diff --git a/.gitignore b/.gitignore
index 4ae60b46c42bb5177b09053f05fc72177c8fab0f..c22e1c12b2d67c2408316b73f470d299a9dcd06e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,4 +47,4 @@ Thumbs.db
.idea
drugsTone-build
-package-lock.json
+package-lock.json
\ No newline at end of file
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index a362738660911993bbf64f74785fc7e0a8ae312b..553ba0a6f9983687d7a1b46c5cafa24857b1c340 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -329,16 +329,16 @@
</a>
</div>
<p-table *ngIf="tableProteins.length > 0" selectionMode="multiple"
- [value]="tableProteins" [selection]="tableSelectedProteins" dataKey="proteinAc"
+ [value]="tableProteins" [selection]="tableSelectedProteins" dataKey="uniprotAc"
(selectionChange)="tableProteinSelection($event)">
<ng-template pTemplate="header">
<tr>
<th class="checkbox-col">
<p-tableHeaderCheckbox></p-tableHeaderCheckbox>
</th>
- <th [pSortableColumn]="'proteinAc'">
+ <th [pSortableColumn]="'uniprotAc'">
UniProt Code
- <p-sortIcon [field]="'proteinAc'"></p-sortIcon>
+ <p-sortIcon [field]="'uniprotAc'"></p-sortIcon>
</th>
<th [pSortableColumn]="'name'">
Gene
@@ -367,7 +367,7 @@
<td>
<p-tableCheckbox [value]="e"></p-tableCheckbox>
</td>
- <td><a href="https://www.uniprot.org/uniprot/{{ e.proteinAc }}" target="_blank">{{ e.proteinAc }}</a></td>
+ <td><a href="https://www.uniprot.org/uniprot/{{ e.uniprotAc }}" target="_blank">{{ e.uniprotAc }}</a></td>
<td>{{e.name}}</td>
<td>{{e.proteinName}}</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index c8899ca189c6e9c54d75e5db0ca257713641d55e..3dd02f0d935d16e45e25b1c0bddf839e7d7132e8 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -379,56 +379,33 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const details = attributes.details || {};
const wrappers: { [key: string]: Wrapper } = {};
for (const node of network.nodes) {
-
- if (nodeTypes[node] === 'protein') {
- this.proteins.push(details[node]);
- wrappers[node] = getWrapperFromNode(details[node]);
- } else if (nodeTypes[node] === 'drug') {
- wrappers[node] = getWrapperFromDrug(details[node]);
+ // backend converts object keys to PascalCase: p_123 --> p123
+ const nodeObjectKey = node.split('_').join('')
+ if (nodeTypes[nodeObjectKey] === 'protein') {
+ this.proteins.push(details[nodeObjectKey]);
+ wrappers[node] = getWrapperFromNode(details[nodeObjectKey]);
+ } else if (nodeTypes[nodeObjectKey] === 'drug') {
+ wrappers[node] = getWrapperFromDrug(details[nodeObjectKey]);
}
- nodes.push(this.mapNode(this.inferNodeType(node), details[node], isSeed[node], scores[node]));
- }
+ nodes.push(this.mapNode(this.inferNodeType(node), wrappers[node], isSeed[nodeObjectKey], scores[nodeObjectKey]));
+ }
for (const edge of network.edges) {
edges.push(this.mapEdge(edge, 'protein-protein', wrappers));
}
-
return {
nodes,
edges,
};
}
- private mapNode(nodeType: WrapperType, details: Node, isSeed?: boolean, score?: number): any {
- /*let nodeLabel;
- // let wrapper: Wrapper;
- let drugType;
- let drugInTrial;*/
- /*if (nodeType === 'protein') {
- const protein = details as Node;
- // wrapper = getWrapperFromNode(protein);
- nodeLabel = protein.name;
- if (!protein.name) {
- nodeLabel = protein.id;
- }
- } else if (nodeType === 'drug') {
- // const drug = details as Drug;
- // wrapper = getWrapperFromDrug(drug);
- drugType = drug.status;
- drugInTrial = drug.inTrial;
- if (drugType === 'approved') {
- nodeLabel = drug.name;
- } else {
- nodeLabel = drug.drugId;
- }
- }*/
- const wrapper = getWrapperFromNode(details)
+ private mapNode(nodeType: WrapperType, wrapper: Wrapper, isSeed?: boolean, score?: number): any {
const node = NetworkSettings.getNodeStyle('gene', isSeed, this.analysis.inSelection(wrapper));
- node.id = details.id;
- node.label = details.name;
