Merge 4f0294e into 2fc0596

.github/workflows/test.yml

@@ -1,30 +1,43 @@
 # This workflow will do a clean install of node dependencies, build the source code and run tests across different versions of node
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions
 
-name: Test
-
 on:
   push:
     branches: 
       - "**"
   pull_request:
     branches: [ master ]
 
+name: Test Coveralls
+
 jobs:
-  test:
 
+  test-coverage:
+    name: Generate coverage report
     runs-on: ubuntu-latest
+    steps:
 
-    strategy:
-      matrix:
-        node-version: [12.x]
+    - uses: actions/checkout@v1
 
-    steps:
-    - uses: actions/checkout@v2
-    - name: Use Node.js ${{ matrix.node-version }}
+    - name: Use Node.js 12.x
       uses: actions/setup-node@v1
       with:
-        node-version: ${{ matrix.node-version }}
-    - run: npm ci
-    - run: npm run build --if-present
-    - run: npm test
+        node-version: 12.x
+
+    - name: npm install, generate coverage report
+      run: |
+        npm ci
+        npm run test-cov
+    - name: Send coverage report to coveralls for visualization
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+  finish:
+    needs: test-coverage
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.github_token }}
+        parallel-finished: true

README.md

@@ -1,6 +1,6 @@
 # BioThings Explorer TRAPI API
 [![Build Status](https://travis-ci.com/kevinxin90/BioThings_Explorer_TRAPI.svg?branch=master)](https://travis-ci.com/kevinxin90/BioThings_Explorer_TRAPI)
-[![Coverage Status](https://coveralls.io/repos/github/kevinxin90/BioThings_Explorer_TRAPI/badge.svg?branch=master)](https://coveralls.io/github/kevinxin90/BioThings_Explorer_TRAPI?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/biothings/BioThings_Explorer_TRAPI/badge.svg?branch=master)](https://coveralls.io/github/biothings/BioThings_Explorer_TRAPI?branch=master)
 
 ## Introduction
 
@@ -76,14 +76,14 @@ If you need to update `npm`, you can make it using `npm`! Cool right? After runn
 
 ## Install
 
-`$ git clone https://github.com/biothings/BioThings_Explorer_TRAPI`
-`$ cd BioThings_Explorer_TRAPI`
-`$ npm install`
+    $ git clone https://github.com/biothings/BioThings_Explorer_TRAPI`
+    $ cd BioThings_Explorer_TRAPI`
+    $ npm install`
 
 
 ## Running the project
 
-`$ npm start`
+    $ npm start
 
 To enable debug mode, which outputs logging statements to the terminal in real time:
 
@@ -93,7 +93,7 @@ To enable debug mode, which outputs logging statements to the terminal in real t
 
 ## Simple build for production
 
-`$ npm build`
+    $ npm build
 
 ## Deploy
 

__test__/integration/KnowledgeGraph.test.js

@@ -6,55 +6,111 @@ describe("Testing KnowledgeGraph Module", () => {
     const gene_node1 = new QNode("n1", { category: "Gene", id: "NCBIGene:1017" });
     const chemical_node1 = new QNode("n3", { category: "ChemicalSubstance" });
     const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 });
-    describe("Testing _createInputNode function", () => {
-        test("test when input with string, should output a hash of 40 characters", () => {
-            const record = {
-                "$reasoner_edge": edge1,
-                "$input": "SYMBOL:CDK2",
-                "id": "CHEMBL.COMPOUND:CHEMBL354634",
-                "$original_input": {
-                    "SYMBOL:CDK2": "NCBIGene:1017"
+    const record = {
+        "$edge_metadata": {
+            trapi_qEdge_obj: edge1,
+            source: "DGIdb",
+            api_name: "BioThings DGIDB API"
+        },
+        "publications": ['PMID:123', 'PMID:1234'],
+        "interactionType": "inhibitor",
+        "$input": {
+            original: "SYMBOL:CDK2",
+            obj: {
+                primaryID: 'NCBIGene:1017',
+                label: "CDK2",
+                dbIDs: {
+                    SYMBOL: "CDK2",
+                    NCBIGene: "1017"
                 },
-                "$input_resolved_identifiers": {
-                    "NCBIGene:1017": {
-                        id: {
-                            label: "CDK2"
-                        }
-                    }
+                curies: ['SYMBOL:CDK2', 'NCBIGene:1017']
+            }
+        },
+        "$output": {
+            original: "CHEMBL.COMPOUND:CHEMBL744",
+            obj: {
+                primaryID: 'CHEMBL.COMPOUND:CHEMBL744',
+                label: "RILUZOLE",
+                dbIDs: {
+                    "CHEMBL.COMPOUND": "CHEMBL744",
+                    "PUBCHEM": "1234",
+                    "name": "RILUZOLE"
                 },
-                "label": "DRUG A"
+                curies: ['CHEMBL.COMPOUND:CHEMBL744', 'PUBCHEM:1234', "name:RILUZOLE"]
             }
+        },
+    }
+    describe("Testing _createInputNode function", () => {
+        test("test when input with string, should output a hash of 40 characters", () => {
             const kg = new KnowledgeGraph();
             const res = kg._createInputNode(record);
-            expect(res).toHaveProperty("NCBIGene:1017");
-            expect(res["NCBIGene:1017"]).toHaveProperty("name", "CDK2");
-            expect(res["NCBIGene:1017"]).toHaveProperty("category", "biolink:Gene");
-            expect(res["NCBIGene:1017"].attributes[0]).toHaveProperty("type", "biolink:id");
+            expect(res).toHaveProperty("category", "biolink:Gene");
+            expect(res).toHaveProperty("name", "CDK2");
+            expect(res.attributes[0]).toHaveProperty("type", "biolink:id");
+            expect(res.attributes[0]).toHaveProperty("value", ["SYMBOL:CDK2", "NCBIGene:1017"])
         })
     })
 
