Merge pull request #63 from biothings/add-qualifiers

Add qualifiers
biothings · Dec 21, 2022 · fc2adba · fc2adba
2 parents 08ae3e0 + bfb2ab4
commit fc2adba
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Showing 2 changed files with 106 additions and 102 deletions.
diff --git a/__test__/integration/integration.test.js b/__test__/integration/integration.test.js
@@ -60,8 +60,8 @@ describe("Integration test", () => {
         test("check response", async () => {
             const query = new q(edges);
             const res = await query.query(false);
-            const mydisease_res = await axios.get("http://mydisease.info/v1/disease/MONDO:0002494?fields=mondo.descendants&dotfield=true");
-            expect(res.length).toEqual(mydisease_res.data["mondo.descendants"].length)
+            const mydisease_res = await axios.get("http://mydisease.info/v1/disease/MONDO:0002494?fields=mondo.children&dotfield=true");
+            expect(res.length).toEqual(mydisease_res.data["mondo.children"].length)
         })
     })
 })
diff --git a/src/builder/trapi_query_builder.js b/src/builder/trapi_query_builder.js
@@ -6,116 +6,120 @@ const nunjucksConfig = require("./nunjucks_config");
 const env = nunjucks.configure({ autoescape: false });
 nunjucksConfig(env);
 module.exports = class TRAPIQueryBuilder {
-    /**
-     * Constructor for Query Builder
-     * @param {object} APIEdge - BTE Edge object with input field provided
-     */
-    constructor(APIEdge) {
-        this.start = 0
-        this.hasNext = false
-        this.APIEdge = APIEdge;
-        this.originalSubmitter;
-    }
+  /**
+   * Constructor for Query Builder
+   * @param {object} APIEdge - BTE Edge object with input field provided
+   */
+  constructor(APIEdge) {
+    this.start = 0;
+    this.hasNext = false;
+    this.APIEdge = APIEdge;
+    this.originalSubmitter;
+  }
 
-    getUrl() {
-        return this.APIEdge.query_operation.server + this.APIEdge.query_operation.path;
-    }
+  getUrl() {
+    return this.APIEdge.query_operation.server + this.APIEdge.query_operation.path;
+  }
 
-    _getUrl(APIEdge, input) {
-        let server = APIEdge.query_operation.server;
-        if (server.endsWith('/')) {
-            server = server.substring(0, server.length - 1)
-        };
-        let path = APIEdge.query_operation.path;
-        if (Array.isArray(APIEdge.query_operation.path_params)) {
-              APIEdge.query_operation.path_params.map(param => {
-                const val = APIEdge.query_operation.params[param];
-                path = path.replace("{" + param + "}", val).replace("{inputs[0]}", input);
-              });
-        }
-        return server + path;
+  _getUrl(APIEdge, input) {
+    let server = APIEdge.query_operation.server;
+    if (server.endsWith("/")) {
+      server = server.substring(0, server.length - 1);
     }
-
-    /**
-     * Construct input based on method and inputSeparator
-     */
-    _getInput(APIEdge) {
-        return APIEdge.input;
+    let path = APIEdge.query_operation.path;
+    if (Array.isArray(APIEdge.query_operation.path_params)) {
+      APIEdge.query_operation.path_params.map(param => {
+        const val = APIEdge.query_operation.params[param];
+        path = path.replace("{" + param + "}", val).replace("{inputs[0]}", input);
+      });
     }
+    return server + path;
+  }
 
-    addSubmitter(submitter) {
-        this.originalSubmitter = submitter;
-    }
+  /**
+   * Construct input based on method and inputSeparator
+   */
+  _getInput(APIEdge) {
+    return APIEdge.input;
+  }
 
