Add qualifiers

__test__/integration/QEdge2BTEEdgeHandler.test.js

@@ -3,25 +3,28 @@ const QEdge = require('../../src/query_edge');
 const NodeUpdateHandler = require('../../src/update_nodes');
 
 describe('Testing NodeUpdateHandler Module', () => {
-  const gene_node1 = new QNode('n1', { categories: ['Gene'], ids: ['NCBIGene:1017'] });
+  const gene_node1 = new QNode({ id: 'n1', categories: ['Gene'], ids: ['NCBIGene:1017'] });
   const node1_equivalent_ids = {
-    'NCBIGene:1017': {
-      db_ids: {
-        NCBIGene: ['1017'],
-        SYMBOL: ['CDK2'],
+    'NCBIGene:1017': [
+      {
+        semanticTypes: [],
+        db_ids: {
+          NCBIGene: ['1017'],
+          SYMBOL: ['CDK2'],
+        },
       },
-    },
+    ],
   };
 
-  const gene_node2 = new QNode('n2', { categories: ['Gene'], ids: ['NCBIGene:1017', 'NCBIGene:1018'] });
-  const gene_node1_with_id_annotated = new QNode('n1', { categories: ['Gene'], ids: ['NCBIGene:1017'] });
+  const gene_node2 = new QNode({ id: 'n2', categories: ['Gene'], ids: ['NCBIGene:1017', 'NCBIGene:1018'] });
+  const gene_node1_with_id_annotated = new QNode({ id: 'n1', categories: ['Gene'], ids: ['NCBIGene:1017'] });
   gene_node1_with_id_annotated.setEquivalentIDs(node1_equivalent_ids);
   //gene_node2.setEquivalentIDs(node2_equivalent_ids);
-  const chemical_node1 = new QNode('n3', { categories: ['SmallMolecule'] });
-  const edge1 = new QEdge('e01', { subject: gene_node1, object: chemical_node1 });
-  const edge2 = new QEdge('e02', { subject: gene_node1_with_id_annotated, object: chemical_node1 });
-  const edge3 = new QEdge('e04', { subject: gene_node2, object: chemical_node1 });
-  const edge4 = new QEdge('e05', { object: gene_node2, subject: chemical_node1 });
+  const chemical_node1 = new QNode({ id: 'n3', categories: ['SmallMolecule'] });
+  const edge1 = new QEdge({ id: 'e01', subject: gene_node1, object: chemical_node1 });
+  const edge2 = new QEdge({ id: 'e02', subject: gene_node1_with_id_annotated, object: chemical_node1 });
+  const edge3 = new QEdge({ id: 'e04', subject: gene_node2, object: chemical_node1 });
+  const edge4 = new QEdge({ id: 'e05', object: gene_node2, subject: chemical_node1 });
 
   describe('Testing _getCuries function', () => {
     test('test edge with one curie input return an array of one', () => {
@@ -36,11 +39,12 @@ describe('Testing NodeUpdateHandler Module', () => {
       expect(res.Gene.length).toEqual(2);
     });
 
-    test('test edge with input node annotated should return an empty array', () => {
-      const nodeUpdater = new NodeUpdateHandler([edge2]);
-      const res = nodeUpdater._getCuries([edge2]);
-      expect(res).toEqual({});
-    });
+    // test deprecated: proper update handling outside of updater ensures minimal redundancy
+    // test('test edge with input node annotated should return an empty array', () => {
+    //   const nodeUpdater = new NodeUpdateHandler([edge2]);
+    //   const res = nodeUpdater._getCuries([edge2]);
+    //   expect(res).toEqual({});
+    // });
 
     test('test edge with input on object end should be handled', () => {
       const nodeUpdater = new NodeUpdateHandler([edge4]);