     describe("Testing _createOutputNode function", () => {
         test("test when input with string, should output a hash of 40 characters", () => {
-            const record = {
-                "$reasoner_edge": edge1,
-                "$input": "SYMBOL:CDK2",
-                "id": "CHEMBL.COMPOUND:CHEMBL354634",
-                "$original_input": {
-                    "SYMBOL:CDK2": "NCBIGene:1017"
-                },
-                "$input_resolved_identifiers": {
-                    "NCBIGene:1017": {
-                        id: {
-                            label: "CDK2"
-                        }
-                    }
-                },
-                "label": "DRUG A"
-            }
             const kg = new KnowledgeGraph();
             const res = kg._createOutputNode(record);
-            expect(res["CHEMBL.COMPOUND:CHEMBL354634"]).toHaveProperty("name", "DRUG A");
-            expect(res["CHEMBL.COMPOUND:CHEMBL354634"]).toHaveProperty("category", "biolink:ChemicalSubstance");
+            expect(res).toHaveProperty("category", "biolink:ChemicalSubstance");
+            expect(res).toHaveProperty("name", "RILUZOLE");
+            expect(res.attributes[0]).toHaveProperty("type", "biolink:id");
+            expect(res.attributes[0]).toHaveProperty("value", ['CHEMBL.COMPOUND:CHEMBL744', 'PUBCHEM:1234', "name:RILUZOLE"])
+        })
+    })
+
+    describe("Testing _createAttributes function", () => {
+        test("test edge attribute provided_by and api are correctly found", () => {
+            const kg = new KnowledgeGraph();
+            const res = kg._createAttributes(record);
+            expect(res.length).toBeGreaterThanOrEqual(2);
+            expect(res[0]).toHaveProperty("name", "provided_by");
+            expect(res[0]).toHaveProperty("type", "biolink:provided_by");
+            expect(res[0]).toHaveProperty("value", "DGIdb");
+            expect(res[1]).toHaveProperty("name", "api");
+            expect(res[1]).toHaveProperty("type", "bts:api");
+            expect(res[1]).toHaveProperty("value", "BioThings DGIDB API");
+        })
+
+        test("test edge attribute other than provided_by and api are correctly found", () => {
+            const kg = new KnowledgeGraph();
+            const res = kg._createAttributes(record);
+            expect(res.length).toBeGreaterThan(2);
+            expect(res[2]).toHaveProperty("name", "publications");
+            expect(res[2]).toHaveProperty("type", "biolink:publications");
+            expect(res[2]).toHaveProperty("value", ['PMID:123', 'PMID:1234']);
+            expect(res[3]).toHaveProperty("name", "interactionType");
+            expect(res[3]).toHaveProperty("type", "bts:interactionType");
+            expect(res[3]).toHaveProperty("value", 'inhibitor');
+        })
+    })
+
+    describe("Testing _createEdge function", () => {
+        test("test edge attribute provided_by and api are correctly found", () => {
+            const kg = new KnowledgeGraph();
+            const res = kg._createAttributes(record);
+            expect(res.length).toBeGreaterThanOrEqual(2);
+            expect(res[0]).toHaveProperty("name", "provided_by");
+            expect(res[0]).toHaveProperty("type", "biolink:provided_by");
+            expect(res[0]).toHaveProperty("value", "DGIdb");
+            expect(res[1]).toHaveProperty("name", "api");
+            expect(res[1]).toHaveProperty("type", "bts:api");
+            expect(res[1]).toHaveProperty("value", "BioThings DGIDB API");
+        })
+
+        test("test edge attribute other than provided_by and api are correctly found", () => {
+            const kg = new KnowledgeGraph();
+            const res = kg._createAttributes(record);
+            expect(res.length).toBeGreaterThan(2);
+            expect(res[2]).toHaveProperty("name", "publications");
+            expect(res[2]).toHaveProperty("type", "biolink:publications");
+            expect(res[2]).toHaveProperty("value", ['PMID:123', 'PMID:1234']);
+            expect(res[3]).toHaveProperty("name", "interactionType");
+            expect(res[3]).toHaveProperty("type", "bts:interactionType");
+            expect(res[3]).toHaveProperty("value", 'inhibitor');
         })
     })
 

