diff --git a/Dockerfile.dev b/Dockerfile.dev
index 92f94e58693701446d1472a5d669f90513d4fdf9..b7be260b872c65073a68c4828ac9fd0e078a9b8f 100644
--- a/Dockerfile.dev
+++ b/Dockerfile.dev
@@ -16,9 +16,14 @@ RUN npm install
COPY . /app/
-RUN npm run build -- --prod --base-href=/covex_dev/
+RUN npm run -- bundle
-RUN cp -r dist/covid19/* /usr/share/nginx/html/
+RUN cp -r website/* /usr/share/nginx/html/
+
+RUN mkdir /usr/share/nginx/html/lib
+RUN cp dist/covid19/bundle-es2015.js /usr/share/nginx/html/lib/
+RUN cp dist/covid19/bundle-es5.js /usr/share/nginx/html/lib/
+RUN cp dist/covid19/styles.scss /usr/share/nginx/html/lib/
COPY nginx/default.conf /etc/nginx/conf.d/
COPY nginx/htpasswd /etc/nginx/htpasswd
diff --git a/package.json b/package.json
index aaac7c835f13e5c69cf6b2f7e3a5426ee315c97d..6a6ede4229c2471c6e171a1ecbdea9a93bb861f8 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,11 @@
"build": "ng build",
"test": "ng test",
"lint": "ng lint && htmlhint",
- "e2e": "ng e2e"
+ "e2e": "ng e2e",
+ "build-prod": "ng build --prod --output-hashing=none",
+ "package-es5": "cd dist/covid19 && cat runtime-es5.js polyfills-es5.js main-es5.js > bundle-es5.js",
+ "package-es2015": "cd dist/covid19 && cat runtime-es2015.js polyfills-es2015.js main-es2015.js > bundle-es2015.js",
+ "bundle": "npm run build-prod covid19 && npm run package-es5 && npm run package-es2015"
},
"private": true,
"dependencies": {
diff --git a/src/app/analysis.service.ts b/src/app/analysis.service.ts
index 780307fdced4f8c610a95acc253f7656aa13922c..23ce8084a92007881179f8b55fc341b98426f564 100644
--- a/src/app/analysis.service.ts
+++ b/src/app/analysis.service.ts
@@ -160,7 +160,7 @@ export class AnalysisService {
const newSelection = [];
nodes.forEach((node) => {
const wrapper: Wrapper = node.wrapper;
- if (wrapper.type === 'host' || wrapper.type === 'virus') {
+ if (wrapper.type === 'protein') {
if (!this.inSelection(wrapper)) {
newSelection.push(wrapper);
}
@@ -204,15 +204,7 @@ export class AnalysisService {
}
public removeAllHostProteins() {
- const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'host');
- for (const wrapper of items) {
- this.selectedItems.delete(wrapper.nodeId);
- }
- this.selectListSubject.next({items, selected: false});
- }
-
- public removeAllViralProteins() {
- const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'virus');
+ const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'protein');
for (const wrapper of items) {
this.selectedItems.delete(wrapper.nodeId);
}
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index e5dd42fb96387cfe095cf42914a9da1c97105367..6ff2bde3fd65f98e35fcf9711bb3bcf912679fd3 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -71,13 +71,6 @@
<i *ngIf="!task.info.parameters.includeNonApprovedDrugs" class="fa fa-times"></i>
</td>
</tr>
- <tr *ngIf="task.info.parameters.ignoreNonSeedBaits !== undefined && task.info.target === 'drug-target'">
- <td>Include non-seed viral proteins</td>
- <td>
- <i *ngIf="!task.info.parameters.ignoreNonSeedBaits" class="fa fa-check"></i>
- <i *ngIf="task.info.parameters.ignoreNonSeedBaits" class="fa fa-times"></i>
- </td>
- </tr>
</tbody>
</table>
</div>
@@ -287,13 +280,6 @@
</button>
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
- <th>
- Closest viral proteins
- </th>
- <th [pSortableColumn]="'closestDistance'">
- Viral protein distance
- <p-sortIcon [field]="'closestDistance'"></p-sortIcon>
- </th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