__test__/integration/QueryEdge.test.js

@@ -2,9 +2,9 @@ const QNode = require('../../src/query_node');
 const QEdge = require('../../src/query_edge');
 
 describe('Testing QueryEdge Module', () => {
-  const gene_node1 = new QNode('n1', { categories: ['Gene'], ids: ['NCBIGene:1017'] });
-  const type_node = new QNode('n2', { categories: ['SmallMolecule'] });
-  const disease1_node = new QNode('n1', { categories: ['Disease'], ids: ['MONDO:000123'] });
+  const gene_node1 = new QNode({ id: 'n1', categories: ['Gene'], ids: ['NCBIGene:1017'] });
+  const type_node = new QNode({ id: 'n2', categories: ['SmallMolecule'] });
+  const disease1_node = new QNode({ id: 'n1', categories: ['Disease'], ids: ['MONDO:000123'] });
   const node1_equivalent_ids = {
     'NCBIGene:1017': {
       db_ids: {
@@ -14,15 +14,15 @@ describe('Testing QueryEdge Module', () => {
     },
   };
 
-  const gene_node2 = new QNode('n2', { categories: 'Gene', ids: ['NCBIGene:1017', 'NCBIGene:1018'] });
-  const gene_node1_with_id_annotated = new QNode('n1', { categories: ['Gene'], ids: ['NCBIGene:1017'] });
+  const gene_node2 = new QNode({ id: 'n2', categories: 'Gene', ids: ['NCBIGene:1017', 'NCBIGene:1018'] });
+  const gene_node1_with_id_annotated = new QNode({ id: 'n1', categories: ['Gene'], ids: ['NCBIGene:1017'] });
   gene_node1_with_id_annotated.setEquivalentIDs(node1_equivalent_ids);
-  const chemical_node1 = new QNode('n3', { categories: ['SmallMolecule'] });
-  const edge1 = new QEdge('e01', { subject: gene_node1, object: chemical_node1 });
-  const edge2 = new QEdge('e02', { subject: gene_node1_with_id_annotated, object: chemical_node1 });
-  const edge3 = new QEdge('e04', { subject: gene_node2, object: chemical_node1 });
-  const edge4 = new QEdge('e05', { object: gene_node2, subject: chemical_node1 });
-  const edge5 = new QEdge('e06', { object: gene_node1_with_id_annotated, subject: chemical_node1 });
+  const chemical_node1 = new QNode({ id: 'n3', categories: ['SmallMolecule'] });
+  const edge1 = new QEdge({ id: 'e01', subject: gene_node1, object: chemical_node1 });
+  const edge2 = new QEdge({ id: 'e02', subject: gene_node1_with_id_annotated, object: chemical_node1 });
+  const edge3 = new QEdge({ id: 'e04', subject: gene_node2, object: chemical_node1 });
+  const edge4 = new QEdge({ id: 'e05', object: gene_node2, subject: chemical_node1 });
+  const edge5 = new QEdge({ id: 'e06', object: gene_node1_with_id_annotated, subject: chemical_node1 });
 
   describe('Testing isReversed function', () => {
     test('test if only the object of the edge has curie defined, should return true', () => {
@@ -36,9 +36,9 @@ describe('Testing QueryEdge Module', () => {
     });
 
     test('test if both subject and object curie not defined, should return false', () => {
-      const node1 = new QNode('n1', { categories: ['Gene'] });
-      const node2 = new QNode('n2', { categories: ['SmallMolecule'] });
-      const edge = new QEdge('e01', { subject: node1, object: node2 });
+      const node1 = new QNode({ id: 'n1', categories: ['Gene'] });
+      const node2 = new QNode({ id: 'n2', categories: ['SmallMolecule'] });
+      const edge = new QEdge({ id: 'e01', subject: node1, object: node2 });
       expect(edge.isReversed()).toBeFalsy();
     });
   });
@@ -77,39 +77,41 @@ describe('Testing QueryEdge Module', () => {
     });
 
     test('test return false if both subject and object has no curies specified', () => {
-      const node1 = new QNode('n1', { categories: ['Gene'] });
-      const node2 = new QNode('n2', { categories: ['SmallMolecule'] });
-      const edge = new QEdge('e01', { subject: node1, object: node2 });
+      const node1 = new QNode({ id: 'n1', categories: ['Gene'] });
+      const node2 = new QNode({ id: 'n2', categories: ['SmallMolecule'] });
+      const edge = new QEdge({ id: 'e01', subject: node1, object: node2 });
       expect(edge.hasInput()).toBeFalsy();
     });
   });
 
