Neo4j Testing (Part 2)

neo4j-test/example.js

@@ -1,36 +1,194 @@
 import { expect } from 'chai';
 import { initDriver, closeDriver } from '../src/neo4j/neo4j-driver.js';
-import { addNode } from '../src/neo4j/neo4j-functions';
-import { deleteAllNodesAndEdges, getGeneNameById, getNumNodes } from '../src/neo4j/test-functions.js';
+import { addEdge, addNode, getInteractions, getNeighbouringNodes, searchByGeneId } from '../src/neo4j/neo4j-functions';
+import { deleteAllNodesAndEdges, getGeneName, getNumNodes, getNumEdges, getEdge } from '../src/neo4j/test-functions.js';
 
-describe('Example set of tests', function () {
+describe('Tests for addNode, addEdge and seachByGeneId', function () {
 
   before('Should create a driver instance and connect to server', async () => {
     await initDriver();
-    await deleteAllNodesAndEdges();
   });
 
-  after('Delete nodes and edges, close driver', async function () {
-    //await deleteAllNodesAndEdges();
+  after('Close driver', async function () {
     await closeDriver();
   });
 
+  beforeEach('Delete nodes and edges', async function () {
+    await deleteAllNodesAndEdges();
+  });
+
   it('Make one node', async function () {
     expect(await getNumNodes()).equal(0);
     await addNode('ncbigene:5597', 'MAPK6');
-    expect(await getGeneNameById('ncbigene:5597')).equal('MAPK6');
+    expect(await getGeneName('ncbigene:5597')).equal('MAPK6');
     expect(await getNumNodes()).equal(1);
   });
 
-  it('Make another node', function () {
+  it('Make an edge between the two nodes', async function () {
+    expect(await getNumEdges()).equal(0);
+    await addNode('ncbigene:207', 'AKT');
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'phosphorylation',
+      'ncbigene:5597',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '34767444',
+      'MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+    expect(await getNumEdges()).equal(1);
+    let edge = await getEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b');
+    expect(edge.type).equal('INTERACTION');
+    expect(edge.properties.type).equal('phosphorylation');
+    expect(edge.properties.sourceId).equal('ncbigene:5597');
+    expect(edge.properties.targetId).equal('ncbigene:207');
+    expect(edge.properties.xref).equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(edge.properties.doi).equal('10.1126/sciadv.abi6439');
+    expect(edge.properties.pmid).equal('34767444');
+    expect(edge.properties.articleTitle).equal('MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+  });
+
+  it('Making a duplicate node fails', async function () {
+    await addNode('ncbigene:207', 'AKT');
+    await addNode('ncbigene:5597', 'MAPK6');
+    expect(await getNumNodes()).equal(2);
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addNode('ncbigene:5597', 'This is a dummy name');
+    expect(await getNumNodes()).equal(2);
+    expect(await getGeneName('ncbigene:5597')).equal('MAPK6');
+  });
+
+  it('Making a duplicate edge fails', async function () {
+    await addNode('ncbigene:207', 'AKT');
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'phosphorylation',
+      'ncbigene:5597',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '34767444',
+      'MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+    expect(await getNumEdges()).equal(1);
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'phosphorylation',
+      'ncbigene:5597',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '34767444',
+      'MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'This is a dummy type',
+      'nc7',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '3444',
+      'MAPK6-AKT signaling ');
+    expect(await getNumEdges()).equal(1);
+    let edge = await getEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b');
+    expect(edge.type).equal('INTERACTION');
+    expect(edge.properties.type).equal('phosphorylation');
+    expect(edge.properties.sourceId).equal('ncbigene:5597');
+    expect(edge.properties.targetId).equal('ncbigene:207');
+    expect(edge.properties.xref).equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(edge.properties.doi).equal('10.1126/sciadv.abi6439');
+    expect(edge.properties.pmid).equal('34767444');
+    expect(edge.properties.articleTitle).equal('MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+  });
+
+  it('Ensure searchGeneById works as expected for MAPK6', async function () {
+    await addNode('ncbigene:207', 'AKT');
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'phosphorylation',
+      'ncbigene:5597',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '34767444',
+      'MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+
+    let mapk6Relationships = await getInteractions('ncbigene:5597');
+
+    expect(mapk6Relationships.length).equal(1);
+    expect(mapk6Relationships[0].type).equal('INTERACTION');
+    expect(mapk6Relationships[0].properties.type).equal('phosphorylation');
+    expect(mapk6Relationships[0].properties.sourceId).equal('ncbigene:5597');
+    expect(mapk6Relationships[0].properties.targetId).equal('ncbigene:207');
+    expect(mapk6Relationships[0].properties.xref).equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(mapk6Relationships[0].properties.doi).equal('10.1126/sciadv.abi6439');
+    expect(mapk6Relationships[0].properties.pmid).equal('34767444');
+    expect(mapk6Relationships[0].properties.articleTitle).equal('MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
 
