Merge pull request #1162 from PathwayCommons/v0.23.0

V0.23.0

.eslintignore

@@ -1,2 +1,3 @@
 node_modules/**/*
-build/*
+build/*
+src/server/routes/api/document/p-limit.js

README.md

@@ -97,6 +97,8 @@ Demo:
 
 Sharing:
 
+- `DOCUMENT_IMAGE_CACHE_SIZE` : number of images to cache in memory
+- `DOCUMENT_IMAGE_PLL_LIMIT` : max number of images to be generated in parallel (expensive)
 - `DOCUMENT_IMAGE_WIDTH` : tweet card image width
 - `DOCUMENT_IMAGE_HEIGHT` : tweet card image height
 - `DOCUMENT_IMAGE_PADDING` : padding around tweet card image (prevents twitter cropping issues)

neo4j-test/add-nodes-edges.js

@@ -0,0 +1,216 @@
+import { expect } from 'chai';
+import { initDriver, closeDriver } from '../src/neo4j/neo4j-driver.js';
+import { addEdge, addNode, getInteractions, getNeighbouringNodes, neighbourhood } from '../src/neo4j/neo4j-functions';
+import { deleteAllNodesAndEdges, getGeneName, getNumNodes, getNumEdges, getEdge } from '../src/neo4j/test-functions.js';
+
+describe('02. Tests for addNode, addEdge and seachByGeneId', function () {
+
+  before('Should create a driver instance and connect to server', async function () {
+    await initDriver();
+  });
+
+  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()).to.equal(0);
+    await addNode('ncbigene:5597', 'MAPK6');
+    expect(await getGeneName('ncbigene:5597')).to.equal('MAPK6');
+    expect(await getNumNodes()).to.equal(1);
+  });
+
+  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()).to.equal(1);
+    let edge = await getEdge('01ef22cc-2a8e-46d4-9060-6bf1c273869b');
+    expect(edge.type).to.equal('INTERACTION');
+    expect(edge.properties.type).to.equal('phosphorylation');
+    expect(edge.properties.sourceId).to.equal('ncbigene:5597');
+    expect(edge.properties.targetId).to.equal('ncbigene:207');
+    expect(edge.properties.sourceComplex).to.equal('');
+    expect(edge.properties.targetComplex).to.equal('');
+    expect(edge.properties.component).to.deep.equal([]);
+    expect(edge.properties.xref).to.equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(edge.properties.doi).to.equal('10.1126/sciadv.abi6439');
+    expect(edge.properties.pmid).to.equal('34767444');
+    expect(edge.properties.articleTitle).to.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()).to.equal(2);
+    await addNode('ncbigene:5597', 'MAPK6');
+    await addNode('ncbigene:5597', 'This is a dummy name');
+    expect(await getNumNodes()).to.equal(2);
+    expect(await getGeneName('ncbigene:5597')).to.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).to.equal('INTERACTION');
+    expect(edge.properties.type).to.equal('phosphorylation');
+    expect(edge.properties.sourceId).to.equal('ncbigene:5597');
+    expect(edge.properties.targetId).to.equal('ncbigene:207');
+    expect(edge.properties.sourceComplex).to.equal('');
+    expect(edge.properties.targetComplex).to.equal('');
+    expect(edge.properties.component).to.deep.equal([]);
+    expect(edge.properties.xref).to.equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(edge.properties.doi).to.equal('10.1126/sciadv.abi6439');
+    expect(edge.properties.pmid).to.equal('34767444');
+    expect(edge.properties.articleTitle).to.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).to.equal(1);
+    expect(mapk6Relationships[0].type).to.equal('phosphorylation');
+    expect(mapk6Relationships[0].sourceId).to.equal('ncbigene:5597');
+    expect(mapk6Relationships[0].targetId).to.equal('ncbigene:207');
+    expect(mapk6Relationships[0].sourceComplex).to.equal('');
+    expect(mapk6Relationships[0].targetComplex).to.equal('');
+    expect(mapk6Relationships[0].component).to.deep.equal([]);
+    expect(mapk6Relationships[0].xref).to.equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(mapk6Relationships[0].doi).to.equal('10.1126/sciadv.abi6439');
+    expect(mapk6Relationships[0].pmid).to.equal('34767444');
+    expect(mapk6Relationships[0].articleTitle).to.equal('MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+
+    let mapk6NeighbouringNodes = await getNeighbouringNodes('ncbigene:5597');
+
+    expect(mapk6NeighbouringNodes.length).to.equal(1);
+    expect(mapk6NeighbouringNodes[0].id).to.equal('ncbigene:207');
+    expect(mapk6NeighbouringNodes[0].name).to.equal('AKT');
+  });
+
+  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).to.equal(1);
+    expect(aktRelationships[0].type).to.equal('phosphorylation');
+    expect(aktRelationships[0].sourceId).to.equal('ncbigene:5597');
+    expect(aktRelationships[0].targetId).to.equal('ncbigene:207');
+    expect(aktRelationships[0].sourceComplex).to.equal('');
+    expect(aktRelationships[0].targetComplex).to.equal('');
+    expect(aktRelationships[0].component).to.deep.equal([]);
+    expect(aktRelationships[0].xref).to.equal('a896d611-affe-4b45-a5e1-9bc560ffceab');
+    expect(aktRelationships[0].doi).to.equal('10.1126/sciadv.abi6439');
+    expect(aktRelationships[0].pmid).to.equal('34767444');
+    expect(aktRelationships[0].articleTitle).to.equal('MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade.');
+
+    let aktNeighbouringNodes = await getNeighbouringNodes('ncbigene:207');
+
+    expect(aktNeighbouringNodes.length).to.equal(1);
+    expect(aktNeighbouringNodes[0].id).to.equal('ncbigene:5597');
+    expect(aktNeighbouringNodes[0].name).to.equal('MAPK6');
+  });
+
+  it('Search for a molecule in an empty database yields null', async function () {
+    expect(await neighbourhood('ncbigene:207')).to.be.null;
+    expect(await getInteractions('ncbigene:207')).to.be.null;
+    expect(await getNeighbouringNodes('ncbigene:207')).to.be.null;
+  });
+
+  it('Search for a non-existing molecule in a non-empty database yields null', 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 neighbourhood('ncbigene:217')).to.be.null;
+    expect(await getInteractions('ncbigene:217')).to.be.null;
+    expect(await getNeighbouringNodes('ncbigene:217')).to.be.null;
+  });
+});

neo4j-test/connect-neo4j.js

@@ -4,7 +4,6 @@ import neo4j from 'neo4j-driver';
 import { closeDriver, getDriver, initDriver } from '../src/neo4j/neo4j-driver.js';
 
 describe('01. Initiate Driver', () => {
-
   it('initDriver Should initialize and return a driver', () => {
     const driver = initDriver();
     expect(driver).an.instanceof(neo4j.Driver);