-  describe('Testing hasInputResolved function', () => {
-    test('test return true if subject has input resolved', () => {
-      const res = edge2.hasInputResolved();
-      expect(res).toBeTruthy();
-    });
+  // Removed because new QEdge has different implementation for hasInputResolved
+  // describe("Testing hasInputResolved function", () => {
+  //     test("test return true if subject has input resolved", () => {
+  //         const res = edge2.hasInputResolved();
+  //         expect(res).toBeTruthy();
+  //     });
 
-    test('test return false if both subject and object do not have input resolved', () => {
-      const res = edge1.hasInputResolved();
-      expect(res).toBeFalsy();
-    });
+  //     test("test return false if both subject and object do not have input resolved", () => {
+  //         const res = edge1.hasInputResolved();
+  //         expect(res).toBeFalsy();
+  //     });
 
-    test("test return true if subject doesn't have input resolved, but object does", () => {
-      const res = edge5.hasInputResolved();
-      expect(res).toBeTruthy();
-    });
-  });
+  //     test("test return true if subject doesn't have input resolved, but object does", () => {
+  //         const res = edge5.hasInputResolved();
+  //         expect(res).toBeTruthy();
+  //     });
+
+  // })
 
   describe('Testing getPredicate function', () => {
     test('test get reverse predicate if query is reversed', () => {
-      const edge = new QEdge('e01', { subject: type_node, object: disease1_node, predicates: ['biolink:treats'] });
+      const edge = new QEdge({ id: 'e01', subject: type_node, object: disease1_node, predicates: ['biolink:treats'] });
       const res = edge.getPredicate();
       expect(res).toContain('treated_by');
     });
 
     test('test get reverse predicate if query is reversed and expanded', () => {
-      const edge = new QEdge('e01', { subject: type_node, object: disease1_node, predicates: ['biolink:affects'] });
+      const edge = new QEdge({ id: 'e01', subject: type_node, object: disease1_node, predicates: ['biolink:affects'] });
       const res = edge.getPredicate();
       expect(res).toContain('affected_by');
       expect(res).toContain('disrupted_by');
@@ -118,7 +120,8 @@ describe('Testing QueryEdge Module', () => {
 
   describe('Testing expandPredicates function', () => {
     test('All predicates are correctly expanded if in biolink model', () => {
-      const edge = new QEdge('e01', {
+      const edge = new QEdge({
+        id: 'e01',
         subject: type_node,
         object: disease1_node,
         predicates: ['biolink:contributes_to'],
@@ -129,7 +132,8 @@ describe('Testing QueryEdge Module', () => {
     });
 
     test('Multiple predicates can be resolved', () => {
-      const edge = new QEdge('e01', {
+      const edge = new QEdge({
+        id: 'e01',
         subject: type_node,
         object: disease1_node,
         predicates: ['biolink:contributes_to'],
@@ -142,7 +146,8 @@ describe('Testing QueryEdge Module', () => {
     });
 
     test('Predicates not in biolink model should return itself', () => {
-      const edge = new QEdge('e01', {
+      const edge = new QEdge({
+        id: 'e01',
         subject: type_node,
         object: disease1_node,
         predicates: 'biolink:contributes_to',
@@ -153,4 +158,42 @@ describe('Testing QueryEdge Module', () => {
       expect(res).toContain('amelio');
     });
   });
+
+  describe('chooseLowerEntityValue', () => {
+    test('Should reverse if subject has more curies', () => {
+      const qEdgeClone = new QEdge(edge1.freeze());
+      qEdgeClone.subject.entity_count = 2;
+      qEdgeClone.object.entity_count = 1;
+
+      qEdgeClone.chooseLowerEntityValue();
+
+      expect(qEdgeClone.isReversed()).toBeTruthy();
+    });
+
+    test("Shouldn't reverse if object has more curies", () => {
+      const qEdgeClone = new QEdge(edge1.freeze());
+      qEdgeClone.subject.entity_count = 1;
+      qEdgeClone.object.entity_count = 2;
+
+      qEdgeClone.chooseLowerEntityValue();
+
+      expect(qEdgeClone.isReversed()).toBeFalsy();
+    });
+
+    test("Shouldn't reverse if both have same number", () => {
+      const qEdgeClone = new QEdge(edge1.freeze());
+      qEdgeClone.subject.entity_count = 2;
+      qEdgeClone.object.entity_count = 2;
+
+      qEdgeClone.chooseLowerEntityValue();
+
+      expect(qEdgeClone.isReversed()).toBeFalsy();
+    });
+  });
+
+  test('getHashedEdgeRepresentation', () => {
+    const qEdge1 = new QEdge({ id: 'e01', subject: type_node, object: disease1_node, predicates: ['biolink:treats'] });
+    const qEdge2 = new QEdge(qEdge1.freeze(), true);
+    expect(qEdge1.getHashedEdgeRepresentation()).not.toEqual(qEdge2.getHashedEdgeRepresentation());
+  });
 });

