diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index 8677a27fe0b01fb4a91b1143607ec36d9846bdc5..95b6ac1be0ec83bd173f16b2b1da72f53ff568f4 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -13,7 +13,7 @@
<div class="field has-addons">
<p class="control" *ngIf="!fullscreen">
<button
- (click)="analysis.removeTask(token); close()"
+ (click)="analysis.removeAnalysis(token, tokenType); close()"
class="button is-rounded is-small is-outlined highlight-danger has-text-danger"
aria-label="delete"
pTooltip="Delete analysis"
@@ -109,13 +109,13 @@
>
<div class="tabs is-centered tabs-header">
<ul>
- <li [class.is-active]="tab === 'table'">
+ <li [class.is-active]="tab === 'table'" *ngIf="tokenType!=='view'">
<a (click)="tab = 'table'">Table</a>
</li>
<li [class.is-active]="tab === 'network'">
<a (click)="tab = 'network'">Network</a>
</li>
- <li [class.is-active]="tab === 'meta'">
+ <li [class.is-active]="tab === 'meta'" *ngIf="tokenType!=='view'">
<a (click)="tab = 'meta'">Parameters</a>
</li>
</ul>
@@ -145,7 +145,8 @@
</div>
<div class="columns m-1">
<div class="column">
- <table class="table parameter-table" *ngIf="['quick', 'super', 'connect', 'connectSelected'].includes(task.info.algorithm)">
+ <table class="table parameter-table"
+ *ngIf="['quick', 'super', 'connect', 'connectSelected'].includes(task.info.algorithm)">
<tbody>
<tr
*ngIf="result && result.geneInteractionDataset !== undefined"
@@ -169,7 +170,8 @@
</tr>
</tbody>
</table>
- <table class="table parameter-table" *ngIf="!['quick', 'super', 'connect', 'connectSelected'].includes(task.info.algorithm)">
+ <table class="table parameter-table"
+ *ngIf="!['quick', 'super', 'connect', 'connectSelected'].includes(task.info.algorithm)">
<tbody>
<tr
*ngIf="result && result.geneInteractionDataset !== undefined"
@@ -191,95 +193,95 @@
{{ result.drugInteractionDataset.version }}]
</td>
</tr>
- <tr *ngIf="task.info.parameters.resultSize !== undefined">
- <td>Result Size</td>
- <td>{{ task.info.parameters.resultSize }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.k !== undefined">
- <td>K</td>
- <td>{{ task.info.parameters.k }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.numTrees !== undefined">
- <td>Number of trees</td>
- <td>{{ task.info.parameters.numTrees }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.tolerance !== undefined">
- <td>Tolerance</td>
- <td>{{ task.info.parameters.tolerance }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.dampingFactor !== undefined">
- <td>Damping Factor</td>
- <td>{{ task.info.parameters.dampingFactor }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.maxDeg !== undefined">
- <td>Maximum Degree</td>
- <td>{{ task.info.parameters.maxDeg }}</td>
- </tr>
- <tr *ngIf="task.info.parameters.hubPenalty !== undefined">
- <td>Hub Penality</td>
- <td>{{ task.info.parameters.hubPenalty }}</td>
- </tr>
- <tr
- *ngIf="
+ <tr *ngIf="task.info.parameters.resultSize !== undefined">
+ <td>Result Size</td>
+ <td>{{ task.info.parameters.resultSize }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.k !== undefined">
+ <td>K</td>
+ <td>{{ task.info.parameters.k }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.numTrees !== undefined">
+ <td>Number of trees</td>
+ <td>{{ task.info.parameters.numTrees }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.tolerance !== undefined">
+ <td>Tolerance</td>
+ <td>{{ task.info.parameters.tolerance }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.dampingFactor !== undefined">
+ <td>Damping Factor</td>
+ <td>{{ task.info.parameters.dampingFactor }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.maxDeg !== undefined">
+ <td>Maximum Degree</td>
+ <td>{{ task.info.parameters.maxDeg }}</td>
+ </tr>
+ <tr *ngIf="task.info.parameters.hubPenalty !== undefined">
+ <td>Hub Penality</td>
+ <td>{{ task.info.parameters.hubPenalty }}</td>
+ </tr>
+ <tr
+ *ngIf="
task.info.parameters.includeIndirectDrugs !== undefined &&
task.info.target === 'drug'
"
- >
- <td>Include indirect drugs</td>
- <td>
- <app-fa-solid-icon
- *ngIf="task.info.parameters.includeIndirectDrugs"
- icon="check"
- title="indirect drugs included"
- classString="has-text-success"
- ></app-fa-solid-icon>
- <app-fa-solid-icon