@@ -328,12 +314,6 @@
</span>
</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
- <td title="{{previewStringArray(e.closestViralProteins, 100)}}">
- {{previewStringArray(e.closestViralProteins, 3)}}
- </td>
- <td>
- {{e.closestDistance}}
- </td>
</tr>
</ng-template>
</p-table>
@@ -380,13 +360,6 @@
Seed
<p-sortIcon [field]="'isSeed'"></p-sortIcon>
</th>
- <th>
- Closest viral proteins
- </th>
- <th [pSortableColumn]="'closestDistance'">
- Closest distance
- <p-sortIcon [field]="'closestDistance'"></p-sortIcon>
- </th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
@@ -407,12 +380,6 @@
<i class="fa fa-times"></i>
</span>
</td>
- <td title="{{previewStringArray(e.closestViralProteins, 100)}}">
- {{previewStringArray(e.closestViralProteins, 3)}}
- </td>
- <td>
- {{e.closestDistance}}
- </td>
</tr>
</ng-template>
</p-table>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index db25357172167037310a3b4d0ce5255ec855e1a5..ca204933f123933c33135b994e4ac9593b7a7808 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -255,7 +255,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const proteinSelection = this.tableSelectedProteins;
const viralProteinSelection = this.tableSelectedViralProteins;
for (const item of items) {
- if (item.type === 'host') {
+ if (item.type === 'protein') {
// TODO: Refactor!
const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.nodeId);
const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.nodeId);
@@ -293,7 +293,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const proteinSelection = [];
const viralProteinSelection = [];
for (const item of items) {
- if (item.type === 'host') {
+ if (item.type === 'protein') {
const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.nodeId);
if (tableItem) {
proteinSelection.push(tableItem);
@@ -369,12 +369,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
public inferNodeType(nodeId: string): WrapperType {
- if (nodeId.indexOf('-') !== -1 || nodeId.indexOf('_') !== -1) {
- return 'virus';
- } else if (nodeId.startsWith('DB')) {
+ if (nodeId.startsWith('DB')) {
return 'drug';
}
- return 'host';
+ return 'protein';
}
public createNetwork(result: any): { edges: any[], nodes: any[] } {
@@ -393,7 +391,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const details = attributes.details || {};
const wrappers: { [key: string]: Wrapper } = {};
for (const node of network.nodes) {
- if (nodeTypes[node] === 'host') {
+ if (nodeTypes[node] === 'protein') {
this.proteins.push(details[node]);
wrappers[node] = getWrapperFromProtein(details[node]);
} else if (nodeTypes[node] === 'drug') {
@@ -417,7 +415,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
let wrapper: Wrapper;
let drugType;
let drugInTrial;
- if (nodeType === 'host') {
+ if (nodeType === 'protein') {
const protein = details as Protein;
wrapper = getWrapperFromProtein(protein);
nodeLabel = protein.name;
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 26cbec22bff0cf7012848e520ad7c7d1dfe3f40a..9d64bd448f771879cbb64f320225984bfe51196f 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -1,5 +1,5 @@
<div *ngIf="wrapper">
- <div *ngIf="wrapper.type === 'host'">
+ <div *ngIf="wrapper.type === 'protein'">
<p>
<b><span>Gene Name: </span></b>
{{ wrapper.data.name }}
@@ -20,17 +20,6 @@
{{ wrapper.data.expressionLevel|number }}
</p>
</div>
- <div *ngIf="wrapper.type === 'virus'">
- <p>
- <b><span>Virus:</span></b>
