Various JQ fixes

__test__/biothings_transformer.test.ts

@@ -57,7 +57,8 @@ describe("test biothings transformer", () => {
       const res = await tf.transform();
       expect(res).toHaveLength(27);
       expect(res[0]).not.toHaveProperty("ref_pmid");
-      expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]);
+      expect(res[0].mappedResponse).toHaveProperty("pubmed", 21873635);
+      // expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]);
     });
   });
 

__test__/data/biothings/mychem_example_edge.json

@@ -1,23 +1,23 @@
 {
   "input": ["DB00188", "DB00184", "DB0000"],
   "query_operation": {
-    "_params": {
+    "params": {
       "fields": "drugbank.enzymes"
     },
-    "_requestBody": {
+    "requestBody": {
       "body": {
         "q": "{inputs[0]}",
         "scopes": "drugbank.id"
       },
       "header": "application/x-www-form-urlencoded"
     },
-    "_supportBatch": true,
-    "_inputSeparator": ",",
-    "_method": "post",
-    "_pathParams": [],
-    "_server": "https://mychem.info/v1",
-    "_path": "/query",
-    "_tags": ["chemical", "drug", "annotation", "query", "translator", "biothings"]
+    "supportBatch": true,
+    "inputSeparator": ",",
+    "method": "post",
+    "pathParams": [],
+    "server": "https://mychem.info/v1",
+    "path": "/query",
+    "tags": ["chemical", "drug", "annotation", "query", "translator", "biothings"]
   },
   "association": {
     "input_id": "DRUGBANK",

__test__/data/biothings/mygene_example_edge.json

@@ -1,22 +1,23 @@
 {
+  "input": "NCBIGene:1017",
   "query_operation": {
-    "_params": {
+    "params": {
       "fields": "go.BP"
     },
-    "_requestBody": {
+    "requestBody": {
       "body": {
         "q": "{inputs[0]}",
         "scopes": "entrezgene"
       },
       "header": "application/x-www-form-urlencoded"
     },
-    "_supportBatch": true,
-    "_inputSeparator": ",",
-    "_method": "post",
-    "_pathParams": [],
-    "_server": "https://mygene.info/v3",
-    "_path": "/query",
-    "_tags": ["gene", "annotation", "query", "translator", "biothings"]
+    "supportBatch": true,
+    "inputSeparator": ",",
+    "method": "post",
+    "pathParams": [],
+    "server": "https://mygene.info/v3",
+    "path": "/query",
+    "tags": ["gene", "annotation", "query", "translator", "biothings"]
   },
   "association": {
     "input_id": "NCBIGene",

data/jq/pair/biothings.jq

@@ -1,22 +1,23 @@
-if $edge.query_operation._method == "post" then
+if $edge.query.method == "post" then
   # if response is not an array, then use response.hits
   if (.response | type) == "array" then .response else .response.hits end |
   reduce .[] as $item ({};
     # if the item is notfound, then proceed to next item & keep current object
     if ($item | keys | contains(["notfound"])) then
       .
     else
-      if $edge.input | type == "object" then
-        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
-      else
-        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input | toArray) as $curie | .[$curie] = .[$curie] + [$item]
-      end
+      generateCurieWithInputs(
+        $edge.input.id;
+        $item.query; 
+        $edge.input.curies
+        | toArray
+        | map(. | split(":") | last)
+      ) as $curie | .[$curie] += [$item]
     end
   )
 else
-  if ($edge.input | type) == "object" then
-    .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
-  else
-    .response as $res | generateCurie($edge.association.input_id; ($edge.input | toArray)[0]) as $curie | {} | .[$curie] = [$res]
-  end
+  .response as $res | generateCurie(
+    $edge.input.id;
+    ($edge.input.curies | toArray | map(. | split(":") | last) | first)
+  ) as $curie | {} | .[$curie] = [$res]
 end

data/jq/pair/ctd.jq

@@ -1,23 +1,14 @@
-reduce .response[] as $item (
-  {}; .[(
-      if ($edge.input | type) == "object" then
-        ($edge.input.queryInputs | toArray)[]
-      else
-        ($edge.input | toArray)[]
-      end
-    ) 
-    | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase))
-    | generateCurie($edge.association.input_id; .)
-  ] = [] 
-  + .[(
-      if ($edge.input | type) == "object" then
-        ($edge.input.queryInputs | toArray)[]
-      else
-        ($edge.input | toArray)[]
-      end
-    )
-    | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase))
-    | generateCurie($edge.association.input_id; .)
-  ] 
-  + [$item]
+(reduce .response[].Input as $id (
+  {}; if (. as $mapping | $id | in($mapping) | not)
+  then
+    ($edge.input.curies | find((. | ascii_upcase) == ($id | split(":") | last | ascii_upcase))) as $fixedID
+    | .[$id] = $fixedID
+  end
+)) as $idMapping # maps response[].Input -> appropriate $edge.input.curies
+| reduce .response[] as $item (
+  {}; if ($idMapping[$item.Input])
+  then
+    (generateCurie($edge.input.id; $idMapping[$item.Input])) as $curie
+    | .[$curie] += [$item]
+  end
 ) | map_values([.])