- *ngIf="!task.info.parameters.includeIndirectDrugs"
- icon="times"
- classString="has-text-danger"
- title="indirect drugs excluded"
- ></app-fa-solid-icon>
- </td>
- </tr>
- <tr
- *ngIf="
+ >
+ <td>Include indirect drugs</td>
+ <td>
+ <app-fa-solid-icon
+ *ngIf="task.info.parameters.includeIndirectDrugs"
+ icon="check"
+ title="indirect drugs included"
+ classString="has-text-success"
+ ></app-fa-solid-icon>
+ <app-fa-solid-icon
+ *ngIf="!task.info.parameters.includeIndirectDrugs"
+ icon="times"
+ classString="has-text-danger"
+ title="indirect drugs excluded"
+ ></app-fa-solid-icon>
+ </td>
+ </tr>
+ <tr
+ *ngIf="
task.info.parameters.includeNonApprovedDrugs !==
undefined && task.info.target === 'drug'
"
- >
- <td>Include non-approved drugs</td>
- <td>
- <app-fa-solid-icon
- *ngIf="task.info.parameters.includeNonApprovedDrugs"
- icon="check"
- title="non-approved drugs included"
- classString="has-text-success"
- ></app-fa-solid-icon>
- <app-fa-solid-icon
- *ngIf="!task.info.parameters.includeNonApprovedDrugs"
- icon="times"
- classString="has-text-danger"
- title="non-approved drugs excluded"
- ></app-fa-solid-icon>
- </td>
- </tr>
- <tr *ngIf="task.info.parameters.customEdges !== undefined">
- <td>Include all displayed edges</td>
- <td>
- <app-fa-solid-icon
- *ngIf="task.info.parameters.customEdges"
- icon="check"
- title="custom edges drugs included"
- classString="has-text-success"
- ></app-fa-solid-icon>
- <app-fa-solid-icon
- *ngIf="!task.info.parameters.customEdges"
- icon="times"
- classString="has-text-danger"
- title="custom edges drugs excluded"
- ></app-fa-solid-icon>
- </td>
- </tr>
+ >
+ <td>Include non-approved drugs</td>
+ <td>
+ <app-fa-solid-icon
+ *ngIf="task.info.parameters.includeNonApprovedDrugs"
+ icon="check"
+ title="non-approved drugs included"
+ classString="has-text-success"
+ ></app-fa-solid-icon>
+ <app-fa-solid-icon
+ *ngIf="!task.info.parameters.includeNonApprovedDrugs"
+ icon="times"
+ classString="has-text-danger"
+ title="non-approved drugs excluded"
+ ></app-fa-solid-icon>
+ </td>
+ </tr>
+ <tr *ngIf="task.info.parameters.customEdges !== undefined">
+ <td>Include all displayed edges</td>
+ <td>
+ <app-fa-solid-icon
+ *ngIf="task.info.parameters.customEdges"
+ icon="check"
+ title="custom edges drugs included"
+ classString="has-text-success"
+ ></app-fa-solid-icon>
+ <app-fa-solid-icon
+ *ngIf="!task.info.parameters.customEdges"
+ icon="times"
+ classString="has-text-danger"
+ title="custom edges drugs excluded"
+ ></app-fa-solid-icon>
+ </td>
+ </tr>
</tbody>
</table>
</div>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 3dd071722b7b14fd45759b9bfd2b3dd825bf182e..0cccfaf786579542cfd546b5789737bc74a4247c 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -26,7 +26,7 @@ import {
} from '../../interfaces';
import {NetworkSettings} from '../../network-settings';
import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
-import {mapCustomEdge} from 'src/app/main-network';
+import {mapCustomEdge, mapNetexEdge, ProteinNetwork} from 'src/app/main-network';
import {DrugstoneConfigService} from 'src/app/services/drugstone-config/drugstone-config.service';
import {NetworkHandlerService} from 'src/app/services/network-handler/network-handler.service';
import {LegendService} from 'src/app/services/legend-service/legend-service.service';
@@ -73,7 +73,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
// private drugNodes: any[] = [];
// private drugEdges: any[] = [];
- public tab: 'meta' | 'network' | 'table' = 'table';
+ public tab: 'meta' | 'network' | 'table' = 'network';
// public adjacentDrugs = false;
// public adjacentDrugList: Node[] = [];
@@ -145,263 +145,474 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}
}
- private async refresh() {
- if (this.token) {
- if (this.tokenType === 'view') {
- this.loadingScreen.stateUpdate(true);
- this.task = await this.getView(this.token);
- console.log(this.task)
- this.analysis.switchSelection(this.token);
- this.loadingScreen.stateUpdate(false);
- } else {
- this.loadingScreen.stateUpdate(true);
- this.task = await this.getTask(this.token);
- this.analysis.switchSelection(this.token);
-
- if (this.task.info.algorithm === 'degree') {
