Merge branch 'main' of https://github.com/biothings/call-apis.js into…

… dev
biothings · Apr 12, 2024 · b93e3f7 · b93e3f7
2 parents d3c967c + ef7b1f9
commit b93e3f7
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Showing 7 changed files with 28 additions and 184 deletions.
diff --git a/package.json b/package.json
@@ -36,6 +36,7 @@
     "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg",
     "biomedical_id_resolver": "workspace:../biomedical_id_resolver",
     "@biothings-explorer/utils": "workspace:../utils",
+    "@biothings-explorer/types": "workspace:../types",
     "@sentry/node": "^7.74.1",
     "axios": "^0.21.4",
     "axios-retry": "^3.8.1",

diff --git a/src/builder/base_query_builder.ts b/src/builder/base_query_builder.ts
@@ -1,5 +1,5 @@
 import { AxiosRequestConfig, Method } from "axios";
-import { QueryParams, APIEdge } from "../types";
+import { QueryParams, APIEdge, QueryHandlerOptions } from "../types";
 
 /**
  * Build API queries serving as input for Axios library based on BTE Edge info
@@ -10,14 +10,16 @@ export default class BaseQueryBuilder {
   APIEdge: APIEdge;
   delayUntil: Date;
   config: AxiosRequestConfig;
+  options: QueryHandlerOptions;
   /**
    * Constructor for Query Builder
    * @param {object} APIEdge - BTE Edge object with input field provided
    */
-  constructor(APIEdge: APIEdge) {
+  constructor(APIEdge: APIEdge, options: QueryHandlerOptions) {
     this.start = 0;
     this.hasNext = false;
     this.APIEdge = APIEdge;
+    this.options = options;
   }
 
   getUrl(): string {

diff --git a/src/builder/builder_factory.ts b/src/builder/builder_factory.ts
@@ -3,20 +3,21 @@ import TRAPIQueryBuilder from "./trapi_query_builder";
 import TemplateQueryBuilder from "./template_query_builder";
 import Debug from "debug";
 const debug = Debug("bte:call-apis:query");
-import type { APIEdge } from "../types";
+import type { APIEdge, QueryHandlerOptions } from "../types";
 
 function builderFactory(
   APIEdge: APIEdge,
+  options: QueryHandlerOptions
 ): TRAPIQueryBuilder | TemplateQueryBuilder | QueryBuilder {
   if ("tags" in APIEdge && APIEdge.tags.includes("bte-trapi")) {
     debug(`using trapi builder now`);
-    return new TRAPIQueryBuilder(APIEdge);
+    return new TRAPIQueryBuilder(APIEdge, options);
   } else if (APIEdge.query_operation.useTemplating) {
     debug("using template builder");
-    return new TemplateQueryBuilder(APIEdge);
+    return new TemplateQueryBuilder(APIEdge, options);
   }
   debug("using default builder");
-  return new QueryBuilder(APIEdge);
+  return new QueryBuilder(APIEdge, options);
 }
 
 export default builderFactory;
diff --git a/src/builder/trapi_query_builder.ts b/src/builder/trapi_query_builder.ts
@@ -1,6 +1,6 @@
-import type { APIEdge, TrapiResponse } from "../types";
+import type { APIEdge } from "../types";
+import { TrapiQuery, TrapiResponse } from "@biothings-explorer/types";
 import { AxiosRequestConfig, Method } from "axios";
-import { TrapiRequest } from "../types";
 import BaseQueryBuilder from "./base_query_builder";
 
 /**
@@ -42,8 +42,8 @@ export default class TRAPIQueryBuilder extends BaseQueryBuilder {
   /**
    * Construct TRAPI request body
    */
-  _getRequestBody(APIEdge: APIEdge, input: string | string[]): TrapiRequest {
-    const queryGraph: TrapiRequest = {
+  _getRequestBody(APIEdge: APIEdge, input: string | string[]): TrapiQuery {
+    const queryBody: TrapiQuery = {
       message: {
         query_graph: {
           nodes: {
@@ -68,20 +68,23 @@ export default class TRAPIQueryBuilder extends BaseQueryBuilder {
     };
     const qualifierConstraints = APIEdge.reasoner_edge?.getQualifierConstraints?.();
     if (qualifierConstraints) {
-      queryGraph.message.query_graph.edges.e01.qualifier_constraints =
+      queryBody.message.query_graph.edges.e01.qualifier_constraints =
         qualifierConstraints;
     }
+    if (this.options.caching === false) {
+      queryBody.bypass_cache = true;
+    }
     const xmaturityMap = {
       ci: "staging",
       test: "test",
       prod: "prod",
       dev: "dev",
     };
     if (process.env.INSTANCE_ENV)
-      queryGraph.submitter += `; bte-${xmaturityMap[process.env.INSTANCE_ENV]}`;
+      queryBody.submitter += `; bte-${xmaturityMap[process.env.INSTANCE_ENV]}`;
     if (this.originalSubmitter)
-      queryGraph.submitter += `; subquery for client "${this.originalSubmitter}"`;
-    return queryGraph;
+      queryBody.submitter += `; subquery for client "${this.originalSubmitter}"`;
+    return queryBody;
   }
 
   /**

diff --git a/src/index.ts b/src/index.ts
@@ -42,7 +42,7 @@ export default class APIQueryDispatcher {
 