__test__/integration/QueryGraphHandler.test.js

@@ -240,22 +240,14 @@ describe('Testing QueryGraphHandler Module', () => {
     });
   });
 
-  describe('test _storeEdges function', () => {
+  describe('test calculateEdges function', () => {
     test('test storeEdges with one hop query', async () => {
       let handler = new QueryGraphHandler(OneHopQuery);
-      let edges = await handler._storeEdges();
-      expect(edges).toHaveProperty('e01');
-      expect(edges).not.toHaveProperty('e02');
-      expect(edges.e01).toBeInstanceOf(QEdge);
-      expect(edges.e01.getSubject()).toBeInstanceOf(QNode2);
-    });
-
-    test('test storeEdges with multi hop query', async () => {
-      let handler = new QueryGraphHandler(FourHopQuery);
-      let edges = await handler._storeEdges();
-      expect(edges).toHaveProperty('e01');
-      expect(edges).toHaveProperty('e02');
-      expect(edges.e01).toBeInstanceOf(QEdge);
+      await handler.calculateEdges();
+      expect(handler.edges).toHaveProperty('e01');
+      expect(handler.edges).not.toHaveProperty('e02');
+      expect(handler.edges.e01).toBeInstanceOf(QEdge);
+      expect(handler.edges.e01.getInputNode()).toBeInstanceOf(QNode2);
     });
   });
 
@@ -264,23 +256,20 @@ describe('Testing QueryGraphHandler Module', () => {
       let handler = new QueryGraphHandler(ThreeHopExplainQuery);
       let edges = await handler.calculateEdges();
       expect(Object.keys(edges)).toHaveLength(3);
-      expect(edges[0]).toHaveLength(1);
-      expect(edges[1]).toHaveLength(1);
-      expect(edges[2]).toHaveLength(1);
     });
   });
   describe('test cycle/duplicate edge detection for query graphs', () => {
     test('Duplicate Edge Graph #1', async () => {
       const handler = new QueryGraphHandler(QueryWithDuplicateEdge1);
-      expect(handler.calculateEdges()).rejects.toThrow(InvalidQueryGraphError);
+      await expect(handler.calculateEdges()).rejects.toThrow(InvalidQueryGraphError);
     });
     test('Query Graph Cycle #1', async () => {
       const handler = new QueryGraphHandler(QueryWithCycle1);
-      expect(handler.calculateEdges()).rejects.toThrow(InvalidQueryGraphError);
+      await expect(handler.calculateEdges()).rejects.toThrow(InvalidQueryGraphError);
     });
     test('Query Graph Cycle #2', async () => {
       const handler = new QueryGraphHandler(QueryWithCycle2);
-      expect(handler.calculateEdges()).rejects.toThrow(InvalidQueryGraphError);
+      await expect(handler.calculateEdges()).rejects.toThrow(InvalidQueryGraphError);
     });
   });
 
@@ -293,7 +282,7 @@ describe('Testing QueryGraphHandler Module', () => {
       const handler = new QueryGraphHandler(QueryWithNullPredicate);
       const edges = await handler.calculateEdges();
       // if this is undefined (not null) then smartapi-kg treats as if the field doesn't exist (desired behavior)
-      expect(edges[0][0].getPredicate()).toBe(undefined);
+      expect(edges[0].getPredicate()).toBe(undefined);
     });
     test('Graph without any ids', async () => {
       const handler = new QueryGraphHandler(QueryWithNullIds);