Update tests and GitHub Workflow

.github/workflows/test_ws_codecov.yml

@@ -13,11 +13,21 @@ jobs:
       id: branch-name
       uses: tj-actions/branch-names@v6
 
-    - 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:

__test__/integration/KnowledgeGraph.test.ts

@@ -1,7 +1,7 @@
 import KGEdge from '../../src/graph/kg_edge';
 import KGNode from '../../src/graph/kg_node';
 import KnowledgeGraph from '../../src/graph/knowledge_graph';
-import { TrapiAttribute } from '../../src/types';
+import { TrapiAttribute } from '@biothings-explorer/types';
 
 describe('Testing KnowledgeGraph Module', () => {
   const nodeInput = new KGNode('PUBCHEM.COMPOUND:2662-n0', {

__test__/integration/QueryEdge.test.ts

@@ -143,7 +143,6 @@ describe('Testing QueryEdge Module', () => {
       expect(res).toContain('contributes_to');
       expect(res).toContain('causes');
       expect(res).toContain('ameliorates');
-      expect(res).toContain('treats');
     });
 
     test('Predicates not in biolink model should return itself', () => {

__test__/integration/QueryResult.test.ts

@@ -43,6 +43,11 @@ describe('Testing QueryResults Module', () => {
           predicate: 'biolink:physically_interacts_with',
           source: 'DGIdb',
           api_name: 'BioThings DGIDB API',
+          "x-translator": {
+            infores: "infores:biothings-dgidb",
+            component: "KP",
+            team: ["Service Provider"]
+          }
         },
         edge1,
       );
@@ -98,6 +103,11 @@ describe('Testing QueryResults Module', () => {
           {
             predicate: 'biolink:gene_associated_with_condition',
             api_name: 'Automat Pharos',
+            "x-translator": {
+              infores: "infores:automat-pharos",
+              component: "KP",
+              team: ["Ranking Agent"]
+            }
           },
           edge1,
         );
@@ -197,6 +207,11 @@ describe('Testing QueryResults Module', () => {
           {
             predicate: 'biolink:gene_associated_with_condition',
             api_name: 'Automat Pharos',
+            "x-translator": {
+              infores: "infores:automat-pharos",
+              component: "KP",
+              team: ["Ranking Agent"]
+            }
           },
           edge1,
         );
@@ -295,6 +310,11 @@ describe('Testing QueryResults Module', () => {
           {
             predicate: 'biolink:gene_associated_with_condition',
             api_name: 'Automat Pharos',
+            "x-translator": {
+              infores: "infores:automat-pharos",
+              component: "KP",
+              team: ["Ranking Agent"]
+            }
           },
           edge1,
         );
@@ -393,6 +413,11 @@ describe('Testing QueryResults Module', () => {
           {
             predicate: 'biolink:gene_associated_with_condition',
             api_name: 'Automat Pharos',
+            "x-translator": {
+              infores: "infores:automat-pharos",
+              component: "KP",
+              team: ["Ranking Agent"]
+            }
           },
           edge1,
         );
@@ -493,6 +518,11 @@ describe('Testing QueryResults Module', () => {
           {
             predicate: 'biolink:gene_associated_with_condition',
             api_name: 'Automat Pharos',
+            "x-translator": {
+              infores: "infores:automat-pharos",
+              component: "KP",
+              team: ["Ranking Agent"]
+            }
           },
           edge1,
         );
@@ -594,6 +624,11 @@ describe('Testing QueryResults Module', () => {
         {
           predicate: 'biolink:gene_associated_with_condition',
           api_name: 'Automat Pharos',
+          "x-translator": {
+            infores: "infores:automat-pharos",
+            component: "KP",
+            team: ["Ranking Agent"]
+          }
         },
         edge1,
       );

