Single Subquery Queue/Thread Messaging Changes

docs/REFERENCE.md

@@ -72,17 +72,17 @@ Several environment variables are supported for various purposes, listed below:
 
 #### `MAX_RECORDS_PER_EDGE`
 
-**Default:** `30000`
+**Default:** `100000`
 
-**Docker Default:** `30000`
+**Docker Default:** `100000`
 
 **Description:** Maximum number of records allowable on a single query edge, after which query execution will be forced to move on to the next edge (or complete if there are no other edges).
 
 #### `MAX_RECORDS_TOTAL`
 
-**Default:** `60000`
+**Default:** `200000`
 
-**Docker Default:** `60000`
+**Docker Default:** `200000`
 
 **Description:** Maximum number of records allowable in a single query execution, after which the query will be terminated.
 

packages/types/__test__/KnowledgeGraph.test.ts

@@ -0,0 +1,156 @@
+import KGEdge from '../src/kg_edge';
+import KGNode from '../src/kg_node';
+import KnowledgeGraph from '../src/knowledge_graph';
+import { TrapiAttribute } from '../src/index';
+
+describe('Testing KnowledgeGraph Module', () => {
+  const nodeInput = new KGNode('PUBCHEM.COMPOUND:2662-n0', {
+    primaryCurie: 'PUBCHEM.COMPOUND:2662',
+    qNodeID: 'n0',
+    curies: [
+      'PUBCHEM.COMPOUND:2662',
+      'CHEMBL.COMPOUND:CHEMBL118',
+      'UNII:JCX84Q7J1L',
+      'CHEBI:41423',
+      'DRUGBANK:DB00482',
+      'MESH:C105934',
+      'MESH:D000068579',
+      'CAS:169590-42-5',
+      'CAS:184007-95-2',
+      'CAS:194044-54-7',
+      'DrugCentral:568',
+      'GTOPDB:2892',
+      'HMDB:HMDB0005014',
+      'KEGG.COMPOUND:C07589',
+      'INCHIKEY:RZEKVGVHFLEQIL-UHFFFAOYSA-N',
+    ],
+    names: ['Celecoxib', 'CELECOXIB', 'celecoxib', '[OBSOLETE] celecoxib'],
+    semanticType: ['biolink:SmallMolecule'],
+    label: 'Celecoxib',
+  });
+
+  const trapiEdgeInput = new KGEdge('PUBCHEM.COMPOUND:2662-biolink:activity_decreased_by-NCBIGene:771', {
+    predicate: 'biolink:activity_decreased_by',
+    subject: 'PUBCHEM.COMPOUND:2662',
+    object: 'NCBIGene:771',
+  });
+
+  trapiEdgeInput.addAdditionalAttributes('edge-attributes', [
+    {
+      attribute_type_id: 'biolink:Attribute',
+      value: 'Ki',
+      value_type_id: 'EDAM:data_0006',
+      original_attribute_name: 'affinity_parameter',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+    {
+      attribute_type_id: 'biolink:knowledge_source',
+      value: ['PHAROS_1_norm_edges.jsonl'],
+      value_type_id: 'EDAM:data_0006',
+      original_attribute_name: 'knowledge_source',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+    {
+      attribute_type_id: 'biolink:aggregator_knowledge_source',
+      value: ['infores:pharos'],
+      value_type_id: 'biolink:InformationResource',
+      original_attribute_name: 'biolink:aggregator_knowledge_source',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+    {
+      attribute_type_id: 'biolink:Attribute',
+      value: 7.75,
+      value_type_id: 'EDAM:data_0006',
+      original_attribute_name: 'affinity',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+    {
+      attribute_type_id: 'biolink:publications',
+      value: [
+        'PMID:20605094',
+        'PMID:21852133',
+        'PMID:16290146',
+        'PMID:23965175',
+        'PMID:23965175',
+        'PMID:24513184',
+        'PMID:25766630',
+        'PMID:23067387',
+      ],
+      value_type_id: 'EDAM:data_0006',
+      original_attribute_name: 'publications',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+    {
+      attribute_type_id: 'biolink:relation',
+      value: 'GAMMA:ki',
+      value_type_id: 'EDAM:data_0006',
+      original_attribute_name: 'relation',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+    {
+      attribute_type_id: 'biolink:aggregator_knowledge_source',
+      value: 'infores:automat.pharos',
+      value_type_id: 'biolink:InformationResource',
+      original_attribute_name: 'biolink:aggregator_knowledge_source',
+      value_url: null,
+      attribute_source: null,
+      description: null,
+    },
+  ]);
+
+  describe('Testing _createNode function', () => {
+    test('test creating node', () => {
+      const kg = new KnowledgeGraph();
+      const res = kg._createNode(nodeInput);
+      expect(res).toHaveProperty('name', 'Celecoxib');
+      expect(res).toHaveProperty('categories');
+      expect(res.categories[0]).toBe('biolink:SmallMolecule');
+      expect(res).toHaveProperty('attributes');
+    });
+  });
+
+  describe('Testing _createAttributes function', () => {
+    test('test edge attributes', () => {
+      const kg = new KnowledgeGraph();
+      const res = kg._createAttributes(trapiEdgeInput);
+      expect(res.length).toBeGreaterThan(0);
+      for (const res_obj of res) {
+        expect(res_obj).toHaveProperty('attribute_type_id');
+        expect(res_obj).toHaveProperty('value');
+        if (res_obj.attribute_type_id.includes('biolink:')) {
+          expect(res_obj).toHaveProperty('value_type_id');
+        }
+      }
+    });
+  });
+
+  describe('Testing _createEdge function', () => {
+    test('test creating edge', () => {
+      const kg = new KnowledgeGraph();
+      const res = kg._createEdge(trapiEdgeInput);
+      expect(res).toHaveProperty('predicate', 'biolink:activity_decreased_by');
+      expect(res).toHaveProperty('subject', 'PUBCHEM.COMPOUND:2662');
+      expect(res).toHaveProperty('object', 'NCBIGene:771');
+      expect(res).toHaveProperty('attributes');
+      for (const res_obj of res.attributes as TrapiAttribute[]) {
+        expect(res_obj).toHaveProperty('attribute_type_id');
+        expect(res_obj).toHaveProperty('value');
+        if (res_obj.attribute_type_id.includes('biolink:')) {
+          expect(res_obj).toHaveProperty('value_type_id');
+        }
+      }
+    });
+  });
+});