Merge pull request #38 from biothings/use-jmes-path

Use JQ
biothings · Oct 24, 2023 · b4188d3 · b4188d3
2 parents e8a3085 + 17496d8
commit b4188d3
Show file tree

Hide file tree

Showing 43 changed files with 25,208 additions and 24,604 deletions.
diff --git a/__test__/base_transformer.test.ts b/__test__/base_transformer.test.ts
@@ -18,9 +18,9 @@ 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
@@ -1,3 +1,4 @@
+import jq_tf from "../built/transformers/jq_transformer";
 import biolink_tf from "../src/transformers/biolink_transformer";
 import fs from "fs";
 import path from "path";
@@ -18,24 +19,24 @@ describe("test biolink transformer", () => {
     };
   });
 
-  test("test biolink wrapper", () => {
-    const tf = new biolink_tf(input, {});
-    const res = tf.wrap(response);
+  test("test biolink wrapper", async () => {
+    const tf = new jq_tf(input, { type: "biolink" });
+    const 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", () => {
-    const tf = new biolink_tf(input, {});
-    const res = tf.wrap({ data: [] });
+  test("test biolink wrapper if no association field as root key", async () => {
+    const tf = new jq_tf(input, { type: "biolink" });
+    const 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: [
         {
           object: {
@@ -47,8 +48,8 @@ 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: [
         {
@@ -58,12 +59,12 @@ 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: [
         {
@@ -73,13 +74,13 @@ 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", () => {
-    const tf = new biolink_tf(input, {});
-    const wrapped_response = tf.wrap(response);
+  test("test biolink jsonTransform function", async () => {
+    const tf = new jq_tf(input, { type: "biolink" });
+    const wrapped_response = await tf.wrap(response);
     const 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
@@ -1,3 +1,4 @@
+import jq_tf from "../src/transformers/jq_transformer";
 import biothings_tf from "../src/transformers/biothings_transformer";
 import fs from "fs";
 import path from "path";
@@ -18,9 +19,9 @@ describe("test biothings transformer", () => {
       };
     });
 
-    test("test biothings wrapper", () => {
-      const tf = new biothings_tf(input, {});
-      const res = tf.pairCurieWithAPIResponse();
+    test("test biothings wrapper", async () => {
+      const tf = new jq_tf(input, { type: "biothings" });
+      const res = await tf.pairCurieWithAPIResponse();
       expect(Object.keys(res)).toHaveLength(2);
       expect(res).toHaveProperty("DRUGBANK:DB00188");
       expect(res["DRUGBANK:DB00188"]).toHaveLength(2);
@@ -43,21 +44,20 @@ describe("test biothings transformer", () => {
       };
     });
 
-    test("test biothings wrapper", () => {
-      const tf = new biothings_tf(input, {});
-      const res = tf.pairCurieWithAPIResponse();
+    test("test biothings wrapper", async () => {
+      const tf = new jq_tf(input, { type: "biothings" });
+      const 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 () => {
-      const tf = new biothings_tf(input, {});
+      const tf = new jq_tf(input, { type: "biothings" });
       const res = await tf.transform();
       expect(res).toHaveLength(27);
       expect(res[0]).not.toHaveProperty("ref_pmid");
-      // TODO: re-enable when this is handled properly
-      // expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]);
+      expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]);
     });
   });
 
@@ -76,9 +76,9 @@ describe("test biothings transformer", () => {
       };
     });
 
-    test("test biothings wrapper", () => {
-      const tf = new biothings_tf(input, {});
-      const res = tf.pairCurieWithAPIResponse();
+    test("test biothings wrapper", async () => {
+      const tf = new jq_tf(input, { type: "biothings" });
+      const 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
@@ -1,7 +1,6 @@
 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", () => {
   let response;
@@ -18,36 +17,36 @@ describe("test ctd transformer", () => {
     };
   });
 
-  test("test ctd wrapper", () => {
-    const tf = new ctd_tf(input, {});
-    const res = tf.wrap(response);
+  test("test ctd wrapper", async () => {
+    const tf = new jq_tf(input, { type: "ctd" });
+    const 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/biolink/edge.json b/__test__/data/biolink/edge.json
@@ -1,56 +1,44 @@
 {
-    "input": "DOID:678",
-    "query_operation": {
-        "params": {
-            "disease_id": "{inputs[0]}",
-            "rows": 200
-        },
-        "path": "/bioentity/disease/{disease_id}/genes",
-        "path_params": [
-            "disease_id"
-        ],
-        "method": "get",
-        "server": "https://api.monarchinitiative.org/api",
-        "tags": [
-            "anatomy",
-            "disease",
-            "gene",
-            "phenotype",
-            "pathway",
-            "annotation",
-            "query",
-            "translator",
-            "biolink"
-        ],
-        "supportBatch": false
+  "input": "DOID:678",
+  "query_operation": {
+    "params": {
+      "disease_id": "{inputs[0]}",
+      "rows": 200
     },
-    "association": {
-        "input_id": "MONDO",
-        "input_type": "Disease",
-        "output_id": "HGNC",
-        "output_type": "Gene",
-        "predicate": "related_to",
-        "api_name": "BioLink API",
-        "smartapi": {
-            "id": "d22b657426375a5295e7da8a303b9893",
-            "meta": {
-                "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d",
-                "github_username": "newgene",
-                "timestamp": "2020-05-28T00:02:40.483712",
-                "uptime_status": "good",
-                "uptime_ts": "2020-06-11T00:05:38.030503",
-                "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml"
-            }
-        }
-    },
-    "response_mapping": {
-        "related_to": {
-            "HGNC": "associations.object.HGNC",
-            "pubmed": "associations.publications.id",
-            "relation": "associations.relation.label",
-            "source": "associations.provided_by",
-            "taxid": "associations.object.taxon.id"
-        }
-    },
-    "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
-}
+    "path": "/bioentity/disease/{disease_id}/genes",
+    "path_params": ["disease_id"],
+    "method": "get",
+    "server": "https://api.monarchinitiative.org/api",
+    "tags": ["anatomy", "disease", "gene", "phenotype", "pathway", "annotation", "query", "translator", "biolink"],
+    "supportBatch": false
+  },
+  "association": {
+    "input_id": "MONDO",
+    "input_type": "Disease",
+    "output_id": "HGNC",
+    "output_type": "Gene",
+    "predicate": "related_to",
+    "api_name": "BioLink API",
+    "smartapi": {
+      "id": "d22b657426375a5295e7da8a303b9893",
+      "meta": {
+        "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d",
+        "github_username": "newgene",
+        "timestamp": "2020-05-28T00:02:40.483712",
+        "uptime_status": "good",
+        "uptime_ts": "2020-06-11T00:05:38.030503",
+        "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml"
+      }
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "HGNC": "associations.object.HGNC",
+      "pubmed": "associations.publications.id",
+      "relation": "associations.relation.label",
+      "source": "associations.provided_by",
+      "taxid": "associations.object.taxon.id"
+    }
+  },
+  "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
+}