+ node.id = wrapper.id;
+ node.label = wrapper.data.name;
node.nodeType = nodeType;
node.isSeed = isSeed;
- node.wrapper = details;
+ node.wrapper = wrapper;
return node;
}
@@ -500,7 +477,8 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
for (const interaction of edges) {
- const edge = {from: interaction.proteinAc, to: interaction.drugId};
+ console.log(interaction)
+ const edge = {from: interaction.uniprotAc, to: interaction.drugId};
this.drugEdges.push(this.mapEdge(edge, 'to-drug'));
}
this.nodeData.nodes.add(Array.from(this.drugNodes.values()));
diff --git a/src/app/components/query-tile/query-tile.component.html b/src/app/components/query-tile/query-tile.component.html
index 43af39b09ad3afa893b05d63a912e84a9efa0986..2afbd5738d3a0a8851c6bd1dec338e3fa743a710 100644
--- a/src/app/components/query-tile/query-tile.component.html
+++ b/src/app/components/query-tile/query-tile.component.html
@@ -4,7 +4,7 @@
<ng-template ng-option-tmp let-item="item">
<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>
+ <span *ngIf="item.type == 'protein'"><small>AC: <b>{{item.data.uniprotAc}}</b></small> </span>
</ng-template>
</ng-select>
</div>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 5f17dca036b7888ab48dd2fb309b73cb07ddad4e..9493b61e4f4839c21f416ebcddca840c6b4f51d1 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -11,6 +11,7 @@ import {
TRUSTRANK
} from '../../services/analysis/analysis.service';
import {Wrapper} from '../../interfaces';
+import { IConfig } from 'src/app/config';
@Component({
selector: 'app-launch-analysis',
@@ -25,6 +26,8 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public target: 'drug' | 'drug-target';
@Input()
public inputNetwork: {nodes: any, edges: any};
+ @Input()
+ public config: IConfig;
@Output()
public showChange = new EventEmitter<boolean>();
@@ -103,15 +106,17 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public async startTask() {
const parameters: any = {
seeds: this.analysis.getSelection().map((item) => item.data.netexId),
+ config: this.config,
+ input_network: this.inputNetwork
};
- parameters.target_or_drugs = this.target === 'drug' ? 'drug' : 'protein';
+ parameters.target = this.target === 'drug' ? 'drug' : 'drug-target';
// pass network data to reconstruct network in analysis result to connect non-proteins to results
// drop interactions in nodes beforehand to no cause cyclic error, information is contained in edges
this.inputNetwork.nodes.forEach(node => {
delete node.interactions
});
- parameters.input_network = this.inputNetwork;
+ console.log(this.inputNetwork)
if (this.algorithm === 'trustrank') {
parameters.damping_factor = this.trustrankDampingFactor;
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 7a9fb7a4feddc5bc852cb050a0bbe6698deae0b0..f894c0085ba521e765b2cf4d108a62b27877cd73 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -98,10 +98,14 @@ export function getNodeId(node: Node) {
/**
* Returns backend_id of Gene object
*/
- return node.id.toString();
+ if ('netexId' in node) {
+ return node['netexId']
+ } else {
+ return node.id
+ }
}
-export function getGeneNodeId(gene: Node) {
+export function getId(gene: Node) {
/**
* Returns the network node id based on a given gene
*/
@@ -115,7 +119,7 @@ export function getWrapperFromNode(gene: Node): Wrapper {
*/
return {
id: getNodeId(gene),
- nodeId: getGeneNodeId(gene),
+ nodeId: getNodeId(gene),
type: 'gene',
data: gene,
};
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 85f5b25de169500c3ed5044d353799744f901240..b3723b06fa2d8dccd91da991ec862896eb1a16ba 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -3,6 +3,7 @@
<app-launch-analysis [(show)]="showAnalysisDialog"
[target]="analysisDialogTarget"
+ [config]="myConfig"
[inputNetwork]="{nodes:proteins, edges:edges}">
</app-launch-analysis>