From 067e7e537165282b2e3de4788b2faef11d3264dd Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Tue, 28 Sep 2021 13:23:30 +0200
Subject: [PATCH] remove necessity of adding edges
---
.../explorer-page/explorer-page.component.ts | 44 ++++++++++---------
src/index.html | 4 +-
2 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index be407ec6..d8968093 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -53,14 +53,15 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public id: undefined | string;
@Input()
- public set config(config: string | undefined |object) {
- if (config== null) {
+ public set config(config: string | undefined | object) {
+ if (config == null) {
return;
}
if (this.id == null)
setTimeout(() => {
this.config = config;
}, 200);
+ console.log(config)
// add settings to config
const configObj = typeof config === 'object' ? config : JSON.parse(config);
this.myConfig = merge(this.myConfig, configObj);
@@ -109,10 +110,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
@Input()
public set network(network: string | undefined | object) {
+ console.log(network)
if (network == null) {
return;
}
- this.networkJSON = typeof network === 'object' ? JSON.stringify(network) : network ;
+ this.networkJSON = typeof network === 'object' ? JSON.stringify(network) : network;
this.createNetwork();
}
@@ -173,7 +175,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public selectedAnalysisToken: string | null = null;
- @Input() inputNetwork = { };
+ @Input() inputNetwork = {};
@Input() set taskId(token: string | null) {
if (token == null || token.length === 0)
@@ -289,17 +291,17 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private async getNetwork() {
const network = JSON.parse(this.networkJSON);
-
if (this.myConfig.identifier === 'ensg') {
// @ts-ignore
network.nodes.forEach(node => {
node.id = this.removeEnsemblVersion(node.id);
});
- // @ts-ignore
- network.edges.forEach(edge => {
- edge.from = this.removeEnsemblVersion(edge.from);
- edge.to = this.removeEnsemblVersion(edge.to);
- });
+ if (network.edges != null)
+ // @ts-ignore
+ network.edges.forEach(edge => {
+ edge.from = this.removeEnsemblVersion(edge.from);
+ edge.to = this.removeEnsemblVersion(edge.to);
+ });
}
// map data to nodes in backend
@@ -315,7 +317,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
// at this point, we have nodes synched with the backend
// use netexIds where posssible, but use original id as node name if no label given
const nodeIdMap = {};
-
network.nodes.forEach((node) => {
// set node label to original id before node id will be set to netex id
node.label = node.label ? node.label : node.id;
@@ -326,14 +327,15 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
// adjust edge labels accordingly and filter
const edges = new Array();
- network.edges.forEach(edge => {
- edge.from = nodeIdMap[edge.from];
- edge.to = nodeIdMap[edge.to];
- // check if edges have endpoints
- if (edge.from !== undefined && edge.to !== undefined) {
- edges.push(edge);
- }
- });
+ if (network.edges != null)
+ network.edges.forEach(edge => {
+ edge.from = nodeIdMap[edge.from];
+ edge.to = nodeIdMap[edge.to];
+ // check if edges have endpoints
+ if (edge.from !== undefined && edge.to !== undefined) {
+ edges.push(edge);
+ }
+ });
// remove edges without endpoints
network.edges = edges;
this.inputNetwork = network;
@@ -833,8 +835,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
setInputNetwork(network: any) {
- if(network == null)
- this.inputNetwork={nodes: this.proteins, edges : this.edges}
+ if (network == null)
+ this.inputNetwork = {nodes: this.proteins, edges: this.edges}
else
this.inputNetwork = network;
}
diff --git a/src/index.html b/src/index.html
index 95e57fd8..81b9ff5d 100644
--- a/src/index.html
+++ b/src/index.html
@@ -44,9 +44,7 @@
<network-expander id="netexp1"
pluginId="2"
- config='{"showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#000000"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590","highlight":{"border":"#F12590","background":"#F12590"}},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
- network='{"nodes":[{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"BRCA1","to":"BRCA2","group":"ggi"},{"from":"ATM","to":"BARD1","group":"ggi"},{"from":"BRCA1","to":"CHEK2","group":"ggi"},{"from":"RAD51C","to":"RAD51D","group":"ggi"},{"from":"STK11","to":"TP53","group":"ggi"},{"from":"TP53","to":"PALB2","group":"ggi"},{"from":"TP53","to":"RAD51D","group":"ggi"},{"from":"TP53","to":"NF1","group":"ggi"},{"from":"TP53","to":"BRCA1","group":"ggi"},{"from":"TP53","to":"BRCA2","group":"ggi"},{"from":"PTEN","to":"BRCA1","group":"ggi"},{"from":"PTEN","to":"BRCA2","group":"ggi"},{"from":"TP53","to":"PTEN","group":"ggi"},{"from":"ATM","to":"PTEN","group":"ggi"},{"from":"CDH1","to":"RAD51D","group":"ggi"},{"from":"CDH1","to":"PALB2","group":"ggi"},{"from":"NBN","to":"BRIP1","group":"ggi"},{"from":"BRIP1","to":"PTEN","group":"ggi"},{"from":"patient-1","to":"BRCA1","group":"genotype"},{"from":"patient-1","to":"TP53","group":"genotype"},{"from":"patient-1","to":"BRCA2","group":"genotype"},{"from":"patient-1","to":"PTEN","group":"genotype"},{"from":"patient-2","to":"TP53","group":"genotype"},{"from":"patient-2","to":"NF1","group":"genotype"},{"from":"patient-2","to":"BARD1","group":"genotype"},{"from":"patient-3","to":"TP53","group":"genotype"},{"from":"patient-3","to":"PTEN","group":"genotype"},{"from":"patient-3","to":"NBN","group":"genotype"},{"from":"patient-1","to":"subtype-1","group":"has-condition"},{"from":"patient-2","to":"subtype-1","group":"has-condition"},{"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'>
- }'></network-expander>
+ network='{"nodes":[{"id": "PTEN"}]}'></network-expander>
</div>
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