-    /**
-     * Construct TRAPI request body
-     */
-    _getRequestBody(APIEdge, input) {
-        const qg = {
-            "message": {
-                "query_graph": {
-                    "nodes": {
-                        "n0": {
-                            "ids": Array.isArray(input) ? input : [input],
-                            "categories": ["biolink:" + APIEdge.association.input_type]
-                        },
-                        "n1": {
-                            "categories": ["biolink:" + APIEdge.association.output_type]
-                        }
-                    },
-                    "edges": {
-                        "e01": {
-                            "subject": "n0",
-                            "object": "n1",
-                            "predicates": ["biolink:" + APIEdge.association.predicate]
-                        }
-                    }
-                }
-            },
-            "submitter": "infores:bte"
-        };
-        const xmaturityMap = {
-            ci: "staging",
-            test: "test",
-            prod: "prod",
-            dev: "dev",
-        }
-        if (process.env.INSTANCE_ENV) qg.submitter += `; bte-${xmaturityMap[process.env.INSTANCE_ENV]}`;
-        if (this.originalSubmitter) qg.submitter += `; subquery for client "${this.originalSubmitter}"`;
-        return qg;
-    }
+  addSubmitter(submitter) {
+    this.originalSubmitter = submitter;
+  }
 
-    /**
-     * Construct the request config for Axios reqeust.
-     */
-    constructAxiosRequestConfig() {
-        const input = this._getInput(this.APIEdge);
-        const config = {
-            url: this._getUrl(this.APIEdge, input),
-            data: this._getRequestBody(this.APIEdge, input),
-            method: this.APIEdge.query_operation.method,
-            headers: {
-                'Content-Type': 'application/json'
+  /**
+   * Construct TRAPI request body
+   */
+  _getRequestBody(APIEdge, input) {
+    const qg = {
+      message: {
+        query_graph: {
+          nodes: {
+            n0: {
+              ids: Array.isArray(input) ? input : [input],
+              categories: ["biolink:" + APIEdge.association.input_type],
             },
-        }
-        this.config = config;
-        return config;
+            n1: {
+              categories: ["biolink:" + APIEdge.association.output_type],
+            },
+          },
+          edges: {
+            e01: {
+              subject: "n0",
+              object: "n1",
+              predicates: ["biolink:" + APIEdge.association.predicate],
+            },
+          },
+        },
+      },
+      submitter: "infores:bte",
+    };
+    const qualifierConstraints = APIEdge.reasoner_edge?.getQualifierConstraints?.();
+    if (qualifierConstraints) {
+      qg.message.query_graph.edges.e01.qualifier_constraints = qualifierConstraints;
     }
+    const xmaturityMap = {
+      ci: "staging",
+      test: "test",
+      prod: "prod",
+      dev: "dev",
+    };
+    if (process.env.INSTANCE_ENV) qg.submitter += `; bte-${xmaturityMap[process.env.INSTANCE_ENV]}`;
+    if (this.originalSubmitter) qg.submitter += `; subquery for client "${this.originalSubmitter}"`;
+    return qg;
+  }
 
-    needPagination(apiResponse) {
-        this.hasNext = false;
-        return false
-    }
+  /**
+   * Construct the request config for Axios reqeust.
+   */
+  constructAxiosRequestConfig() {
+    const input = this._getInput(this.APIEdge);
+    const config = {
+      url: this._getUrl(this.APIEdge, input),
+      data: this._getRequestBody(this.APIEdge, input),
+      method: this.APIEdge.query_operation.method,
+      headers: {
+        "Content-Type": "application/json",
+      },
+    };
+    this.config = config;
+    return config;
+  }
 
-    getNext() {
-        const config = this.constructAxiosRequestConfig(this.APIEdge);
-        return config;
-    }
+  needPagination(apiResponse) {
+    this.hasNext = false;
+    return false;
+  }
+
+  getNext() {
+    const config = this.constructAxiosRequestConfig(this.APIEdge);
+    return config;
+  }
 
-    getConfig() {
-        if (this.hasNext === false) {
-            return this.constructAxiosRequestConfig(this.APIEdge);
-        }
-        return this.getNext();
+  getConfig() {
+    if (this.hasNext === false) {
+      return this.constructAxiosRequestConfig(this.APIEdge);
     }
-}
+    return this.getNext();
+  }
+};