Use JQ

__test__/base_transformer.test.ts

@@ -21,9 +21,9 @@ describe("test base transformer", () => {
         }
     })
 
-    test("Test pairInputWithAPIResponse function", () => {
+    test("Test pairInputWithAPIResponse function", async () => {
         const tf = new base_tf(input, {});
-        const res = tf.pairCurieWithAPIResponse();
+        const res = await tf.pairCurieWithAPIResponse();
         expect(res).toHaveProperty("DOID:9562");
         expect(res["DOID:9562"]).toHaveLength(1);
     })

__test__/biolink_transformers.test.ts

@@ -1,6 +1,6 @@
 import {describe, expect, test} from '@jest/globals';
 
-import biolink_tf from "../src/transformers/biolink_transformer";
+import jq_tf from "../built/transformers/jq_transfomer";
 import fs from "fs";
 import path from "path";
 import { JSONDoc } from '../src/json_transform/types';
@@ -21,24 +21,24 @@ describe("test biolink transformer", () => {
         }
     })
 
-    test("test biolink wrapper", () => {
-        let tf = new biolink_tf(input, {});
-        let res = tf.wrap(response);
+    test("test biolink wrapper", async () => {
+        let tf = new jq_tf(input, { type: "biolink" });
+        let res = await tf.wrap(response);
         expect(res.associations[0].object.HGNC).toBe("10956");
         expect(res.associations[0].publications[0].id).toBe("21685912");
         expect(res.associations[1]).not.toHaveProperty("publications");
         expect(res.associations[1]).not.toHaveProperty("provided_by");
     });
 
-    test("test biolink wrapper if no association field as root key", () => {
-        let tf = new biolink_tf(input, {});
-        let res = tf.wrap({ "data": [] });
+    test("test biolink wrapper if no association field as root key", async () => {
+        let tf = new jq_tf(input, { type: "biolink" });
+        let res = await tf.wrap({ "data": [] });
         expect(res).toEqual({ "data": [] })
     });
 
-    test("test biolink wrapper if no object id should be prefixed", () => {
-        const tf = new biolink_tf(input, {});
-        const res = tf.wrap(
+    test("test biolink wrapper if no object id should be prefixed", async () => {
+        const tf = new jq_tf(input, { type: "biolink" });
+        const res = await tf.wrap(
             {
                 associations: [
                     {
@@ -51,8 +51,8 @@ describe("test biolink transformer", () => {
         expect(res.associations[0].object.MONDO).toEqual("MONDO:12345")
     });
 
-    test("test biolink wrapper if no object field present", () => {
-        const tf = new biolink_tf(input, {});
+    test("test biolink wrapper if no object field present", async () => {
+        const tf = new jq_tf(input, { type: "biolink" });
         const fake_response = {
             associations: [
                 {
@@ -62,12 +62,12 @@ describe("test biolink transformer", () => {
                 }
             ]
         }
-        const res = tf.wrap(fake_response);
+        const res = await tf.wrap(fake_response);
         expect(res).toEqual(fake_response)
     });
 
-    test("test biolink wrapper if no object.id field present", () => {
-        const tf = new biolink_tf(input, {});
+    test("test biolink wrapper if no object.id field present", async () => {
+        const tf = new jq_tf(input, { type: "biolink" });
         const fake_response = {
             associations: [
                 {
@@ -77,13 +77,13 @@ describe("test biolink transformer", () => {
                 }
             ]
         }
-        const res = tf.wrap(fake_response);
+        const res = await tf.wrap(fake_response);
         expect(res).toEqual(fake_response)
     });
 
-    test("test biolink jsonTransform function", () => {
-        let tf = new biolink_tf(input, {});
-        const wrapped_response = tf.wrap(response);
+    test("test biolink jsonTransform function", async () => {
+        let tf = new jq_tf(input, { type: "biolink" });
+        const wrapped_response = await tf.wrap(response);
         let res: JSONDoc = tf.jsonTransform(wrapped_response);
         expect(res).toHaveProperty("related_to");
         expect(res.related_to[0].HGNC).toEqual("10956");

__test__/biothings_transformer.test.ts

@@ -21,9 +21,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
+        test("test biothings wrapper", async () => {
             let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(2);
             expect(res).toHaveProperty("DRUGBANK:DB00188");
             expect(res["DRUGBANK:DB00188"]).toHaveLength(2);
@@ -46,9 +46,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
+        test("test biothings wrapper", async () => {
             let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("NCBIGene:1017");
             expect(res["NCBIGene:1017"]).toHaveLength(1);
@@ -78,9 +78,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
+        test("test biothings wrapper", async () => {
             let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("PUBCHEM:11373846");
             expect(res["PUBCHEM:11373846"]).toHaveLength(1);