- {{ wrapper.data.virusName.replace('V', 'V-') }}
- <span class="icon is-small"><i class="fas fa-virus"></i></span>
- </p>
- <p>
- <b><span>Effect: </span></b>
- {{ wrapper.data.effectName }}
- </p>
- </div>
<div *ngIf="wrapper.type === 'drug'">
<p>
<b><span>Name: </span></b>
diff --git a/src/app/components/query-tile/query-tile.component.html b/src/app/components/query-tile/query-tile.component.html
index 93bdd6289e73db3b68f390e7be664827dfd8bbd9..b053d67c0db4c7941b5446c139eb92f0c76dc82e 100644
--- a/src/app/components/query-tile/query-tile.component.html
+++ b/src/app/components/query-tile/query-tile.component.html
@@ -2,11 +2,9 @@
<ng-select [items]="queryItems" bindLabel="backendId" bindValue="data" [virtualScroll]="true" class="custom"
placeholder="Search..." [hideSelected]="true" [searchFn]="querySearch" (change)="select($event)" data-tooltip="Find proteins in the network.">
<ng-template ng-option-tmp let-item="item">
- <b *ngIf="item.type == 'host'"> {{item.data.name}}</b>
- <b *ngIf="item.type == 'virus'"> {{item.data.effectName}}</b> <br/>
- <span><small *ngIf="item.type === 'virus'">Viral Protein</small><small *ngIf="item.type === 'host'">Host Protein</small> | </span>
- <span *ngIf="item.type == 'host'"><small>AC: <b>{{item.data.proteinAc}}</b></small> </span>
- <span *ngIf="item.type == 'virus'"><small><b>{{item.data.virusName.replace('V', 'V-')}}</b></small></span>
+ <b *ngIf="item.type == 'protein'"> {{item.data.name}}</b>
+ <span><small *ngIf="item.type === 'protein'">Host Protein</small> | </span>
+ <span *ngIf="item.type == 'protein'"><small>AC: <b>{{item.data.proteinAc}}</b></small> </span>
</ng-template>
</ng-select>
</div>
diff --git a/src/app/config.ts b/src/app/config.ts
index f6d3e60372cc6f473e8975223b4224e7877ae38c..34a5a918cbbb1de0c39d47bc9d762a7bb4b4651f 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -5,7 +5,6 @@ export interface IConfig {
showLeftSidebar: boolean;
showOverview: boolean;
showQuery: boolean;
- showFilter: boolean;
showItemSelector: boolean;
showSimpleAnalysis: boolean;
showAdvAnalysis: boolean;
@@ -21,7 +20,6 @@ export const defaultConfig: IConfig = {
showLeftSidebar: true,
showOverview: true,
showQuery: true,
- showFilter: true,
showItemSelector: true,
showSimpleAnalysis: false,
showAdvAnalysis: true,
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.html b/src/app/dialogs/launch-analysis/launch-analysis.component.html
index 3fee026fc4f868ca4af6eed60d03058abe28fab1..9133d7867a755f960a20b53d8c9d9d538d23db5e 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -13,13 +13,6 @@
<button (click)="close()" class="delete" aria-label="close"></button>
</header>
<section class="modal-card-body">
- <div *ngIf="target === 'drug' && hasBaits">
- <div class="notification is-warning warning">
- You have selected <i class="fa fa-virus"></i> viral proteins.
- When finding drugs, make sure you have selected <i class="fa fa-dna"></i> host proteins only.
- </div>
- </div>
-
<div *ngIf="!analysis.canLaunchTask()">
<div class="notification is-warning warning">
You can only run {{maxTasks}} tasks at once. Please wait for one of them to finish or delete it from the task
@@ -97,15 +90,6 @@
</p>
</div>
- <div class="field" *ngIf="target === 'drug-target'">
- <label class="label">Include non-seed viral proteins</label>
- <app-toggle textOn="Include" textOff="Ignore"
- tooltipOn="Include viral proteins that are not seeds."
- tooltipOff="Exclude viral proteins that are not seeds."