+    let mapk6NeighbouringNodes = await getNeighbouringNodes('ncbigene:5597');
+
+    expect(mapk6NeighbouringNodes.length).equal(1);
+    expect(mapk6NeighbouringNodes[0].labels[0]).equal('Gene');
+    expect(mapk6NeighbouringNodes[0].properties.id).equal('ncbigene:207');
+    expect(mapk6NeighbouringNodes[0].properties.name).equal('AKT');
   });
 
-  it('Make an edge between the two nodes', function () {
+  it('Ensure searchGeneById works as expected for AKT', async function () {
+    await addNode('ncbigene:207', 'AKT');
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'phosphorylation',
+      'ncbigene:5597',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '34767444',
+      'MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+
+    let aktRelationships = await getInteractions('ncbigene:207');
 
+    expect(aktRelationships.length).equal(1);
+    expect(aktRelationships[0].type).equal('INTERACTION');
+    expect(aktRelationships[0].properties.type).equal('phosphorylation');
+    expect(aktRelationships[0].properties.sourceId).equal('ncbigene:5597');
+    expect(aktRelationships[0].properties.targetId).equal('ncbigene:207');
+    expect(aktRelationships[0].properties.xref).equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(aktRelationships[0].properties.doi).equal('10.1126/sciadv.abi6439');
+    expect(aktRelationships[0].properties.pmid).equal('34767444');
+    expect(aktRelationships[0].properties.articleTitle).equal('MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+
+    let aktNeighbouringNodes = await getNeighbouringNodes('ncbigene:207');
+
+    expect(aktNeighbouringNodes.length).equal(1);
+    expect(aktNeighbouringNodes[0].labels[0]).equal('Gene');
+    expect(aktNeighbouringNodes[0].properties.id).equal('ncbigene:5597');
+    expect(aktNeighbouringNodes[0].properties.name).equal('MAPK6');
+  });
+
+  it('Search for a gene in an empty database yields empty array', async function () {
+    let nonexistent = await searchByGeneId('ncbigene:207');
+    expect(nonexistent.length).equal(0);
+    nonexistent = await getInteractions('ncbigene:207');
+    expect(nonexistent.length).equal(0);
+    nonexistent = await getNeighbouringNodes('ncbigene:207');
+    expect(nonexistent.length).equal(0);
   });
 
-  it('Ensure searchGeneById works as expected', function () {
+  it('Search for a non-existing gene in a non-empty database yields empty array', async function () {
+    await addNode('ncbigene:207', 'AKT');
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b',
+      'phosphorylation',
+      'ncbigene:5597',
+      'ncbigene:207',
+      'a896d611-affe-4b45-a5e1-9bc560ffceab',
+      '10.1126/sciadv.abi6439',
+      '34767444',
+      'MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
 
+    let nonexistent = await searchByGeneId('ncbigene:217');
+    expect(nonexistent.length).equal(0);
+    nonexistent = await getInteractions('ncbigene:217');
+    expect(nonexistent.length).equal(0);
+    nonexistent = await getNeighbouringNodes('ncbigene:217');
+    expect(nonexistent.length).equal(0);
   });
+
 });

src/neo4j/.env

@@ -1 +1,2 @@
-GRAPHDB_IMAGE_TAG=5.4.0
+GRAPHDB_IMAGE_TAG=5.4.0
+RETHINKDB_IMAGE_TAG=latest

src/neo4j/docker-compose.yml

@@ -1,5 +1,5 @@
 version: "3.8"
-services: 
+services:
   graphdb:
     image: neo4j:${GRAPHDB_IMAGE_TAG:-latest}
     restart: unless-stopped
@@ -18,11 +18,24 @@ services:
       NEO4J_PLUGINS: '["apoc"]'
     networks:
       - graphdb-config-network
+  db:
+    image: pathwaycommons/rethinkdb-docker:${RETHINKDB_IMAGE_TAG:-latest}
+    restart: unless-stopped
+    container_name: db
+    ports:
+      - "8080:8080"
+      - "28015:28015"
+      - "29015:29015"
+    volumes:
+      - db-data:/data
+    networks:
+      - graphdb-config-network
 