__test__/integration/QEdge2BTEEdgeHandler.test.js

@@ -7,7 +7,7 @@ describe("Testing QEdge2BTEEdgeHandler Module", () => {
     const gene_node1 = new QNode("n1", { category: "Gene", curie: "NCBIGene:1017" });
     const node1_equivalent_ids = {
         "NCBIGene:1017": {
-            db_ids: {
+            dbIDs: {
                 NCBIGene: ["1017"],
                 SYMBOL: ['CDK2']
             }
@@ -16,13 +16,13 @@ describe("Testing QEdge2BTEEdgeHandler Module", () => {
     gene_node1.setEquivalentIDs(node1_equivalent_ids);
     const node2_equivalent_ids = {
         "NCBIGene:1017": {
-            db_ids: {
+            dbIDs: {
                 NCBIGene: ["1017"],
                 SYMBOL: ['CDK2']
             }
         },
         "NCBIGene:1018": {
-            db_ids: {
+            dbIDs: {
                 NCBIGene: ["1018"],
                 SYMBOL: ['CDK3']
             }

__test__/integration/QueryResult.test.js

@@ -6,41 +6,54 @@ describe("Testing QueryResults Module", () => {
     const gene_node1 = new QNode("n1", { category: "Gene", id: "NCBIGene:1017" });
     const chemical_node1 = new QNode("n3", { category: "ChemicalSubstance" });
     const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 });
+    const record = {
+        "$edge_metadata": {
+            trapi_qEdge_obj: edge1,
+            source: "DGIdb",
+            api_name: "BioThings DGIDB API"
+        },
+        "publications": ['PMID:123', 'PMID:1234'],
+        "interactionType": "inhibitor",
+        "$input": {
+            original: "SYMBOL:CDK2",
+            obj: {
+                primaryID: 'NCBIGene:1017',
+                label: "CDK2",
+                dbIDs: {
+                    SYMBOL: "CDK2",
+                    NCBIGene: "1017"
+                },
+                curies: ['SYMBOL:CDK2', 'NCBIGene:1017']
+            }
+        },
+        "$output": {
+            original: "CHEMBL.COMPOUND:CHEMBL744",
+            obj: {
+                primaryID: 'CHEMBL.COMPOUND:CHEMBL744',
+                label: "RILUZOLE",
+                dbIDs: {
+                    "CHEMBL.COMPOUND": "CHEMBL744",
+                    "PUBCHEM": "1234",
+                    "name": "RILUZOLE"
+                },
+                curies: ['CHEMBL.COMPOUND:CHEMBL744', 'PUBCHEM:1234', "name:RILUZOLE"]
+            }
+        },
+    }
     describe("Testing _createNodeBindings function", () => {
         test("test when input with string, should output a hash of 40 characters", () => {
-            const record = {
-                "$reasoner_edge": edge1,
-                "$input": "SYMBOL:CDK2",
-                "id": "CHEMBL.COMPOUND:CHEMBL354634",
-                "$original_input": {
-                    "SYMBOL:CDK2": "NCBIGene:1017"
-                }
-            }
             const queryResult = new QueryResult();
             const res = queryResult._createNodeBindings(record);
             expect(res).toHaveProperty("n1");
             expect(res).toHaveProperty("n3");
             expect(res.n1[0].id).toEqual("NCBIGene:1017");
-            expect(res.n3[0].id).toEqual("CHEMBL.COMPOUND:CHEMBL354634");
+            expect(res.n3[0].id).toEqual("CHEMBL.COMPOUND:CHEMBL744");
 
         })
     })
 
     describe("Testing _createEdgeBindings function", () => {
         test("test when input with string, should output a hash of 40 characters", () => {
-            const record = {
-                "$reasoner_edge": edge1,
-                "$input": "SYMBOL:CDK2",
-                "id": "CHEMBL.COMPOUND:CHEMBL354634",
-                "$original_input": {
-                    "SYMBOL:CDK2": "NCBIGene:1017"
-                },
-                "$association": {
-                    api_name: "MyChem.info API",
-                    source: "drugbank",
-                    predicate: "physically_interacts_with"
-                }
-            }
             const queryResult = new QueryResult();
             const res = queryResult._createEdgeBindings(record);
             expect(res).toHaveProperty("e01");
@@ -50,19 +63,6 @@ describe("Testing QueryResults Module", () => {
 
     describe("Testing update function", () => {
         test("test when input with string, should output a hash of 40 characters", () => {
-            const record = {
-                "$reasoner_edge": edge1,
-                "$input": "SYMBOL:CDK2",
-                "id": "CHEMBL.COMPOUND:CHEMBL354634",
-                "$original_input": {
-                    "SYMBOL:CDK2": "NCBIGene:1017"
-                },
-                "$association": {
-                    api_name: "MyChem.info API",
-                    source: "drugbank",
-                    predicate: "physically_interacts_with"
-                }
-            }
             const queryResult = new QueryResult();
             queryResult.update([record]);
             expect(queryResult.results.length).toEqual(1);