- [(value)]="trustrankIncludeViralNonSeeds">
- </app-toggle>
- </div>
-
<div class="box">
<article class="media">
<div class="media-left">
@@ -181,14 +165,6 @@
</p>
</div>
- <div class="field" *ngIf="target === 'drug-target'">
- <label class="label">Include non-seed viral proteins</label>
- <app-toggle textOn="Include" textOff="Ignore"
- tooltipOn="Include viral proteins that are not seeds."
- tooltipOff="Exclude viral proteins that are not seeds."
- [(value)]="closenessIncludeViralNonSeeds"></app-toggle>
- </div>
-
<div class="box">
<article class="media">
<div class="media-left">
@@ -236,14 +212,6 @@
</p>
</div>
- <div class="field" *ngIf="target === 'drug-target'">
- <label class="label">Include non-seed viral proteins</label>
- <app-toggle textOn="Include" textOff="Ignore"
- tooltipOn="Include viral proteins that are not seeds."
- tooltipOff="Exclude viral proteins that are not seeds."
- [(value)]="degreeIncludeViralNonSeeds"></app-toggle>
- </div>
-
<div class="box">
<article class="media">
<div class="media-left">
@@ -353,14 +321,6 @@
</p>
</div>
- <div class="field">
- <label class="label">Include non-seed viral proteins</label>
- <app-toggle textOn="Include" textOff="Ignore"
- tooltipOn="Include viral proteins that are not seeds."
- tooltipOff="Exclude viral proteins that are not seeds."
- [(value)]="betweennessIncludeViralNonSeeds"></app-toggle>
- </div>
-
<div class="box">
<article class="media">
<div class="media-left">
@@ -381,13 +341,6 @@
</div>
<div *ngIf="algorithm==='keypathwayminer'">
- <div *ngIf="hasBaits">
- <div class="notification is-warning warning">
- You have selected <i class="fa fa-virus"></i> viral proteins.
- If you want to use KeyPathwayMiner, please remove them because it cannot process them.
- </div>
- </div>
-
<div class="field">
<label class="label" for="keypathwayminer-k">Additional proteins</label>
<div class="control">
@@ -491,14 +444,6 @@
</p>
</div>
- <div class="field" *ngIf="target === 'drug-target'">
- <label class="label">Include non-seed viral proteins</label>
- <app-toggle textOn="Include" textOff="Ignore"
- tooltipOn="Include viral proteins that are not seeds."
- tooltipOff="Exclude viral proteins that are not seeds."
- [(value)]="multisteinerIncludeViralNonSeeds"></app-toggle>
- </div>
-
</div>
<p class="doc-link">
@@ -511,7 +456,7 @@
<footer class="modal-card-foot">
<button (click)="startTask(); close()" class="button is-success is-rounded has-tooltip"
data-tooltip="Run the analysis."