   _constructQueries(APIEdges: APIEdge[]) {
     return APIEdges.map(edge => {
-      const built = queryBuilder(edge);
+      const built = queryBuilder(edge, this.options);
       if (built instanceof TRAPIQueryBuilder) {
         built.addSubmitter?.(this.options.submitter);
       }

diff --git a/src/types.ts b/src/types.ts
@@ -1,8 +1,8 @@
 import { SmartAPIKGOperationObject } from "@biothings-explorer/smartapi-kg";
-import { SmartAPISpec } from "@biothings-explorer/smartapi-kg";
 import { Record } from "@biothings-explorer/api-response-transform";
 import { StampedLog } from "@biothings-explorer/utils";
 import { SRIBioEntity } from "biomedical_id_resolver";
+import { TrapiQualifierConstraint } from "@biothings-explorer/types";
 
 /* TODO: most of these are temporarily pulled from other packages
  * Instead, they should be pulled out into a new package ('@biothings-explorer/types' or similar).
@@ -19,173 +19,6 @@ export interface BiothingsResponse {
   max_total?: number;
 }
 
-export interface TrapiQNode {
-  ids?: string[];
-  categories?: string[];
-  is_set?: boolean;
-  constraints?: TrapiAttributeConstraint[];
-}
-
-export interface TrapiQEdge {
-  knowledge_type?: string;
-  predicates?: string[];
-  subject: string;
-  object: string;
-  attribute_constraints?: TrapiAttributeConstraint[];
-  qualifier_constraints?: TrapiQualifierConstraint[];
-}
-
-export interface TrapiQueryGraph {
-  nodes: {
-    [QNodeID: string]: TrapiQNode;
-  };
-  edges: {
-    [QEdgeID: string]: TrapiQEdge;
-  };
-}
-
-export interface TrapiSource {
-  resource_id: string;
-  resource_role: string;
-  upstream_resource_ids?: string[];
-}
-
-export interface TrapiKGNodes {
-  [nodeID: string]: TrapiKGNode;
-}
-
-export interface TrapiKGEdges {
-  [edgeID: string]: TrapiKGEdge;
-}
-
-export interface TrapiKnowledgeGraph {
-  nodes: TrapiKGNodes;
-  edges: TrapiKGEdges;
-}
-
-export interface TrapiKGEdge {
-  predicate: string;
-  subject: string;
-  object: string;
-  attributes?: TrapiAttribute[];
-  qualifiers?: TrapiQualifier[];
-  sources: TrapiSource[];
-}
-
-export interface TrapiKGNode {
-  categories: string[];
-  name: string;
-  attributes?: TrapiAttribute[];
-}
-
-export interface TrapiAttribute {
-  attribute_type_id: string;
-  original_attribute_name?: string;
-  value: string | string[] | number | number[];
-  value_type_id?: string;
-  attribute_source?: string | null;
-  value_url?: string | null;
-  attributes?: TrapiAttribute;
-  [additionalProperties: string]:
-  | string
-  | string[]
-  | null
-  | TrapiAttribute
-  | number
-  | number[];
-}
-
-export interface TrapiQualifier {
-  qualifier_type_id: string;
-  qualifier_value: string | string[];
-}
-
-export interface TrapiQualifierConstraint {
-  qualifier_set: TrapiQualifier[];
-}
-
-export interface TrapiAttributeConstraint {
-  id: string;
-  name: string;
-  not: boolean;
-  operator: string;
-  value: string | string[] | number | number[];
-}
-
-export interface TrapiNodeBinding {
-  id: string;
-  query_id?: string;
-  attributes?: TrapiAttribute[];
-}
-
-export interface TrapiEdgeBinding {
-  id: string;
-  attributes?: TrapiAttribute[];
-}
-
-export interface TrapiAnalysis {
-  resource_id?: string;
-  score?: number;
-  edge_bindings: {
-    [qEdgeID: string]: TrapiEdgeBinding[];
-  };
-  support_graphs?: string[];
-  scoring_method?: string;
-  attributes?: TrapiAttribute[];
-}
-
-export interface TrapiAuxiliaryGraph {
-  edges: string[];
-  attributes?: TrapiAttribute[];
-}
-
-export interface TrapiPfocrFigure {
-  figureUrl: string;
-  pmc: string;
-  matchedCuries: string[];
-  score: number;
-}
-
-export interface TrapiResult {
-  node_bindings: {
-    [qNodeID: string]: TrapiNodeBinding[];
-  };
-  analyses: TrapiAnalysis[];
-  pfocr?: TrapiPfocrFigure[];
-}
-
-export interface TrapiAuxGraphCollection {
-  [supportGraphID: string]: TrapiAuxiliaryGraph;
-}
-
-export interface TrapiResponse {
-  description?: string;
-  schema_version?: string;
-  biolink_version?: string;
-  workflow?: { id: string }[];
-  message: {
-    query_graph: TrapiQueryGraph;
-    knowledge_graph: TrapiKnowledgeGraph;
-    auxiliary_graphs?: TrapiAuxGraphCollection;
-    results: TrapiResult[];
-  };
-  logs: TrapiLog[];
-}
-
-export interface TrapiLog {
-  timestamp: string;
-  level: string;
-  message: string;
-  code: string;
-}
-
-export interface TrapiRequest {
-  message: {
-    query_graph: any;
-  };
-  submitter?: string;
-}
-
 export interface JSONDoc {
   [key1: string]: any;
   [key2: number]: any;

diff --git a/tsconfig.json b/tsconfig.json
@@ -8,7 +8,8 @@
       "@biothings-explorer/smartapi-kg": ["../smartapi-kg"],
       "@biothings-explorer/api-response-transform": ["../api-response-transform"],
       "biomedical_id_resolver": ["../biomedical_id_resolver"],
-      "@biothings-explorer/utils": ["../utils"]
+      "@biothings-explorer/utils": ["../utils"],
+      "@biothings-explorer/types": ["../types"]
     }
   },
   "include": ["./src/**/*"],
@@ -25,6 +26,9 @@
     },
     {
       "path": "../utils"
+    },
+    {
+      "path": "../types"
     }
   ]
 }