 volumes:
   graphdb-data:
   graphdb-plugins:
-
+  db-data:
+
 networks:
   graphdb-config-network:
     driver: bridge

src/neo4j/index.js

@@ -0,0 +1,2 @@
+// export { addDocumentToNeo4j } from './neo4j-document'; This function does not yet exist
+export { addNode, addEdge, searchByGeneId } from './neo4j-functions';

src/neo4j/neo4j-functions.js

@@ -1,14 +1,17 @@
-import neo4j from 'neo4j-driver';
 import { giveConnectedInfoByGeneId, makeNodeQuery, makeRelationshipQuery } from './query-strings';
 import { getDriver } from './neo4j-driver';
 
+/**
+ * @param { String } id in the form of "dbName:dbId", ex: "ncbigene:207"
+ * @param { String } name 
+ * @returns 
+ */
 export async function addNode(id, name) {
     const driver = getDriver();
     let session;
     try {
         session = driver.session({ database: "neo4j" });
-        // eslint-disable-next-line no-unused-vars
-        let result = await session.executeWrite(tx => {
+        await session.executeWrite(tx => {
             return tx.run(makeNodeQuery, {
                 id: id.toLowerCase(),
                 name: name
@@ -23,13 +26,23 @@ export async function addNode(id, name) {
     return;
 }
 
+/**
+ * @param { String } id interaction element's UUID (NOT document id)
+ * @param { String } type 
+ * @param { String } sourceId in the form of "dbName:dbId", ex: "ncbigene:207"
+ * @param { String } targetId in the form of "dbName:dbId", ex: "ncbigene:207"
+ * @param { String } xref document UUID
+ * @param { String } doi 
+ * @param { String } pmid 
+ * @param { String } articleTitle 
+ * @returns 
+ */
 export async function addEdge(id, type, sourceId, targetId, xref, doi, pmid, articleTitle) {
     const driver = getDriver();
     let session;
     try {
         session = driver.session({ database: "neo4j" });
-        // eslint-disable-next-line no-unused-vars
-        let result = await session.executeWrite(tx => {
+        await session.executeWrite(tx => {
             return tx.run(makeRelationshipQuery, {
                 id: id.toLowerCase(),
                 type: type,
@@ -50,28 +63,57 @@ export async function addEdge(id, type, sourceId, targetId, xref, doi, pmid, art
     return;
 }
 
+/**
+ * @param { String } id in the form of "dbName:dbId", ex: "ncbigene:207"
+ * @returns An object with 2 fields: relationships (array) and neighbouring nodes (array) or null
+ */
 export async function searchByGeneId(id) {
     const driver = getDriver();
     let session;
+    let record;
     try {
         session = driver.session({ database: "neo4j" });
         let result = await session.executeRead(tx => {
             return tx.run(giveConnectedInfoByGeneId, { id: id });
         });
-        let nodes = result.records.map(row => {
-            return row.get('m');
-        });
-        let edges = result.records.map(row => {
-            return row.get('r');
-        });
-        console.log(nodes);
-        console.log(edges);
+        if (result) {
+            record = result.records;
+        } else {
+            record = null;
+        }
     } catch (error) {
         console.error(error);
         throw error;
     } finally {
         await session.close();
     }
-    return;
+    return record;
 }
 
+/**
+ * @param { String } id in the form of "dbName:dbId", ex: "ncbigene:207"
+ * @returns an array of nodes that are neighbours to the specified gene
+ */
+export async function getNeighbouringNodes(id) {
+    let record = await searchByGeneId(id);
+    if (record.length == 0) {
+        return record;
+    }
+    return record.map(row => {
+        return row.get('m');
+    });
+}
+
+/**
+ * @param {*} id in the form of "dbName:dbId", ex: "ncbigene:207"
+ * @returns an array of relationships leading away from/leading to the specified gene
+ */
+export async function getInteractions(id) {
+    let record = await searchByGeneId(id);
+    if (record.length == 0) {
+        return record;
+    }
+    return record.map(row => {
+        return row.get('r');
+    });
+}