- [disabled]="(target === 'drug' && hasBaits) || !analysis.canLaunchTask() || (algorithm === 'keypathwayminer' && hasBaits)">
+ [disabled]="!analysis.canLaunchTask()">
<span class="icon">
<i class="fa fa-rocket"></i>
</span>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 077516b76de0e1894f1fee0009df9b1a186e1e88..9026cdaf2d6bcbcfe745d0d2c35a4055ebbd1cac 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -9,7 +9,6 @@ import {
QuickAlgorithmType,
TRUSTRANK
} from '../../analysis.service';
-import {Dataset} from '../../interfaces';
@Component({
selector: 'app-launch-analysis',
@@ -74,15 +73,9 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public multisteinerMaxDeg = 0;
public multisteinerHubPenalty = 0.0;
- public hasBaits;
-
public maxTasks = MAX_TASKS;
constructor(public analysis: AnalysisService) {
- this.hasBaits = !!analysis.getSelection().find((i) => i.type === 'virus');
- analysis.subscribeList(() => {
- this.hasBaits = !!analysis.getSelection().find((i) => i.type === 'virus');
- });
}
ngOnInit(): void {
@@ -108,7 +101,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
seeds: this.analysis.getSelection().map((item) => item.backendId),
};
- parameters.target_or_drugs = this.target === 'drug' ? 'drugs' : 'PPI';
+ parameters.target_or_drugs = this.target === 'drug' ? 'PPDr' : 'PPI';
if (this.algorithm === 'trustrank') {
parameters.damping_factor = this.trustrankDampingFactor;
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 3e5bcc41c8cf6792d983f324d79456e72fb995f2..230bb223c1acbabf0ec1b368f7574b048d317332 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -92,7 +92,7 @@ export function getWrapperFromProtein(protein: Protein): Wrapper {
return {
backendId: getProteinBackendId(protein),
nodeId: getProteinNodeId(protein),
- type: 'host',
+ type: 'protein',
data: protein,
};
}
@@ -106,7 +106,7 @@ export function getWrapperFromDrug(drug: Drug): Wrapper {
};
}
-export type WrapperType = 'host' | 'virus' | 'drug';
+export type WrapperType = 'protein' | 'drug';
export interface Wrapper {
backendId: string;
diff --git a/src/app/network-settings.ts b/src/app/network-settings.ts
index e74902c237f2f299cdaeaa8d8018904f2845dd03..83a622c31f9e00db24565e2b8091288f24b93490 100644
--- a/src/app/network-settings.ts
+++ b/src/app/network-settings.ts
@@ -80,20 +80,16 @@ export class NetworkSettings {
private static drugInTrialShape = 'triangle';
static getNodeSize(wrapperType: WrapperType) {
- if (wrapperType === 'host') {
+ if (wrapperType === 'protein') {
return this.hostSize;
- } else if (wrapperType === 'virus') {
- return this.virusSize;
} else if (wrapperType === 'drug') {
return this.drugSize;
}
}
static getNodeShape(wrapperType: WrapperType, drugInTrial?: boolean) {
- if (wrapperType === 'host') {
+ if (wrapperType === 'protein') {
return this.hostShape;
- } else if (wrapperType === 'virus') {
- return this.virusShape;
} else if (wrapperType === 'drug') {
if (drugInTrial) {
return this.drugInTrialShape;
@@ -125,13 +121,11 @@ export class NetworkSettings {
}
}
- static getColor(color: 'host' | 'virus' | 'approvedDrug' | 'unapprovedDrug' | 'hostFont' | 'virusFont' | 'drugFont' |
+ static getColor(color: 'protein' | 'approvedDrug' | 'unapprovedDrug' | 'hostFont' | 'virusFont' | 'drugFont' |
'nonSeedHost' | 'nonSeedVirus' | 'selectedForAnalysis' | 'selectedForAnalysisText' |
'edgeHostVirus' | 'edgeHostVirusHighlight' | 'edgeHostDrug' | 'edgeHostDrugHighlight') {
- if (color === 'host') {
+ if (color === 'protein') {
return this.hostColor;
- } else if (color === 'virus') {
- return this.virusColor;
} else if (color === 'approvedDrug') {