- this.tableDrugScoreTooltip =
- 'Normalized number of direct interactions of the drug with the seeds. ' +
- 'The higher the score, the more relevant the drug.';
- this.tableProteinScoreTooltip =
- 'Normalized number of direct interactions of the protein with the seeds. ' +
- 'The higher the score, the more relevant the protein.';
- } else if (this.task.info.algorithm === 'closeness' || this.task.info.algorithm === 'quick' || this.task.info.algorithm === 'super') {
- this.tableDrugScoreTooltip =
- 'Normalized inverse mean distance of the drug to the seeds. ' +
- 'The higher the score, the more relevant the drug.';
- this.tableProteinScoreTooltip =
- 'Normalized inverse mean distance of the protein to the seeds. ' +
- 'The higher the score, the more relevant the protein.';
- } else if (this.task.info.algorithm === 'trustrank') {
- this.tableDrugScoreTooltip =
- 'Amount of ‘trust’ on the drug at termination of the algorithm. ' +
- 'The higher the score, the more relevant the drug.';
- this.tableProteinScoreTooltip =
- 'Amount of ‘trust’ on the protein at termination of the algorithm. ' +
- 'The higher the score, the more relevant the protein.';
- } else if (this.task.info.algorithm === 'proximity') {
- this.tableDrugScoreTooltip =
- 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
- 'The lower the score, the more relevant the drug.';
- this.tableProteinScoreTooltip =
- 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
- 'The lower the score, the more relevant the drug.';
+ private async refreshView() {
+ this.loading = true;
+ this.loadingScreen.stateUpdate(true);
+ this.getView(this.token).then(async view => {
+ this.task = view;
+ this.result = view;
+ this.drugstoneConfig.set_analysisConfig(view.config);
+ this.analysis.switchSelection(this.token);
+ this.loadingScreen.stateUpdate(false);
+
+
+ // Reset
+ this.nodeData = {nodes: null, edges: null};
+ // this.networkHandler.activeNetwork.networkEl.nativeElement.innerHTML = '';
+ // this.networkHandler.activeNetwork.networkInternal = null;
+ // Create+
+ return new Promise<any>(async (resolve, reject) => {
+ const nodes = view.network.nodes;
+ let edges = view.network.edges;
+
+ if (this.drugstoneConfig.config.autofillEdges && nodes.length) {
+ const node_map = {};
+ nodes.filter(n => n.drugstoneType === 'protein').forEach(node => {
+ if (typeof node.drugstoneId === 'string') {
+ if (node_map[node.drugstoneId]) {
+ node_map[node.drugstoneId].push(node.id);
+ } else {
+ node_map[node.drugstoneId] = [node.id];
+ }
+ } else {
+ node.drugstoneId.forEach(n => {
+ if (node_map[n]) {
+ node_map[n].push(node.id);
+ } else {
+ node_map[n] = [node.id];
+ }
+ });
+ }
+ });
+ const netexEdges = await this.netex.fetchEdges(nodes, this.drugstoneConfig.config.interactionProteinProtein, this.drugstoneConfig.config.licensedDatasets);
+ edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.drugstoneConfig.currentConfig(), node_map)).flatMap(e => e));
}
- if (this.task && this.task.info && this.task.info.done) {
+ const edge_map = {};
+
+ edges = edges.filter(edge => {
+ if (edge_map[edge.to] && edge_map[edge.to].indexOf(edge.from) !== -1) {
+ return false;
+ }
+ if (edge_map[edge.from] && edge_map[edge.from].indexOf(edge.to) !== -1) {
+ return false;
+ }
+ if (!edge_map[edge.from]) {
+ edge_map[edge.from] = [edge.to];
+ } else {
+ edge_map[edge.from].push(edge.to);
+ }
+ return true;
+ });
+
+ // @ts-ignore
+ if (!this.drugstoneConfig.selfReferences) {
+ edges = edges.filter(el => el.from !== el.to);
+ }
- this.loading = true;
- this.netex.getTaskResult(this.token).then(async result => {
- this.drugstoneConfig.set_analysisConfig(result.parameters.config);
- this.result = result;
- if (this.result.parameters.target === 'drug') {
- this.legendService.add_to_context('drug');
+ this.networkHandler.activeNetwork.inputNetwork = {nodes: nodes, edges: edges};
+ this.nodeData.nodes = new vis.DataSet(nodes);
+ this.nodeData.edges = new vis.DataSet(edges);
+ const container = this.networkHandler.activeNetwork.networkEl.nativeElement;
+ const isBig = nodes.length > 100 || edges.length > 100;
+ const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
+ // @ts-ignore
