResolved();
            expect(res).toBeTruthy();
        });

    })

    describe("Testing getPredicate function", () => {
        test("test get reverse predicate if query is reversed", () => {
            const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicates: "biolink:treats" });
            const res = edge.getPredicate();
            expect(res).toContain("treated_by");
        });

        test("test get reverse predicate if query is reversed and expanded", () => {
            const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicates: "biolink:affects" });
            const res = edge.getPredicate();
            expect(res).toContain("affected_by");
            expect(res).toContain("disrupted_by");
        });
    })

    describe("Testing expandPredicates function", () => {
        test("All predicates are correctly expanded if in biolink model", () => {
            const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicates: "biolink:contributes_to" });
            const res = edge.expandPredicates(["contributes_to"])
            expect(res).toContain("contributes_to");
            expect(res).toContain("causes");
        });

        test("Multiple predicates can be resolved", () => {
            const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicates: "biolink:contributes_to" });
            const res = edge.expandPredicates(["contributes_to", "ameliorates"])
            expect(res).toContain("contributes_to");
            expect(res).toContain("causes");
            expect(res).toContain("ameliorates");
            expect(res).toContain("treats");
        });

        test("Predicates not in biolink model should return itself", () => {
            const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicates: "biolink:contributes_to" });
            const res = edge.expandPredicates(["contributes_to", "amelio"])
            expect(res).toContain("contributes_to");
            expect(res).toContain("causes");
            expect(res).toContain("amelio");
        });
    })

})