__test__/integration/graph/graph.test.ts

@@ -109,11 +109,11 @@ describe('Test graph class', () => {
     expect(g.nodes['inputPrimaryCurie'].qNodeID).toEqual('qg1');
     expect(Array.from(g.nodes['inputPrimaryCurie'].targetNodes)).toEqual(['outputPrimaryCurie']);
     expect(Array.from(g.nodes['inputPrimaryCurie'].targetQNodeIDs)).toEqual(['qg2']);
-    expect(g.edges).toHaveProperty('95fe2a8089c0d79ea093b97c5991f7ba');
-    expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].apis)).toEqual(['API1']);
-    expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].sources).toHaveProperty('source1');
-    expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].publications)).toEqual(['PMID:1', 'PMID:2']);
-    expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].attributes).toHaveProperty('relation', new Set(['relation1']));
+    expect(g.edges).toHaveProperty('2c826c3663b91f65a1cba70f06c7fc65');
+    expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].apis)).toEqual(['API1']);
+    expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].sources).toHaveProperty('source1');
+    expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].publications)).toEqual(['PMID:1', 'PMID:2']);
+    expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].attributes).toHaveProperty('relation', new Set(['relation1']));
   });
 
   test('Multiple query results are correctly updated for two edges having same input, predicate and output', () => {
@@ -130,17 +130,17 @@ describe('Test graph class', () => {
     expect(Array.from(g.nodes['inputPrimaryCurie'].targetNodes)).toEqual(['outputPrimaryCurie']);
     expect(Array.from(g.nodes['inputPrimaryCurie'].targetQNodeIDs)).toEqual(['qg2']);
 
-    expect(g.edges).toHaveProperty('95fe2a8089c0d79ea093b97c5991f7ba');
-    expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].apis)).toEqual(['API1']);
-    expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].sources).toHaveProperty('source1');
-    expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].publications)).toEqual(['PMID:1', 'PMID:2']);
-    expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].attributes).toHaveProperty('relation', new Set(['relation1']));
+    expect(g.edges).toHaveProperty('2c826c3663b91f65a1cba70f06c7fc65');
+    expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].apis)).toEqual(['API1']);
+    expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].sources).toHaveProperty('source1');
+    expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].publications)).toEqual(['PMID:1', 'PMID:2']);
+    expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].attributes).toHaveProperty('relation', new Set(['relation1']));
 
-    expect(g.edges).toHaveProperty('9d334cb674d5671364c45cc8403184c6');
-    expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].apis)).toEqual(['API2']);
-    expect(g.edges['9d334cb674d5671364c45cc8403184c6'].sources).toHaveProperty('source2');
-    expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].publications)).toEqual(['PMC:1', 'PMC:2']);
-    expect(g.edges['9d334cb674d5671364c45cc8403184c6'].attributes).toHaveProperty('relation', new Set(['relation2']));
+    expect(g.edges).toHaveProperty('827c366e2e3088b3f4a90dd88a524f15');
+    expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].apis)).toEqual(['API2']);
+    expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].sources).toHaveProperty('source2');
+    expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].publications)).toEqual(['PMC:1', 'PMC:2']);
+    expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].attributes).toHaveProperty('relation', new Set(['relation2']));
   });
 
   test('Multiple query results for different edges are correctly updated', () => {
@@ -157,37 +157,37 @@ describe('Test graph class', () => {
     expect(Array.from(g.nodes['inputPrimaryCurie'].targetNodes)).toEqual(['outputPrimaryCurie']);
     expect(Array.from(g.nodes['inputPrimaryCurie'].targetQNodeIDs)).toEqual(['qg2']);
 
-    expect(g.edges).toHaveProperty('95fe2a8089c0d79ea093b97c5991f7ba');
-    expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].apis)).toEqual(['API1']);
-    expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].sources).toHaveProperty('source1');
-    expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].publications)).toEqual(['PMID:1', 'PMID:2']);
-    expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].attributes).toHaveProperty('relation', new Set(['relation1']));
+    expect(g.edges).toHaveProperty('2c826c3663b91f65a1cba70f06c7fc65');
+    expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].apis)).toEqual(['API1']);
+    expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].sources).toHaveProperty('source1');
+    expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].publications)).toEqual(['PMID:1', 'PMID:2']);
+    expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].attributes).toHaveProperty('relation', new Set(['relation1']));
 