+ options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
+ // @ts-ignore
+ for (const g of Object.values(options.groups)) {
+ // @ts-ignore
+ delete g.renderer;
+ }
+ if (this.drugstoneConfig.config.physicsOn) {
+ this.drugstoneConfig.config.physicsOn = !isBig;
+ }
+ this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
+
+ if (isBig) {
+ resolve(nodes);
+ }
+ this.networkHandler.activeNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
+ if (!this.drugstoneConfig.config.physicsOn || this.networkHandler.activeNetwork.isBig()) {
+ this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
+ }
+ this.networkHandler.updateAdjacentNodes(this.networkHandler.activeNetwork.isBig()).then(() => {
+ resolve(nodes);
+ });
+ });
+ }).then(() => {
+ this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
+ this.showDetailsChange.emit(null);
+ });
+
+ this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
+ const nodeIds: Array<string> = properties.nodes;
+ if (nodeIds.length > 0) {
+ const nodeId = nodeIds[0];
+ const node = this.nodeData.nodes.get(nodeId);
+ if (node.drugstoneId === undefined || node.nodeType === 'drug' || node.drugstoneType !== 'protein') {
+ this.analysis.unmappedNodeToast();
+ return;
+ }
+ const wrapper = getWrapperFromNode(node);
+ if (this.analysis.inSelection(wrapper)) {
+ this.analysis.removeItems([wrapper]);
+ this.analysis.getCount();
} else {
- this.legendService.add_to_context('drugTarget');
+ this.analysis.addItems([wrapper]);
+ this.analysis.getCount();
}
- const nodeAttributes = this.result.nodeAttributes || {};
-
- this.networkHandler.activeNetwork.seedMap = nodeAttributes.isSeed || {};
-
- // Reset
- this.nodeData = {nodes: null, edges: null};
- this.networkHandler.activeNetwork.networkEl.nativeElement.innerHTML = '';
- this.networkHandler.activeNetwork.networkInternal = null;
- // Create
- await this.createNetwork(this.result).then(nw => {
- return new Promise<any>((resolve, reject) => {
-
- const nodes = nw.nodes;
- const edges = nw.edges;
- this.networkHandler.activeNetwork.inputNetwork = {nodes: nodes, edges: edges};
- this.nodeData.nodes = new vis.DataSet(nodes);
- this.nodeData.edges = new vis.DataSet(edges);
- const container = this.networkHandler.activeNetwork.networkEl.nativeElement;
- const isBig = nodes.length > 100 || edges.length > 100;
- const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
- // @ts-ignore
- options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
- // @ts-ignore
- for (const g of Object.values(options.groups)) {
- // @ts-ignore
- delete g.renderer;
- }
- if (this.drugstoneConfig.config.physicsOn) {
- this.drugstoneConfig.config.physicsOn = !isBig;
- }
- this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
+ }
+ });
+
+ this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
+ if (properties.nodes.length === 0 && properties.edges.length === 1) {
+ // clicked on one edge
+ const edgeId = properties.edges[0];
+ this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
+ } else {
+ this.networkHandler.activeNetwork.activeEdge = null;
+ const selectedNodes = this.nodeData.nodes.get(properties.nodes);
+ if (selectedNodes.length > 0) {
+ this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
+ } else {
+ this.showDetailsChange.emit(null);
+ }
+ }
+ });
+ this.analysis.subscribeList((items, selected) => {
+ // return if analysis panel is closed or no nodes are loaded
+ if (!this.token) {
+ return;
+ }
+
+ if (selected !== null) {
+ const updatedNodes: Node[] = [];
+ for (const item of items) {
+ const node = this.nodeData.nodes.get(item.id);
+ if (!node) {
+ continue;
+ }
+ const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([item.id]);
+ node.x = pos[item.id].x;
+ node.y = pos[item.id].y;
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
+ const nodeStyled = NetworkSettings.getNodeStyle(
+ node,
+ this.drugstoneConfig.currentConfig(),
+ isSeed,
+ selected,
+ this.networkHandler.activeNetwork.getGradient(item.id),
+ this.networkHandler.activeNetwork.nodeRenderer
+ );
+ updatedNodes.push(nodeStyled);
+ }
+ this.nodeData.nodes.update(updatedNodes);
+
+ const proteinSelection = this.tableSelectedProteins;
+ for (const item of items) {
+ // TODO: Refactor!
