Merge branch 'use-jmes-path' of https://github.com/biothings/api-resp…

…one-transform.js into dev
biothings · Oct 19, 2023 · dbf8aac · dbf8aac
2 parents 23182bc + 549e415
commit dbf8aac
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Showing 27 changed files with 351 additions and 112 deletions.
diff --git a/__test__/base_transformer.test.ts b/__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);
     })

diff --git a/__test__/biolink_transformers.test.ts b/__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_transformer";
 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");

diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts
@@ -1,5 +1,5 @@
 
-import biothings_tf from "../src/transformers/biothings_transformer";
+import jq_tf from "../src/transformers/jq_transformer";
 import {describe, expect, test} from '@jest/globals';
 import fs from "fs";
 import path from "path";
@@ -21,9 +21,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
-            let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+        test("test biothings wrapper", async () => {
+            let tf = new jq_tf(input, {type: "biothings"});
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(2);
             expect(res).toHaveProperty("DRUGBANK:DB00188");
             expect(res["DRUGBANK:DB00188"]).toHaveLength(2);
@@ -46,16 +46,16 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
-            let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+        test("test biothings wrapper", async () => {
+            let tf = new jq_tf(input, {type: "biothings"});
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("NCBIGene:1017");
             expect(res["NCBIGene:1017"]).toHaveLength(1);
         })
 
         test("test biothings transform", async () => {
-            let tf = new biothings_tf(input, {});
+            let tf = new jq_tf(input, {type: "biothings"});
             let res = await tf.transform();
             expect(res).toHaveLength(27);
             expect(res[0]).not.toHaveProperty('ref_pmid');
@@ -78,9 +78,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
-            let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+        test("test biothings wrapper", async () => {
+            let tf = new jq_tf(input, {type: "biothings"});
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("PUBCHEM:11373846");
             expect(res["PUBCHEM:11373846"]).toHaveLength(1);

diff --git a/__test__/ctd_transformer.test.ts b/__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_transformer";
 
 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");
+        expect(res.data[0].DiseaseID).toEqual("MESH: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;

diff --git a/__test__/data/biothings/drug_response_example_edge.json b/__test__/data/biothings/drug_response_example_edge.json
@@ -8,7 +8,7 @@
             "size": "1000"
         },
         "_supportBatch": false,
-        "method": "get",
+        "_method": "get",
         "_pathParams": [],
         "_server": "https://biothings.ncats.io/drug_response_kp",
         "_path": "/query",

diff --git a/__test__/data/biothings/mychem_example_edge.json b/__test__/data/biothings/mychem_example_edge.json
@@ -17,7 +17,7 @@
         },
         "_supportBatch": true,
         "_inputSeparator": ",",
-        "method": "post",
+        "_method": "post",
         "_pathParams": [],
         "_server": "https://mychem.info/v1",
         "_path": "/query",

diff --git a/__test__/data/biothings/mygene_example_edge.json b/__test__/data/biothings/mygene_example_edge.json
@@ -12,7 +12,7 @@
         },
         "_supportBatch": true,
         "_inputSeparator": ",",
-        "method": "post",
+        "_method": "post",
         "_pathParams": [],
         "_server": "https://mygene.info/v3",
         "_path": "/query",

diff --git a/__test__/ebi_protein_transformer.test.ts b/__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_transformer";
 
 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);
   });
 });
diff --git a/__test__/opentarget_transformer.test.ts b/__test__/opentarget_transformer.test.ts
@@ -1,7 +1,7 @@
 import {describe, expect, test} from '@jest/globals';
+import jq_tf from "../built/transformers/jq_transformer";
 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");
     })

diff --git a/__test__/semmed_transformer.test.ts b/__test__/semmed_transformer.test.ts
@@ -17,9 +17,9 @@ 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();
@@ -39,7 +39,7 @@ 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]);

diff --git a/__test__/transformers.test.ts b/__test__/transformers.test.ts
@@ -162,9 +162,9 @@ 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();

diff --git a/data/jq/pair/biothings.jq b/data/jq/pair/biothings.jq
@@ -0,0 +1,22 @@
+if $edge.query_operation._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
+    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
+end
diff --git a/data/jq/pair/ctd.jq b/data/jq/pair/ctd.jq
@@ -0,0 +1,23 @@
+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]
+) | map_values([.])