-    expect(g.edges).toHaveProperty('9d334cb674d5671364c45cc8403184c6');
-    expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].apis)).toEqual(['API2']);
-    expect(g.edges['9d334cb674d5671364c45cc8403184c6'].sources).toHaveProperty('source2');
-    expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].publications)).toEqual(['PMC:1', 'PMC:2']);
-    expect(g.edges['9d334cb674d5671364c45cc8403184c6'].attributes).toHaveProperty('relation', new Set(['relation2']));
+    expect(g.edges).toHaveProperty('827c366e2e3088b3f4a90dd88a524f15');
+    expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].apis)).toEqual(['API2']);
+    expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].sources).toHaveProperty('source2');
+    expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].publications)).toEqual(['PMC:1', 'PMC:2']);
+    expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].attributes).toHaveProperty('relation', new Set(['relation2']));
 
-    expect(g.edges).toHaveProperty('4fe2d5d3e03e0f78f272745caf6b627d');
-    expect(Array.from(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].apis)).toEqual(['API3']);
-    expect(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].sources).toHaveProperty('source3');
-    expect(Array.from(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].publications)).toEqual(['PMC:3', 'PMC:4']);
-    expect(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].attributes).toHaveProperty('relation', new Set(['relation3']));
+    expect(g.edges).toHaveProperty('3138ca0afca791770ed38c243dea2116');
+    expect(Array.from(g.edges['3138ca0afca791770ed38c243dea2116'].apis)).toEqual(['API3']);
+    expect(g.edges['3138ca0afca791770ed38c243dea2116'].sources).toHaveProperty('source3');
+    expect(Array.from(g.edges['3138ca0afca791770ed38c243dea2116'].publications)).toEqual(['PMC:3', 'PMC:4']);
+    expect(g.edges['3138ca0afca791770ed38c243dea2116'].attributes).toHaveProperty('relation', new Set(['relation3']));
   });
 
   test('Multiple attributes with the same name are merged', () => {
     const g = new graph();
     g.update([record3, record3a]);
 
-    expect(g.edges).toHaveProperty('4fe2d5d3e03e0f78f272745caf6b627d');
-    expect(Array.from(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].publications)).toEqual([
+    expect(g.edges).toHaveProperty('3138ca0afca791770ed38c243dea2116');
+    expect(Array.from(g.edges['3138ca0afca791770ed38c243dea2116'].publications)).toEqual([
       'PMC:3',
       'PMC:4',
       'PMC:6',
       'PMC:7',
     ]);
-    expect(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].attributes).toHaveProperty(
+    expect(g.edges['3138ca0afca791770ed38c243dea2116'].attributes).toHaveProperty(
       'relation',
       new Set(['relation3', 'relation3a', 'relation3b']),
     );

__test__/unittest/inferred_mode.test.ts

@@ -201,6 +201,7 @@ describe('Test InferredQueryHandler', () => {
           },
         },
         template: 'Chem-treats-DoP.json',
+        qualifiers: {}
       },
     ];
 
@@ -549,7 +550,7 @@ describe('Test InferredQueryHandler', () => {
     expect(creativeLimitHit).toBeTruthy();
     expect(Object.keys(combinedResponse.message.results)).toHaveLength(3);
     expect(combinedResponse.message.results['fakeCompound1-fakeDisease1'].analyses[0].score).toEqual(
-      0.8421052631578949,
+      0.7836531040612146,
     );
     expect(combinedResponse.message.results['fakeCompound3-fakeDisease1'].analyses[0].score).toEqual(0.2);
     expect(combinedResponse.logs).toHaveLength(3);
@@ -712,7 +713,7 @@ describe('Test InferredQueryHandler', () => {
     expect(Object.keys(mergedResults1)).toHaveLength(1);
     expect(creativeLimitHit1).toBeTruthy();
     expect(combinedResponse.message.results['fakeCompound1-fakeDisease1'].analyses[0].score).toEqual(
-      0.8421052631578949,
+      0.7836531040612146,
     );
   });
 

src/index.ts

@@ -38,6 +38,7 @@ export { default as QEdge } from './query_edge';
 export { default as QNode } from './query_node';
 export { default as InvalidQueryGraphError } from './exceptions/invalid_query_graph_error';
 export * from './qedge2apiedge';
+export {TrapiQueryGraph, TrapiResponse, TrapiResult};  // better readability
 
 export default class TRAPIQueryHandler {
   logs: StampedLog[];