Merge branch 'main' of https://github.com/biothings/smartapi-kg.js in…

…to dev

.github/workflows/test_cov.yml

@@ -1,6 +1,6 @@
 on: ["push", "pull_request"]
 
-name: Test Codecov
+name: Test in workspace
 
 jobs:
 
@@ -9,7 +9,24 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-    - uses: actions/checkout@v1
+    - name: Get branch name
+      id: branch-name
+      uses: tj-actions/[email protected]
+
+    - 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
@@ -23,10 +40,14 @@ jobs:
 
     - name: pnpm install, generate coverage report
       run: |
+        pnpm run clone
+        pnpm run git checkout ${{ steps.branch-name.outputs.current_branch }}
         pnpm i
-        pnpm run test-cov
+        pnpm --filter smartapi-kg test-cov
 
     - name: Send coverage report to codecov for visualization
       uses: codecov/codecov-action@v3
       with:
+        working-directory: ./packages/@biothings-explorer/smartapi-kg
+        files: ./coverage/lcov.info
         verbose: true

package.json

@@ -73,6 +73,7 @@
     "@babel/runtime": "^7.23.2",
     "@commitlint/cli": "^17.8.1",
     "@commitlint/config-conventional": "^11.0.0",
+    "@biothings-explorer/utils": "workspace:../utils",
     "axios": "^0.21.4",
     "camelcase": "^6.3.0",
     "core-js": "^3.33.1",

src/operations_builder/sync_operations_builder_with_reasoner.ts

@@ -7,6 +7,7 @@ import { PredicatesMetadata } from "../types";
 import Debug from "debug";
 const debug = Debug("bte:smartapi-kg:SyncOperationsBuilderWithReasoner");
 import { SmartAPISpec } from "../parser/types";
+import { biolink } from "@biothings-explorer/utils";
 
 declare global {
   var missingAPIs: SmartAPISpec[];
@@ -45,11 +46,12 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
     }
     //predicates are store as OBJ:{SUBJ:[predicates]}
     //parses each layer accordingly
+    let injectedOps = 0;
     Object.keys(metadata.predicates).map(obj => {
       Object.keys(metadata.predicates[obj]).map(sbj => {
         if (Array.isArray(metadata.predicates[obj][sbj])) {
           metadata.predicates[obj][sbj].map(pred => {
-            ops.push({
+            const op = {
               association: {
                 input_type: this.removeBioLinkPrefix(sbj),
                 input_id: metadata?.nodes?.[sbj]?.id_prefixes,
@@ -64,11 +66,11 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
                   typeof pred === "string" || !pred.qualifiers
                     ? undefined
                     : Object.fromEntries(
-                        pred.qualifiers.map((q: any) => [
-                          this.removeBioLinkPrefix(q.qualifier_type_id),
-                          q.applicable_values.map(this.removeBioLinkPrefix),
-                        ]),
-                      ),
+                      pred.qualifiers.map((q: any) => [
+                        this.removeBioLinkPrefix(q.qualifier_type_id),
+                        q.applicable_values.map(this.removeBioLinkPrefix),
+                      ]),
+                    ),
                 "x-translator": metadata.association["x-translator"],
                 "x-trapi": metadata.association["x-trapi"],
               },
@@ -84,11 +86,70 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
                 inputSeparator: ",",
                 tags: [...metadata.tags, ...["bte-trapi"]],
               },
-            });
+            };
+            ops.push(op);
+            if (
+              !this._options.apiList ||
+              !this._options.apiList.include.find(
+                api => api.id === metadata.association.smartapi.id,
+              )?.includeFlipped
+            ) {
+              return;
+            }
+            // Add inverse metaEdge if includeFlipped is true
+            const inverse_op = {
+              ...op,
+              association: {
+                ...op.association,
+                input_type: this.removeBioLinkPrefix(obj),
+                input_id: metadata?.nodes?.[obj]?.id_prefixes,
+                output_type: this.removeBioLinkPrefix(sbj),
+                output_id: metadata?.nodes?.[sbj]?.id_prefixes,
+                predicate: biolink.reverse(
+                  this.removeBioLinkPrefix(
+                    typeof pred === "string" ? pred : pred.predicate,
+                  ),
+                ),
+                qualifiers:
+                  typeof pred === "string" || !pred.qualifiers
+                    ? undefined
+                    : Object.fromEntries(
+                      pred.qualifiers.map((q: any) => {
+                        let newQualifierType: string = q.qualifier_type_id;
+                        let newQualifier: string[] = q.applicable_values.map(
+                          this.removeBioLinkPrefix,
+                        );
+                        if (newQualifierType.includes("predicate")) {
+                          newQualifier = newQualifier.map(biolink.reverse);
+                        }
+                        if (newQualifierType.includes("subject")) {
+                          newQualifierType = newQualifierType.replace(
+                            "subject",
+                            "object",
+                          );
+                        } else if (newQualifierType.includes("object")) {
+                          newQualifierType = newQualifierType.replace(
+                            "object",
+                            "subject",
+                          );
+                        }
+
+                        return [newQualifierType, newQualifier];
+                      }),
+                    ),
+              },
+            };
+            if (inverse_op.association.predicate) {
+              ops.push(inverse_op);
+              injectedOps += 1;
+            }
           });
         }
       });
     });
+    if (injectedOps) {
+      debug(`Injected ${injectedOps} inverse operations for ${metadata.association.api_name}`);
+    }
     if (!(typeof this._options.apiList === "undefined")) {
       return ops.filter(op => {
         const includeSmartAPI = this._options.apiList.include.find(
@@ -150,7 +211,7 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
 
   private fetch(): PredicatesMetadata[] {
     if (this._options.predicates) {
-        return this._options.predicates;
+      return this._options.predicates;
     }
 
     const file = fs.readFileSync(this._predicates_file_path, "utf-8");
@@ -166,7 +227,7 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
       this._options.component,
       this._options.apiList,
       this._file_path,
-      this._options.smartapiSpecs
+      this._options.smartapiSpecs,
     );
     const nonTRAPIOps = this.loadOpsFromSpecs(specs);
     const predicatesMetadata = this.fetch();
@@ -177,7 +238,7 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
       undefined,
       undefined,
       this._file_path,
-      this._options.smartapiSpecs
+      this._options.smartapiSpecs,
     ).filter(
       spec =>
         "info" in spec &&

src/types.ts

@@ -9,6 +9,7 @@ export interface apiListItem {
   id?: string;
   infores?: string;
   name: string;
+  includeFlipped?: boolean; // Automatically generate flipped MetaEdges (TRAPI only)
 }
 
 export interface apiListObject {

tsconfig.json

@@ -13,7 +13,10 @@
     "esModuleInterop": true,
     "resolveJsonModule": true,
     "strict": false,
-    "noImplicitAny": false
+    "noImplicitAny": false,
+    "paths": {
+      "@biothings-explorer/utils": ["../utils"],
+    }
   },
   "include": [
     "./src/**/*",
@@ -23,5 +26,10 @@
   "exclude": [
     "node_modules",
     "__tests__/"
+  ],
+  "references": [
+    {
+      "path": "../utils"
+    }
   ]
 }