Merge branch 'main' into parallel-creative

biothings · Sep 6, 2024 · fa427b6 · fa427b6
2 parents 657cddc + 273b866
commit fa427b6
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Showing 10 changed files with 160 additions and 50 deletions.
diff --git a/.github/workflows/test_ws_codecov.yml b/.github/workflows/test_ws_codecov.yml
@@ -13,11 +13,21 @@ jobs:
       id: branch-name
       uses: tj-actions/[email protected]
 
-    - uses: actions/checkout@v3
+    - name: Checkout to specific branch
+      uses: actions/checkout@v3
+      id: specific-checkout
+      continue-on-error: true
       with:
         repository: biothings/biothings_explorer
         ref: ${{ steps.branch-name.outputs.current_branch }}
 
+    - name: Checkout to main if above failed
+      if: steps.specific-checkout.outcome == 'failure'
+      uses: actions/checkout@v3
+      with:
+        repository: biothings/biothings_explorer
+        ref: main
+
     - name: Use Node.js 18.x
       uses: actions/setup-node@v3
       with:

diff --git a/__test__/data/mygene_example_edge.json b/__test__/data/mygene_example_edge.json
@@ -29,6 +29,7 @@
     "api_name": "MyGene.info API",
     "smartapi": {},
     "x-translator": {
+      "infores": "infores:mygene-info",
       "component": "KP",
       "team": ["Service Provider"]
     }

diff --git a/__test__/unittest/query_builder.test.ts b/__test__/unittest/query_builder.test.ts
@@ -299,7 +299,10 @@ describe("test query builder class", () => {
       // @ts-expect-error TODO: change after APIEdge split from query_graph_handler
       const builder = new qb(edge);
       const res = builder.needPagination(response);
-      expect(res).toBeFalsy();
+      expect(res).toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
 
     test("biothings tagged api with post method should return false", () => {
@@ -316,7 +319,10 @@ describe("test query builder class", () => {
       // @ts-expect-error TODO: change after APIEdge split from query_graph_handler
       const builder = new qb(edge);
       const res = builder.needPagination(response);
-      expect(res).toBeFalsy();
+      expect(res).toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
 
     test("biothings tagged api with get method and needs pagniation should return true", () => {
@@ -333,7 +339,10 @@ describe("test query builder class", () => {
       // @ts-expect-error TODO: change after APIEdge split from query_graph_handler
       const builder = new qb(edge);
       const res = builder.needPagination(response);
-      expect(res).toBeTruthy();
+      expect(res).not.toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
 
     test("biothings tagged api with get method and doesn't need pagniation should return false", () => {
@@ -350,7 +359,10 @@ describe("test query builder class", () => {
       // @ts-expect-error TODO: change after APIEdge split from query_graph_handler
       const builder = new qb(edge);
       const res = builder.needPagination(response);
-      expect(res).toBeFalsy();
+      expect(res).toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
   });
 });
diff --git a/__test__/unittest/template_query_builder.test.ts b/__test__/unittest/template_query_builder.test.ts
@@ -5,6 +5,7 @@
 import qb from "../../src/builder/template_query_builder";
 import path from "path";
 import fs from "fs";
+import { QueryHandlerOptions } from "../../src/types";
 
 describe("test query builder class", () => {
   describe("test _getUrl function", () => {
@@ -15,8 +16,9 @@ describe("test query builder class", () => {
           path: "/query",
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getUrl(edge, "hello");
       expect(res).toBe("https://google.com/query");
@@ -29,8 +31,9 @@ describe("test query builder class", () => {
           path: "/query",
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getUrl(edge, "hello");
       expect(res).toBe("https://google.com/query");
@@ -48,8 +51,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getUrl(edge, "hello");
       expect(res).toBe("https://google.com/1017/query");
@@ -67,8 +71,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getUrl(edge, { queryInputs: "hello" });
       expect(res).toBe("https://google.com/hello/json/query");
@@ -77,7 +82,8 @@ describe("test query builder class", () => {
     test("if _getUrl nunjucks templates are filled", () => {
       const edge_path = path.resolve(__dirname, "../data/multi_input_edge.json");
       const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
-      const builder = new qb(edge);
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder._getUrl(edge, {
         specialpath: "/querytest",
         id: "MONDO:0005252",
@@ -96,8 +102,9 @@ describe("test query builder class", () => {
           supportBatch: true,
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getInput(edge);
       expect(res).toEqual(edge.input);
@@ -110,8 +117,9 @@ describe("test query builder class", () => {
           supportBatch: true,
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getInput(edge);
       expect(res).toEqual(["kevin", "xin"]);
@@ -124,8 +132,9 @@ describe("test query builder class", () => {
           supportBatch: false,
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getInput(edge);
       expect(res).toEqual(edge.input);
@@ -144,8 +153,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getParams(edge, { queryInputs: "1017" });
       expect(res).toHaveProperty("geneid");
@@ -164,8 +174,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getParams(edge, "1017");
       expect(res).not.toHaveProperty("geneid");
@@ -184,8 +195,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getParams(edge, { queryInputs: "1017" });
       expect(res).not.toHaveProperty("geneid");
@@ -204,8 +216,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getParams(edge, "1017");
       expect(res.output).toEqual(1);
@@ -215,7 +228,8 @@ describe("test query builder class", () => {
       const edge_path = path.resolve(__dirname, "../data/multi_input_edge.json");
       const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
 