+ const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.id);
+ const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
+ if (selected && found === -1 && tableItem) {
+ proteinSelection.push(tableItem);
+ }
+ if (!selected && found !== -1 && tableItem) {
+ proteinSelection.splice(found, 1);
+ }
+ }
+ this.tableSelectedProteins = [...proteinSelection];
+ } else {
+ // else: selected is null
+ const updatedNodes = [];
+ this.nodeData.nodes.forEach((node) => {
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
+ if (!isSeed) {
+ return;
+ }
+ const nodeStyled = NetworkSettings.getNodeStyle(
+ node,
+ this.drugstoneConfig.currentConfig(),
+ isSeed,
+ selected,
+ this.networkHandler.activeNetwork.getGradient(node.id),
+ this.networkHandler.activeNetwork.nodeRenderer
+ );
+ updatedNodes.push(nodeStyled);
+ });
+ this.nodeData.nodes.update(updatedNodes);
+
+ const proteinSelection = [];
+ for (const item of items) {
+ const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
+ if (tableItem) {
+ proteinSelection.push(tableItem);
+ }
+ }
+ this.tableSelectedProteins = [...proteinSelection];
+ }
+ });
+ this.emitVisibleItems(true);
+ });
+ });
+ }
- if (isBig) {
- resolve(nodes);
- }
- this.networkHandler.activeNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
- if (!this.drugstoneConfig.config.physicsOn || this.networkHandler.activeNetwork.isBig()) {
- this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
- }
- this.networkHandler.updateAdjacentNodes(this.networkHandler.activeNetwork.isBig()).then(() => {
- resolve(nodes);
- });
- });
- }).then(nodes => {
- this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
- this.tableDrugs.forEach((r) => {
- r.rawScore = r.score;
- });
- // @ts-ignore
- this.tableDrugs.sort((a, b) => b.score - a.score);
- this.rankTable(this.tableDrugs);
- this.tableProteins = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'protein');
- this.tableSelectedProteins = [];
- this.tableProteins.forEach((r) => {
- r.rawScore = r.score;
- r.isSeed = this.networkHandler.activeNetwork.seedMap[r.id];
- const wrapper = getWrapperFromNode(r);
- if (this.analysis.inSelection(wrapper)) {
- this.tableSelectedProteins.push(r);
- }
- });
- this.tableProteins.sort((a, b) => b.score - a.score);
- this.rankTable(this.tableProteins);
+ private async refreshTask() {
+ this.loadingScreen.stateUpdate(true);
+ this.task = await this.getTask(this.token);
+ this.analysis.switchSelection(this.token);
+
+ if (this.task.info.algorithm === 'degree') {
+ this.tableDrugScoreTooltip =
+ 'Normalized number of direct interactions of the drug with the seeds. ' +
+ 'The higher the score, the more relevant the drug.';
+ this.tableProteinScoreTooltip =
+ 'Normalized number of direct interactions of the protein with the seeds. ' +
+ 'The higher the score, the more relevant the protein.';
+ } else if (this.task.info.algorithm === 'closeness' || this.task.info.algorithm === 'quick' || this.task.info.algorithm === 'super') {
+ this.tableDrugScoreTooltip =
+ 'Normalized inverse mean distance of the drug to the seeds. ' +
+ 'The higher the score, the more relevant the drug.';
+ this.tableProteinScoreTooltip =
+ 'Normalized inverse mean distance of the protein to the seeds. ' +
+ 'The higher the score, the more relevant the protein.';
+ } else if (this.task.info.algorithm === 'trustrank') {
+ this.tableDrugScoreTooltip =
+ 'Amount of ‘trust’ on the drug at termination of the algorithm. ' +
+ 'The higher the score, the more relevant the drug.';
+ this.tableProteinScoreTooltip =
+ 'Amount of ‘trust’ on the protein at termination of the algorithm. ' +
+ 'The higher the score, the more relevant the protein.';
+ } else if (this.task.info.algorithm === 'proximity') {
+ this.tableDrugScoreTooltip =
+ 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
+ 'The lower the score, the more relevant the drug.';
+ this.tableProteinScoreTooltip =
+ 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
+ 'The lower the score, the more relevant the drug.';
+ }
+
+ if (this.task && this.task.info && this.task.info.done) {
+
+ this.loading = true;
+ this.netex.getTaskResult(this.token).then(async result => {
+ this.drugstoneConfig.set_analysisConfig(result.parameters.config);
+ this.result = result;
