Use JQ

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";
@@ -31,7 +32,8 @@ export class Transformer {
         } 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)
         } else if (tags.includes("biothings")) {

src/transformers/jq_transfomer.ts

@@ -0,0 +1,18 @@
+import BaseTransformer from "./transformer";
+
+const jq = require('node-jq');
+
+const filterStrings = {
+  'ebi': '(select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")',
+  'ctd': '((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}',
+  'opentarget': '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)',
+  'biolink': '[del(.associations), {associations: [select(.associations != null) | .associations | .[] | select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) | .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] ]}] | add'
+}
+
+export default class JQTransformer extends BaseTransformer {
+  async wrap (res) {
+    res = JSON.parse(await jq.run(filterStrings[this.config.type], res, { input: 'json' }));
+    console.log("THIS IS WHAT WILL BE RETURNED", res.associations[1] )
+    return res;
+  }
+}

src/transformers/opentarget_transformer.ts

@@ -1,14 +1,16 @@
 import BaseTransformer from "./transformer";
-
+import jq from "node-jq";
 
 export default class OpenTargetTransformer extends BaseTransformer {
-    wrap(res) {
-        res.data = res.data.map(item => {
-            if ('drug' in item && "id" in item.drug && typeof item.drug.id === "string" && item.drug.id.includes("CHEMBL")) {
-                item.drug.id = item.drug.id.split('/').slice(-1)[0];
-            }
-            return item;
-        });
-        return res;
+    async wrap(res) {
+//         res.data = res.data.map(item => {
+//             if ('drug' in item && "id" in item.drug && typeof item.drug.id === "string" && item.drug.id.includes("CHEMBL")) {
+//                 item.drug.id = item.drug.id.split('/').slice(-1)[0];
+//             }
+//             return item;
+//         });
+//         return res;
+        const filterString = '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)';
+        return await jq.run(filterString, res);
     }
 }

src/transformers/transformer.ts

@@ -169,7 +169,7 @@ export default class BaseTransformer {
         await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
             if (Array.isArray(curieResponses) && curieResponses.length > 0) {
                 await async.eachSeries(curieResponses, async response => {
-                    const predicateResponse = this.jsonTransform(this.wrap(response));
+                    const predicateResponse = this.jsonTransform(await this.wrap(response));
                     await async.eachSeries(Object.entries(predicateResponse), async ([predicate, mappedResponses]) => {
                         if (Array.isArray(mappedResponses) && mappedResponses.length > 0) {
                             await async.eachSeries(mappedResponses, async (mappedResponse: any[]) => {