return this.approvedDrugColor;
} else if (color === 'unapprovedDrug') {
@@ -158,10 +152,8 @@ export class NetworkSettings {
}
static getFont(wrapperType: WrapperType, drugInTrial?: boolean) {
- if (wrapperType === 'host') {
+ if (wrapperType === 'protein') {
return {color: this.hostFontColor, size: this.hostFontSize};
- } else if (wrapperType === 'virus') {
- return {color: this.virusFontColor, size: this.virusFontSize};
} else if (wrapperType === 'drug') {
if (!drugInTrial) {
return {color: this.drugFontColor, size: this.drugFontSize};
@@ -188,20 +180,12 @@ export class NetworkSettings {
nodeShape = NetworkSettings.getNodeShape(nodeType);
nodeSize = NetworkSettings.getNodeSize(nodeType);
nodeFont = NetworkSettings.getFont(nodeType);
- if (nodeType === 'host') {
+ if (nodeType === 'protein') {
nodeColor = NetworkSettings.getColor(nodeType);
- nodeFont = NetworkSettings.getFont('host');
+ nodeFont = NetworkSettings.getFont('protein');
if (!isSeed) {
nodeColor = NetworkSettings.getColor('nonSeedHost');
}
- } else if (nodeType === 'virus') {
- nodeColor = NetworkSettings.getColor(nodeType);
- if (nodeType === 'virus') {
- nodeFont = NetworkSettings.getFont('virus');
- if (!isSeed) {
- nodeColor = NetworkSettings.getColor('nonSeedVirus');
- }
- }
} else if (nodeType === 'drug') {
if (drugType === 'approved') {
nodeColor = NetworkSettings.getColor('approvedDrug');
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 443f47dc311f19ec176a5e78d0eb54dd1d31a6fd..ba67fd3595ffd55b8e65c618cb2e4437d2d54e23 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -171,14 +171,13 @@
<p class="card-header-title">
<span class="icon">
<i *ngIf="!selectedWrapper" class="fas fa-info" aria-hidden="true"></i>
- <i *ngIf="selectedWrapper && selectedWrapper.type === 'host'" class="fas fa-dna" aria-hidden="true"></i>
- <i *ngIf="selectedWrapper && selectedWrapper.type === 'virus'" class="fas fa-virus" aria-hidden="true"></i>
+ <i *ngIf="selectedWrapper && selectedWrapper.type === 'protein'" class="fas fa-dna" aria-hidden="true"></i>
<i *ngIf="selectedWrapper && selectedWrapper.type === 'drug'" class="fas fa-capsules"
aria-hidden="true"></i>
</span>
<span *ngIf="!selectedWrapper">No item selected</span>
<span *ngIf="selectedWrapper">
- <span *ngIf="selectedWrapper.type === 'host'">Protein</span>
+ <span *ngIf="selectedWrapper.type === 'protein'">Host Protein</span>
<span *ngIf="selectedWrapper.type === 'drug'">Drug</span>
</span>
</p>
@@ -274,7 +273,7 @@
<span class="icon">
<i class="fas fa-flask" aria-hidden="true"></i>
</span>
- Advanced Analysis
+ Analysis
</p>
<a (click)="collapseAnalysis = !collapseAnalysis" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
@@ -407,12 +406,10 @@
<tr *ngFor="let p of analysis.getSelection()">
<td>
<span class="icon">
- <i class="fa fa-dna" *ngIf="p.type == 'host'"></i>
- <i class="fa fa-virus" *ngIf="p.type =='virus'"></i>
+ <i class="fa fa-dna" *ngIf="p.type == 'protein'"></i>
</span>
</td>
- <td *ngIf="p.type == 'virus'">{{p.data.effectName}}</td>
- <td *ngIf="p.type == 'host'">{{p.data.name}}</td>
+ <td *ngIf="p.type == 'protein'">{{p.data.name}}</td>
<td>
<button (click)="analysis.removeItems([p])" class="button is-small is-danger is-outlined has-tooltip"
data-tooltip="Remove from selection.">
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index d42cf73363857a219f66f76adcddd40d255a11fe..66f901e69948b935e55fae5fb6e4e76465bd78bf 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -67,7 +67,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public selectedWrapper: Wrapper | null = null;
public collapseAnalysisQuick = true;