__test__/ctd_transformer.test.ts

@@ -1,8 +1,7 @@
 import {describe, expect, test} from '@jest/globals';
 import fs from "fs";
 import path from "path";
-
-import ctd_tf from "../src/transformers/ctd_transformer";
+import jq_tf from "../built/transformers/jq_transfomer";
 
 describe("test ctd transformer", () => {
 
@@ -20,36 +19,36 @@ describe("test ctd transformer", () => {
         }
     })
 
-    test("test ctd wrapper", () => {
-        let tf = new ctd_tf(input, {});
-        let res = tf.wrap(response);
+    test("test ctd wrapper", async () => {
+        let tf = new jq_tf(input, { type: "ctd" });
+        let res = await tf.wrap(response);
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(2);
         expect(res.data[0].PubMedIDs).toEqual(["21559390"]);
         expect(res.data[0].DiseaseID).toEqual("D008545");
     })
 
-    test("test ctd wrapper if pubmed id field is not string", () => {
-        const tf = new ctd_tf(input, {});
+    test("test ctd wrapper if pubmed id field is not string", async () => {
+        const tf = new jq_tf(input, { type: "ctd" });
         const fake = [
             {
                 DiseaseID: "MESH:D008545"
             }
         ]
-        const res = tf.wrap(fake);
+        const res = await tf.wrap(fake);
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(1);
         expect(res.data[0].PubMedIDs).toBeUndefined;
     })
 
-    test("test ctd wrapper if disease id field is not string", () => {
-        const tf = new ctd_tf(input, {});
+    test("test ctd wrapper if disease id field is not string", async () => {
+        const tf = new jq_tf(input, { type: "ctd" });
         const fake = [
             {
                 PubMedID: "12345"
             }
         ]
-        const res = tf.wrap(fake);
+        const res = await tf.wrap(fake);
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(1);
         expect(res.data[0].DiseaseIDs).toBeUndefined;

__test__/ebi_protein_transformer.test.ts

@@ -1,7 +1,7 @@
 import { describe, expect, test } from "@jest/globals";
 import fs from "fs";
 import path from "path";
-import ebi_tf from "../src/transformers/ebi_protein_transformer";
+import jq_tf from "../src/transformers/jq_transfomer";
 
 describe("test EBI Protein transformer", () => {
   let response;
@@ -18,9 +18,9 @@ describe("test EBI Protein transformer", () => {
     };
   });
 
-  test("test ebi wrapper", () => {
-    let tf = new ebi_tf(input, {});
-    let res = tf.wrap(response);
+  test("test ebi wrapper", async () => {
+    let tf = new jq_tf(input, {type: "ebi"});
+    let res = await tf.wrap(response);
     expect(res.comments[0].reaction.dbReferences).toHaveLength(1);
   });
 });

__test__/opentarget_transformer.test.ts

@@ -1,7 +1,7 @@
 import {describe, expect, test} from '@jest/globals';
+import jq_tf from "../built/transformers/jq_transfomer";
 import fs from "fs";
 import path from "path";
-import opentarget_tf from "../src/transformers/opentarget_transformer";
 
 describe("test opentarget transformer", () => {
 
@@ -20,15 +20,15 @@ describe("test opentarget transformer", () => {
     })
 
 // skip these tests since we're not ingesting opentargets right now
-    test.skip("test opentarget wrapper", () => {
-        let tf = new opentarget_tf(input, {});
-        let res = tf.wrap(response);
+    test.skip("test opentarget wrapper", async () => {
+        let tf = new jq_tf(input, { type: "opentarget" });
+        let res = await tf.wrap(response);
         expect(res).toHaveProperty("data");
         expect(res.data[0].drug.id).toEqual("CHEMBL220492");
     })
 
-    test.skip("test opentarget wrapper if id field is not chembl", () => {
-        let tf = new opentarget_tf(input, {});
+    test.skip("test opentarget wrapper if id field is not chembl", async () => {
+        let tf = new jq_tf(input, { type: "opentarget" });
         const fake = {
             data: [
                 {
@@ -38,7 +38,7 @@ describe("test opentarget transformer", () => {
                 }
             ]
         }
-        let res = tf.wrap(fake);
+        let res = await tf.wrap(fake);
         expect(res).toHaveProperty("data");
         expect(res.data[0].drug.id).toEqual("http://identifiers.org/drugbank/DB0001");
     })