+ if (this.result.parameters.target === 'drug') {
+ this.legendService.add_to_context('drug');
+ } else {
+ this.legendService.add_to_context('drugTarget');
+ }
+ const nodeAttributes = this.result.nodeAttributes || {};
+
+ this.networkHandler.activeNetwork.seedMap = nodeAttributes.isSeed || {};
+
+ // Reset
+ this.nodeData = {nodes: null, edges: null};
+ this.networkHandler.activeNetwork.networkEl.nativeElement.innerHTML = '';
+ this.networkHandler.activeNetwork.networkInternal = null;
+ // Create
+ await this.createNetwork(this.result).then(nw => {
+ return new Promise<any>((resolve, reject) => {
+
+ const nodes = nw.nodes;
+ const edges = nw.edges;
+ this.networkHandler.activeNetwork.inputNetwork = {nodes: nodes, edges: edges};
+ this.nodeData.nodes = new vis.DataSet(nodes);
+ this.nodeData.edges = new vis.DataSet(edges);
+ const container = this.networkHandler.activeNetwork.networkEl.nativeElement;
+ const isBig = nodes.length > 100 || edges.length > 100;
+ const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
+ // @ts-ignore
+ options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
+ // @ts-ignore
+ for (const g of Object.values(options.groups)) {
+ // @ts-ignore
+ delete g.renderer;
+ }
+ if (this.drugstoneConfig.config.physicsOn) {
+ this.drugstoneConfig.config.physicsOn = !isBig;
+ }
+ this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
- this.tableHasScores = ['trustrank', 'closeness', 'degree', 'betweenness', 'quick', 'super']
- .indexOf(this.task.info.algorithm) !== -1;
- if (this.tableHasScores) {
- this.toggleNormalization(true);
+ if (isBig) {
+ resolve(nodes);
+ }
+ this.networkHandler.activeNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
+ if (!this.drugstoneConfig.config.physicsOn || this.networkHandler.activeNetwork.isBig()) {
+ this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
+ }
+ this.networkHandler.updateAdjacentNodes(this.networkHandler.activeNetwork.isBig()).then(() => {
+ resolve(nodes);
+ });
+ });
+ }).then(nodes => {
+
+ this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
+ this.tableDrugs.forEach((r) => {
+ r.rawScore = r.score;
+ });
+ // @ts-ignore
+ this.tableDrugs.sort((a, b) => b.score - a.score);
+ this.rankTable(this.tableDrugs);
+ this.tableProteins = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'protein');
+ this.tableSelectedProteins = [];
+ this.tableProteins.forEach((r) => {
+ r.rawScore = r.score;
+ r.isSeed = this.networkHandler.activeNetwork.seedMap[r.id];
+ const wrapper = getWrapperFromNode(r);
+ if (this.analysis.inSelection(wrapper)) {
+ this.tableSelectedProteins.push(r);
+ }
+ });
+ this.tableProteins.sort((a, b) => b.score - a.score);
+ this.rankTable(this.tableProteins);
+
+ this.tableHasScores = ['trustrank', 'closeness', 'degree', 'betweenness', 'quick', 'super']
+ .indexOf(this.task.info.algorithm) !== -1;
+ if (this.tableHasScores) {
+ this.toggleNormalization(true);
+ }
+ this.networkHandler.activeNetwork.networkInternal.setData({nodes: undefined, edge: undefined});
+ setTimeout(() => {
+ this.networkHandler.activeNetwork.networkInternal.setData(this.nodeData);
+ }, 1000);
+
+ this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
+ this.showDetailsChange.emit(null);
+ });
+
+ this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
+ const nodeIds: Array<string> = properties.nodes;
+ if (nodeIds.length > 0) {
+ const nodeId = nodeIds[0];
+ const node = this.nodeData.nodes.get(nodeId);
+ if (node.drugstoneId === undefined || node.nodeType === 'drug' || node.drugstoneType !== 'protein') {
+ this.analysis.unmappedNodeToast();
+ return;
}
- this.networkHandler.activeNetwork.networkInternal.setData({nodes: undefined, edge: undefined});
- setTimeout(() => {
- this.networkHandler.activeNetwork.networkInternal.setData(this.nodeData);
- }, 1000);
+ const wrapper = getWrapperFromNode(node);
+ if (this.analysis.inSelection(wrapper)) {
+ this.analysis.removeItems([wrapper]);
+ this.analysis.getCount();
+ } else {
+ this.analysis.addItems([wrapper]);
+ this.analysis.getCount();
+ }
+ }
+ });
- this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
+ this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
+ if (properties.nodes.length === 0 && properties.edges.length === 1) {
+ // clicked on one edge
