Merge branch 'main' of https://github.com/biothings/bte-server into k…

…g-refactor

__test__/integration/TRAPIv1.test.ts

@@ -0,0 +1,154 @@
+import app from "../../src/app";
+import request from "supertest";
+import fs from "fs";
+import path from "path";
+
+//V1 tests are now skipped.
+describe.skip("Testing v1 endpoints", () => {
+ const example_folder = path.resolve(__dirname, "../../../../examples/v1");
+ const clinical_risk_kp_folder = path.resolve(__dirname, "../../../../examples/v1/multiomics/clinical_risk_kp");
+ const old_spec_folder = path.resolve(__dirname, "../../../../examples/v0.9.2");
+ const drug2disease_query = JSON.parse(
+ fs.readFileSync(path.join(clinical_risk_kp_folder, "query_drug_to_disease.json"), { encoding: "utf8" }),
+ );
+ const gene2chemical_query = JSON.parse(
+ fs.readFileSync(path.join(example_folder, "query_chemicals_physically_interacts_with_genes.json"), {
+ encoding: "utf8",
+ }),
+ );
+ const disease2gene_query = JSON.parse(
+ fs.readFileSync(path.join(example_folder, "query_genes_relate_to_disease.json"), { encoding: "utf8" }),
+ );
+ const query_using_earlier_trapi_spec = JSON.parse(
+ fs.readFileSync(path.join(old_spec_folder, "query_genes_relate_to_disease.json"), { encoding: "utf8" }),
+ );
+ const query_without_category = JSON.parse(
+ fs.readFileSync(path.join(example_folder, "query_without_input_category.json"), { encoding: "utf8" }),
+ );
+
+ test("GET /v1/predicates", async () => {
+ await request(app)
+ .get("/v1/predicates")
+ .expect(200)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body).toHaveProperty("biolink:Gene");
+ expect(response.body["biolink:Gene"]).toHaveProperty("biolink:SmallMolecule");
+ expect(response.body["biolink:Gene"]["biolink:SmallMolecule"]).toContain("biolink:related_to");
+ });
+ });
+
+ test("GET /v1/smartapi/{smartapi_id}/predicates", async () => {
+ await request(app)
+ .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates")
+ .expect(200)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body).toHaveProperty("biolink:Gene");
+ expect(response.body["biolink:Gene"]).toHaveProperty("biolink:SmallMolecule");
+ });
+ });
+
+ test("POST /v1/query with gene2chemical query", async () => {
+ await request(app)
+ .post("/v1/query")
+ .send(gene2chemical_query)
+ .set("Accept", "application/json")
+ .expect(200)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body.message).toHaveProperty("query_graph");
+ expect(response.body.message).toHaveProperty("knowledge_graph");
+ expect(response.body.message.knowledge_graph).toHaveProperty("nodes");
+ expect(response.body.message.knowledge_graph).toHaveProperty("edges");
+ expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:1017");
+ });
+ });
+
+ test("POST /v1/query with clinical risk kp query", async () => {
+ await request(app)
+ .post("/v1/query")
+ .send(drug2disease_query)
+ .set("Accept", "application/json")
+ .expect(200)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body.message).toHaveProperty("query_graph");
+ expect(response.body.message).toHaveProperty("knowledge_graph");
+ expect(response.body.message.knowledge_graph).toHaveProperty("nodes");
+ expect(response.body.message.knowledge_graph).toHaveProperty("edges");
+ expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0001583");
+ });
+ });
+
+ test("POST /v1/query with query graph defined in old trapi standard", async () => {
+ await request(app)
+ .post("/v1/query")
+ .send(query_using_earlier_trapi_spec)
+ .set("Accept", "application/json")
+ .expect(400)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body).toHaveProperty("error", "Your input query graph is invalid");
+ });
+ });
+
+ test("POST /v1/query with disease2gene query", async () => {
+ await request(app)
+ .post("/v1/query")
+ .send(disease2gene_query)
+ .set("Accept", "application/json")
+ .expect(200)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body).toHaveProperty("message");
+ expect(response.body.message).toHaveProperty("query_graph");
+ expect(response.body.message).toHaveProperty("knowledge_graph");
+ expect(response.body.message.knowledge_graph).toHaveProperty("nodes");
+ expect(response.body.message.knowledge_graph).toHaveProperty("edges");
+ expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0005737");
+ });
+ });
+
+ test("POST /v1/query with query that doesn't provide input category", async () => {
+ await request(app)
+ .post("/v1/query")
+ .send(query_without_category)
+ .set("Accept", "application/json")
+ .expect(200)
+ .expect("Content-Type", /json/)
+ .then(response => {
+ expect(response.body).toHaveProperty("message");
+ expect(response.body.message).toHaveProperty("query_graph");
+ expect(response.body.message).toHaveProperty("knowledge_graph");
+ expect(response.body.message.knowledge_graph).toHaveProperty("nodes");
+ expect(response.body.message.knowledge_graph).toHaveProperty("edges");
+ expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0016575");
+ expect(response.body.message.knowledge_graph.nodes).toHaveProperty("UMLS:C0008780");
+ expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty(
+ "category",
+ "biolink:PhenotypicFeature",
+ );
+ });
+ });
+
+ // test("POST /v1/query with query that needs to expand node", async () => {
+ // console.log("expanded node", expand_node);
+ // await request(app)
+ // .post("/v1/query")
+ // .send(expand_node)
+ // .set('Accept', 'application/json')
+ // .expect(200)
+ // .expect('Content-Type', /json/)
+ // .then(response => {
+ // console.log(response.body.message.knowledge_graph);
+ // expect(response.body).toHaveProperty("message");
+ // expect(response.body.message).toHaveProperty("query_graph");
+ // expect(response.body.message).toHaveProperty("knowledge_graph");
+ // expect(response.body.message.knowledge_graph).toHaveProperty("nodes");
+ // expect(response.body.message.knowledge_graph).toHaveProperty("edges");
+ // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("REACT:R-HSA-109582");
+ // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("GO:0000082");
+ // })
+ // })
+});