__test__/semmed_transformer.test.ts

@@ -76,9 +76,9 @@ describe("test semmed transformer", () => {
         }
     });
 
-    test("test semmed pairCurieWithAPIResponse", () => {
+    test("test semmed pairCurieWithAPIResponse", async () => {
         let tf = new semmed_tf(input, {});
-        let res = tf.pairCurieWithAPIResponse();
+        let res = await tf.pairCurieWithAPIResponse();
         expect(res["UMLS:C1332823"][0]['umls']).toBe("C1332823");
         expect(res).toHaveProperty('UMLS:C1332823');
         expect(res["UMLS:123"]).toBeUndefined();
@@ -98,7 +98,7 @@ describe("test semmed transformer", () => {
 
     test("add edge info", async () => {
         let tf = new semmed_tf(input, {});
-        let res = tf.pairCurieWithAPIResponse();
+        let res = await tf.pairCurieWithAPIResponse();
         let rec = res["UMLS:C1332823"][0];
         rec = tf.wrap(rec);
         let result = await tf.formatRecords("UMLS:C1332823", rec["positively_regulates"][0]);

__test__/transformers.test.ts

@@ -147,9 +147,9 @@ describe("test biothings transformer", () => {
         }
     });
 
-    test("test biothings pairCurieWithAPIResponse", () => {
+    test("test biothings pairCurieWithAPIResponse", async () => {
         let tf = new biothings_tf(input, {});
-        let res = tf.pairCurieWithAPIResponse();
+        let res = await tf.pairCurieWithAPIResponse();
         expect(res["UMLS:C1332823"][0]['umls']).toBe("C1332823");
         expect(res).toHaveProperty('UMLS:C1332823');
         expect(res["123"]).toBeUndefined();

package.json

@@ -54,7 +54,8 @@
     "common-path-prefix": "^3.0.0",
     "husky": "^4.3.8",
     "jsonata": "^1.8.4",
-    "lodash": "^4.17.21"
+    "lodash": "^4.17.21",
+    "node-jq": "^2.3.4"
   },
   "husky": {
     "hooks": {

src/index.ts

@@ -7,6 +7,7 @@ import OpenTargetTransformer from "./transformers/opentarget_transformer";
 import BaseTransformer from "./transformers/transformer";
 import TRAPITransformer from './transformers/trapi_transformer';
 import EBIProteinTransformer from './transformers/ebi_protein_transformer'
+import JQTransformer from "./transformers/jq_transfomer";
 import { BTEQueryObject } from "./types";
 const debug = require("debug")("bte:api-response-transform:index");
 export { Record } from "./record";
@@ -26,18 +27,30 @@ export class Transformer {
         debug(`api name ${api}`);
         let tags = this.data.edge.query_operation.tags;
         debug(`api tags: ${tags}`);
-        if (tags.includes('bte-trapi')) {
+
+        // if (!this.data.edge.query_operation.transformer) {
+        //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
+        // } 
+
+        if (this.data.edge.query_operation?.transformer?.pair_jq || this.data.edge.query_operation?.transformer?.wrap_jq) {
+            // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
+            this.tf = new JQTransformer(this.data, { 
+              ...this.config, 
+              wrap: this.data.edge.query_operation.transformer.wrap_jq, 
+              pair: this.data.edge.query_operation.transformer.pair_jq 
+            })
+        } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);
-        } else if (api.startsWith('SEMMED')) {
-            this.tf = new SemmedTransformer(this.data, this.config);
         } else if (api === 'BioLink API') {
-            this.tf = new BiolinkTransformer(this.data, this.config);
+            // this.tf = new BiolinkTransformer(this.data, this.config);
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" })
         } else if (api === 'EBI Proteins API') {
-            this.tf = new EBIProteinTransformer(this.data, this.config)
+            // this.tf = new EBIProteinTransformer(this.data, this.config)
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" })
         } else if (tags.includes("biothings")) {
-            this.tf = new BioThingsTransformer(this.data, this.config);
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" })
         } else if (tags.includes("ctd")) {
-            this.tf = new CTDTransformer(this.data, this.config);
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" });
         } else if (tags.includes("opentarget")) {
             this.tf = new OpenTargetTransformer(this.data, this.config)
         } else {