+ const edgeId = properties.edges[0];
+ this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
+ } else {
+ this.networkHandler.activeNetwork.activeEdge = null;
+ const selectedNodes = this.nodeData.nodes.get(properties.nodes);
+ if (selectedNodes.length > 0) {
+ this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
+ } else {
this.showDetailsChange.emit(null);
- });
+ }
+ }
+ });
- this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
- const nodeIds: Array<string> = properties.nodes;
- if (nodeIds.length > 0) {
- const nodeId = nodeIds[0];
- const node = this.nodeData.nodes.get(nodeId);
- if (node.drugstoneId === undefined || node.nodeType === 'drug' || node.drugstoneType !== 'protein') {
- this.analysis.unmappedNodeToast();
- return;
- }
- const wrapper = getWrapperFromNode(node);
- if (this.analysis.inSelection(wrapper)) {
- this.analysis.removeItems([wrapper]);
- this.analysis.getCount();
- } else {
- this.analysis.addItems([wrapper]);
- this.analysis.getCount();
- }
+ this.analysis.subscribeList((items, selected) => {
+ // return if analysis panel is closed or no nodes are loaded
+ if (!this.token) {
+ return;
+ }
+
+ if (selected !== null) {
+ const updatedNodes: Node[] = [];
+ for (const item of items) {
+ const node = this.nodeData.nodes.get(item.id);
+ if (!node) {
+ continue;
}
- });
-
- this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
- if (properties.nodes.length === 0 && properties.edges.length === 1) {
- // clicked on one edge
- const edgeId = properties.edges[0];
- this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
- } else {
- this.networkHandler.activeNetwork.activeEdge = null;
- const selectedNodes = this.nodeData.nodes.get(properties.nodes);
- if (selectedNodes.length > 0) {
- this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
- } else {
- this.showDetailsChange.emit(null);
- }
+ const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([item.id]);
+ node.x = pos[item.id].x;
+ node.y = pos[item.id].y;
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
+ const nodeStyled = NetworkSettings.getNodeStyle(
+ node,
+ this.drugstoneConfig.currentConfig(),
+ isSeed,
+ selected,
+ this.networkHandler.activeNetwork.getGradient(item.id),
+ this.networkHandler.activeNetwork.nodeRenderer
+ );
+ updatedNodes.push(nodeStyled);
+ }
+ this.nodeData.nodes.update(updatedNodes);
+
+ const proteinSelection = this.tableSelectedProteins;
+ for (const item of items) {
+ // TODO: Refactor!
+ const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.id);
+ const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
+ if (selected && found === -1 && tableItem) {
+ proteinSelection.push(tableItem);
}
- });
-
- this.analysis.subscribeList((items, selected) => {
- // return if analysis panel is closed or no nodes are loaded
- if (!this.token) {
+ if (!selected && found !== -1 && tableItem) {
+ proteinSelection.splice(found, 1);
+ }
+ }
+ this.tableSelectedProteins = [...proteinSelection];
+ } else {
+ // else: selected is null
+ const updatedNodes = [];
+ this.nodeData.nodes.forEach((node) => {
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
+ if (!isSeed) {
return;
}
+ const nodeStyled = NetworkSettings.getNodeStyle(
+ node,
+ this.drugstoneConfig.currentConfig(),
+ isSeed,
+ selected,
+ this.networkHandler.activeNetwork.getGradient(node.id),
+ this.networkHandler.activeNetwork.nodeRenderer
+ );
+ updatedNodes.push(nodeStyled);
+ });
+ this.nodeData.nodes.update(updatedNodes);
- if (selected !== null) {
- const updatedNodes: Node[] = [];
- for (const item of items) {
- const node = this.nodeData.nodes.get(item.id);
- if (!node) {
- continue;
- }
- const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([item.id]);
- node.x = pos[item.id].x;
- node.y = pos[item.id].y;
- const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
- const nodeStyled = NetworkSettings.getNodeStyle(
- node,
- this.drugstoneConfig.currentConfig(),
- isSeed,
- selected,
- this.networkHandler.activeNetwork.getGradient(item.id),
- this.networkHandler.activeNetwork.nodeRenderer
- );
- updatedNodes.push(nodeStyled);
- }
- this.nodeData.nodes.update(updatedNodes);
-
- const proteinSelection = this.tableSelectedProteins;
- for (const item of items) {
- // TODO: Refactor!