- public collapseAnalysis = false;
+ public collapseAnalysis = true;
public collapseDetails = true;
public collapseTask = true;
public collapseSelection = true;
@@ -299,7 +299,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private mapHostProteinToNode(hostProtein: Protein): any {
const wrapper = getWrapperFromProtein(hostProtein);
- const node = NetworkSettings.getNodeStyle('host', true, this.analysis.inSelection(wrapper));
+ const node = NetworkSettings.getNodeStyle('protein', true, this.analysis.inSelection(wrapper));
let nodeLabel = hostProtein.name;
if (hostProtein.name.length === 0) {
nodeLabel = hostProtein.proteinAc;
@@ -365,7 +365,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
gProfilerLink(): string {
const queryString = this.analysis.getSelection()
- .filter(wrapper => wrapper.type === 'host')
+ .filter(wrapper => wrapper.type === 'protein')
.map(wrapper => wrapper.data.proteinAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
diff --git a/src/index.html b/src/index.html
index 870537e3d928c752e812a4aa81673f4160416ce4..5fc741c8cbffb2c5b2794657dd5615369ae5de72 100644
--- a/src/index.html
+++ b/src/index.html
@@ -1,14 +1,6 @@
<!doctype html>
<html lang="en">
<head>
-<style>
- .my-legend-1{
- width: 10%;
- }
-</style>
-
-
-
<meta charset="utf-8">
<title>Network Expander</title>
<base href="/">
@@ -25,16 +17,14 @@
<input type="checkbox" onclick=changeConfigStr('{"showOverview":'+this.checked+'}') checked /> Show overview<br>
<input type="checkbox" onclick=changeConfigStr('{"showQuery":'+this.checked+'}') /> Show query<br>
-<input type="checkbox" onclick=changeConfigStr('{"showFilter":'+this.checked+'}') /> Show filter<br>
<input type="checkbox" onclick=changeConfigStr('{"showLeftSidebar":'+this.checked+'}') checked /> Show sidebar<br>
<br>
-<button onclick="changeConfig()">Hide sidebar</button>
<button onclick="setNetwork('netexp1')">Add proteins</button>
-<div style="border: 3px solid red">
- <network-expander id="netexp1" config='{"legendClass": "my-legend-1", "showQuery": false, "showFilter": false}' onload="init1()" style="height: 100vh"></network-expander>
+<div>
+ <network-expander id="netexp1" config='{"legendClass": "my-legend-1", "showQuery": false}' onload="init1()" style="height: 100vh"></network-expander>
</div>
<!--
@@ -43,8 +33,6 @@
</div>
-->
-
-
<script>
function init1() {
document.getElementsByClassName('my-legend-1')[0].onclick = function() {this.remove()};
diff --git a/src/styles.scss b/src/styles.scss
index 1cfb339b6a2df523957dff31b50a61aea0d7d8d2..11392e29ad65977d98c76561e268299213bde206 100644
--- a/src/styles.scss
+++ b/src/styles.scss
@@ -16,6 +16,8 @@ $info: $primary;
@import "~primeng/resources/primeng.min.css";
@import "~primeicons/primeicons.css";
+$height: '1000px';
+
nav.navbar {
height: 60px;
}
@@ -53,7 +55,7 @@ input.checkbox {
}
div.covex.sidebar {
- height: calc(100% - 70px);
+ height: calc(#{$height} - 70px);
overflow-y: auto;
overflow-x: hidden;
width: 340px;
@@ -109,7 +111,7 @@ div.card.network {
}
div.network {
- height: calc(100% - 200px);
+ height: calc(#{$height} - 200px);
}
div.parent {
@@ -134,7 +136,7 @@ div.center {
div.covex.explorer {
- height: calc(100% - 70px);
+ height: calc(#{$height} - 70px);
margin-left: 10px;
margin-right: 10px;
}
diff --git a/website/index.html b/website/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..0ccf46fa801aad83232e5c543f9f967687f44662
--- /dev/null
+++ b/website/index.html
@@ -0,0 +1,12 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+ <meta charset="UTF-8">
+ <title>DrugsToNe</title>
+</head>
+<body>
+
+DrugsToNe!
+
+</body>
+</html>