data/jq/utils.jq

@@ -46,3 +46,6 @@ def list_filter_all(filter_strs): if (. | type) == "array" then [.[] | if . | al
 
 # filters the list that is supplied on any conditions
 def list_filter_any(filter_strs): if (. | type) == "array" then [.[] | if . | any_filter(filter_strs) then . else empty end] else empty end;
+
+# essential Array.find()
+def find(cond): . as $iter | 0 | until((. == ($iter | length)) or ($iter[.] | cond); . + 1) | if (. == ($iter | length)) then false else $iter[.] end;

src/jq_utils.ts

@@ -1,8 +1,12 @@
 import { JQVariable, BTEKGOperationObject } from "./types";
 import Path from "path";
 import fs from "fs";
+import { toArray } from "./utils";
 
-const functions = fs.readFileSync(Path.resolve(`${__dirname}/../data/jq/utils.jq`), { encoding: "utf8" });
+const functions = fs.readFileSync(
+  Path.resolve(`${__dirname}/../data/jq/utils.jq`),
+  { encoding: "utf8" },
+);
 
 function generateVariables(variables: JQVariable[]) {
   let variableString = "";
@@ -12,12 +16,6 @@ function generateVariables(variables: JQVariable[]) {
   return variableString;
 }
 
-export function generateFilterString(filterString: string, edge: BTEKGOperationObject) {
-  const variables = [
-    {
-      name: "$edge",
-      value: JSON.stringify(edge),
-    },
-  ];
-  return `${functions}\n${generateVariables(variables)}${filterString}`;
+export function generateFilterString(filterString: string) {
+  return `${functions}\n${filterString}`;
 }

src/transformers/jq_transformer.ts

@@ -5,6 +5,7 @@ import Path from "path";
 
 import * as jq from "node-jq"; // If converted to import, ts compile breaks it (imports default as undefined)
 import { JSONDoc, PairedResponse } from "../json_transform/types";
+import { toArray } from "../utils";
 
 // Get prefab JQ strings from data/jq
 const filterStringsWrap = Object.fromEntries(
@@ -24,33 +25,42 @@ const filterStringsPair = Object.fromEntries(
 export default class JQTransformer extends BaseTransformer {
   // TODO more specific typing?
   async wrap(res: JSONDoc | JSONDoc[]): Promise<JSONDoc> {
-    if (this.config.wrap)
-      res = JSON.parse(
-        (await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: "json" })) as string,
-      );
-    else if (filterStringsWrap[this.config.type])
-      res = JSON.parse(
-        (await jq.run(generateFilterString(filterStringsWrap[this.config.type], this.edge), res, {
-          input: "json",
-        })) as string,
-      );
-    else res = super.wrap(res);
-
-    return res;
+    let filterString: string | undefined = this.config.wrap ?? filterStringsWrap[this.config.type];
+    if (typeof filterString === "undefined") return super.wrap(res);
+    filterString = generateFilterString(filterString);
+    return JSON.parse(
+      (await jq.run(filterString, res, {
+        input: "json",
+      })) as string,
+    );
   }
 
   async pairCurieWithAPIResponse(): Promise<PairedResponse> {
-    if (this.config.pair)
-      return JSON.parse(
-        (await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: "json" })) as string,
-      );
-    else if (filterStringsPair[this.config.type])
-      return JSON.parse(
-        (await jq.run(generateFilterString(filterStringsPair[this.config.type], this.edge), this.data, {
-          input: "json",
-        })) as string,
-      );
-
-    return super.pairCurieWithAPIResponse();
+    let filterString: string | undefined = this.config.pair ?? filterStringsPair[this.config.type];
+    if (typeof filterString === "undefined") return super.pairCurieWithAPIResponse();
+    const data = {
+      response: this.data.response,
+      edge: {
+        query: {
+          method: this.edge.query_operation.method,
+        },
+        input: {
+          id: this.edge.association.input_id,
+          type: this.edge.association.input_type,
+          // input is array or is object with queryInputs
+          curies:
+            Array.isArray(this.edge.input) || typeof this.edge.input === "string"
+              ? toArray(this.edge.input)
+              : toArray(this.edge.input.queryInputs),
+        },
+        predicate: this.edge.association.predicate,
+        output: {
+          id: this.edge.association.output_id,
+          type: this.edge.association.output_type,
+        },
+      },
+    };
+    filterString = `.edge as $edge | ${generateFilterString(filterString)}`;
+    return JSON.parse((await jq.run(filterString, data, { input: "json" })) as string);
   }
 }