-      const builder = new qb(edge);
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder._getParams(edge, {
         specialpath: "/querytest",
         id: "MONDO:0005252",
@@ -243,8 +257,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getRequestBody(edge, "1017");
       expect(res).toBeUndefined;
@@ -263,8 +278,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getRequestBody(edge, "1017");
       expect(res).toEqual("geneid=hello&output=1");
@@ -283,8 +299,9 @@ describe("test query builder class", () => {
           },
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
       const res = builder._getRequestBody(edge, { queryInputs: "1017" });
       expect(res).toEqual("geneid=hello&output=1017");
@@ -294,7 +311,8 @@ describe("test query builder class", () => {
       const edge_path = path.resolve(__dirname, "../data/multi_input_edge.json");
       const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
 
-      const builder = new qb(edge);
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder._getRequestBody(edge, {
         specialpath: "/querytest",
         id: "MONDO:0005252",
@@ -320,8 +338,9 @@ describe("test query builder class", () => {
           method: "get",
         },
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder.constructAxiosRequestConfig();
       expect(res.url).toEqual("https://google.com/1017/query");
       expect(res.params).not.toHaveProperty("geneid");
@@ -343,10 +362,14 @@ describe("test query builder class", () => {
         total: 1000,
         hits: new Array(400),
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder.needPagination(response);
-      expect(res).toBeFalsy();
+      expect(res).toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
 
     test("biothings tagged api with post method should return false", () => {
@@ -361,10 +384,14 @@ describe("test query builder class", () => {
         total: 1000,
         hits: new Array(400),
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder.needPagination(response);
-      expect(res).toBeFalsy();
+      expect(res).toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
 
     test("biothings tagged api with get method and needs pagniation should return true", () => {
@@ -378,10 +405,14 @@ describe("test query builder class", () => {
         total: 1000,
         hits: new Array(400),
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder.needPagination(response);
-      expect(res).toBeTruthy();
+      expect(res).not.toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
 
     test("biothings tagged api with get method and doesn't need pagniation should return false", () => {
@@ -395,10 +426,14 @@ describe("test query builder class", () => {
         total: 1000,
         hits: new Array(1000),
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new qb(edge);
+      const builder = new qb(edge, queryHandlerOptions);
       const res = builder.needPagination(response);
-      expect(res).toBeFalsy();
+      expect(res).toMatchObject({
+        paginationStart: 0,
+        paginationSize: 0
+      });
     });
   });
 });
diff --git a/__test__/unittest/trapi_query_builder.test.ts b/__test__/unittest/trapi_query_builder.test.ts
@@ -3,6 +3,7 @@
  */
 
 import TRAPIQueryBuilder from "../../src/builder/trapi_query_builder";
+import { QueryHandlerOptions } from "../../src/types";
 
 describe("test trapi query builder class", () => {
   describe("test getConfig function", () => {
@@ -19,8 +20,9 @@ describe("test trapi query builder class", () => {
         },
         input: ["123", "456"],
       };
+      const queryHandlerOptions: QueryHandlerOptions = {caching: false};
       // @ts-expect-error TODO: change after extracting APIEdge from query_graph_handler
-      const builder = new TRAPIQueryBuilder(edge);
+      const builder = new TRAPIQueryBuilder(edge, queryHandlerOptions);
       const res = builder.getConfig();
       expect(res).toHaveProperty("url", "https://google.com/query");
       expect(res.data.message.query_graph.nodes.n0.ids).toEqual(["123", "456"]);

diff --git a/src/builder/base_query_builder.ts b/src/builder/base_query_builder.ts
@@ -85,9 +85,9 @@ export default class BaseQueryBuilder {
     return config;
   }
 
-  needPagination(apiResponse: unknown): number {
+  needPagination(apiResponse: unknown): {paginationStart: number, paginationSize: number} {
     // implemented in subclasses
-    return 0;
+    return {paginationSize: 0, paginationStart: 0};
   }
 
   getNext(): AxiosRequestConfig {