build: migrate to pnpm+turbo

Author: tokebe

.gitignore

@@ -47,6 +47,9 @@ typings/
 # TypeScript cache
 *.tsbuildinfo
 
+# Turbo cache
+.turbo
+
 # Optional npm cache directory
 .npm
 
@@ -104,4 +107,4 @@ dist
 .tern-port
 
 # Javascript build folder
-built/
+built/

package.json

@@ -3,15 +3,15 @@
   "version": "1.18.0",
   "description": "A nodejs module to query TRAPI Query Graph",
   "main": "built/index.js",
+  "types": "built/index.d.ts",
   "scripts": {
     "test": "jest --env=node",
     "test-cov": "jest --coverage --env=node",
-    "build": "tsc",
+    "build": "tsc -b",
     "coveralls": "jest --coverage --env=node && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage",
     "format": "prettier --write \"src/**/*.*s\" \"built/**/*.js\"",
     "lint": "eslint './src/**/*.ts'",
     "prepare": "npm run build",
-    "prepublishOnly": "npm test",
     "version": "npm run format && git add -A src",
     "postversion": "git push && git push --tags",
     "release": "npm run format && standard-version",
@@ -35,23 +35,27 @@
   },
   "homepage": "https://github.com/biothings/bte_trapi_query_graph_handler#readme",
   "devDependencies": {
+    "@types/debug": "^4.1.10",
+    "@types/jest": "^29.5.6",
+    "@types/lodash": "^4.14.200",
     "coveralls": "^3.1.0",
     "ioredis-mock": "^8.2.2",
     "jest": "^26.6.3",
     "jest-util": "^26.6.2",
     "prettier": "^2.2.1",
     "standard-version": "^9.1.1",
-    "ts-jest": "^26.5.4",
-    "typescript": "^4.2.3"
+    "ts-jest": "^26.5.6",
+    "typescript": "^5.2.2"
   },
   "dependencies": {
+    "@biothings-explorer/api-response-transform": "file:../api-response-transform",
     "@biothings-explorer/call-apis": "file:../call-apis",
     "@biothings-explorer/node-expansion": "file:../node-expansion",
     "@biothings-explorer/smartapi-kg": "file:../smartapi-kg",
     "@sentry/node": "^7.72.0",
     "async": "^3.2.1",
-    "biolink-model": "file:../../biolink-model",
-    "biomedical_id_resolver": "file:../../biomedical_id_resolver",
+    "biolink-model": "file:../biolink-model",
+    "biomedical_id_resolver": "file:../biomedical_id_resolver",
     "chi-square-p-value": "^1.0.5",
     "debug": "^4.3.1",
     "ioredis": "^5.0.6",

src/query_node.ts

@@ -4,7 +4,7 @@ import * as utils from './utils';
 import biolink from './biolink';
 import Debug from 'debug';
 import InvalidQueryGraphError from './exceptions/invalid_query_graph_error';
-import { SRIBioEntity } from '../../../biomedical_id_resolver/built/common/types';
+import { SRIBioEntity } from 'biomedical_id_resolver';
 const debug = Debug('bte:biothings-explorer-trapi:QNode');
 
 export interface QNodeInfo {
@@ -31,7 +31,7 @@ export interface ExpandedCuries {
 export default class QNode {
   id: string;
   categories: string[];
-  equivalentIDs: SRIResolvedSet;
+  equivalentIDs?: SRIResolvedSet;
   expandedCategories: string[];
   equivalentIDsUpdated: boolean;
   curie: string[];
@@ -285,7 +285,7 @@ export default class QNode {
   }
 
   hasEquivalentIDs(): boolean {
-    return !(typeof this.equivalentIDs === 'undefined' || this.equivalentIDs === {});
+    return !(typeof this.equivalentIDs === 'undefined');
   }
 
   getEntityCount(): number {

src/update_nodes.ts

@@ -1,6 +1,6 @@
 import { resolveSRI } from 'biomedical_id_resolver';
 import Debug from 'debug';
-import { ResolverInput, SRIResolverOutput } from '../../../biomedical_id_resolver/built/common/types';
+import { ResolverInput, SRIResolverOutput } from 'biomedical_id_resolver';
 import { Record } from '@biothings-explorer/api-response-transform';
 import QEdge from './query_edge';
 import { NodeNormalizerResultObj } from '../../api-response-transform/built';

tsconfig.json

@@ -12,7 +12,13 @@
     "resolveJsonModule": true,
     "strict": false,
     "noImplicitAny": false,
-    "skipLibCheck": true
+    "skipLibCheck": true,
+    "paths": {
+      "@biothings-explorer/call-apis": ["../call-apis"],
+      "biolink-model": ["../biolink-model"],
+      "biomedical_id_resolver": ["../biomedical_id_resolver"],
+      "@biothings-explorer/smartapi-kg": ["../smartapi-kg"]
+    }
   },
   "include": ["./src/**/*", "./src/biolink.json", "./src/smartapi_specs.json", "./src/predicates.json"],
   "exclude": ["node_modules", "__tests__/"],
@@ -21,14 +27,13 @@
       "path": "../call-apis"
     },
     {
-      "path": "../../biomedical_id_resolver"
+      "path": "../biomedical_id_resolver"
     },
     {
       "path": "../smartapi-kg"
     },
     {
-      "path": "../../biolink-model"
+      "path": "../biolink-model"
     }
-
   ]
 }