- const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.id);
- const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
- if (selected && found === -1 && tableItem) {
- proteinSelection.push(tableItem);
- }
- if (!selected && found !== -1 && tableItem) {
- proteinSelection.splice(found, 1);
- }
- }
- this.tableSelectedProteins = [...proteinSelection];
- } else {
- // else: selected is null
- const updatedNodes = [];
- this.nodeData.nodes.forEach((node) => {
- const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
- if (!isSeed) {
- return;
- }
- const nodeStyled = NetworkSettings.getNodeStyle(
- node,
- this.drugstoneConfig.currentConfig(),
- isSeed,
- selected,
- this.networkHandler.activeNetwork.getGradient(node.id),
- this.networkHandler.activeNetwork.nodeRenderer
- );
- updatedNodes.push(nodeStyled);
- });
- this.nodeData.nodes.update(updatedNodes);
-
- const proteinSelection = [];
- for (const item of items) {
- const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
- if (tableItem) {
- proteinSelection.push(tableItem);
- }
- }
- this.tableSelectedProteins = [...proteinSelection];
+ const proteinSelection = [];
+ for (const item of items) {
+ const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
+ if (tableItem) {
+ proteinSelection.push(tableItem);
}
- });
- this.emitVisibleItems(true);
- }).then(() => {
- if (!['quick', 'super', 'connect', 'connectSelected'].includes(this.task.info.algorithm)) {
- return;
}
- this.netex.getAlgorithmDefaults(this.task.info.algorithm).then(response => {
- this.algorithmDefault = response;
- });
- }).catch(console.error);
+ this.tableSelectedProteins = [...proteinSelection];
+ }
});
- this.loadingScreen.stateUpdate(false);
- });
- }
- }
+ this.emitVisibleItems(true);
+ }).then(() => {
+ if (!['quick', 'super', 'connect', 'connectSelected'].includes(this.task.info.algorithm)) {
+ return;
+ }
+ this.netex.getAlgorithmDefaults(this.task.info.algorithm).then(response => {
+ this.algorithmDefault = response;
+ });
+ }).catch(console.error);
+ });
+ this.loadingScreen.stateUpdate(false);
+ });
}
+ }
+ private async refresh() {
+ if (this.token) {
+ if (this.tokenType === 'view') {
+ await this.refreshView();
+ } else {
+ await this.refreshTask();
+ }
+ }
}
diff --git a/src/app/components/analysis-panel/view-list/view-list.component.html b/src/app/components/analysis-panel/view-list/view-list.component.html
index f9d5b9328fd8bc48afefaac85322e7ce53e37fdf..0ed31cf8ff8a553d28f57cb23981424b5480af2e 100644
--- a/src/app/components/analysis-panel/view-list/view-list.component.html
+++ b/src/app/components/analysis-panel/view-list/view-list.component.html
@@ -4,50 +4,19 @@
[ngClass]="{ 'text-normal': drugstoneConfig.smallStyle }"
>
<a
- *ngFor="let task of analysis.selectionTokens"
+ *ngFor="let task of analysis.viewInfos"
class="list-item box small-box"
- [class.is-active]="task === token"
+ [class.is-active]="task.token === token"
>
-<!-- <div *ngIf="!task">-->
-<!-- <div class="columns mb-0">-->
-<!-- <div class="column">-->
-<!-- <app-fa-solid-icon-->
-<!-- classString="is-pulled-right has-text-warning"-->
-<!-- icon="pause"-->
-<!-- ></app-fa-solid-icon>-->
-<!-- </div>-->
-<!-- </div>-->
-<!-- <div class="columns mb-0">-->
-<!-- <div class="column pt-0 pb-0">-->
-<!-- <a-->
-<!-- (click)="analysis.removeSelection(task)"-->
-<!-- class="has-text-danger is-pulled-right"-->
-<!-- >-->
-<!-- <app-fa-solid-icon icon="trash"></app-fa-solid-icon>-->
-<!-- </a>-->
-<!-- </div>-->
-<!-- </div>-->
-<!-- </div>-->
<div
*ngIf="task"
- (click)="open(task)"
+ (click)="open(task.token)"
pTooltip="Show selection view"
[tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-top'"
tooltipPosition="top"
>
<div class="columns mb-0">
<div class="column is-8">
-<!-- <span class="is-capitalized"-->
-<!-- ><app-fa-solid-icon-->
-<!-- icon="crosshairs"-->
-<!-- *ngIf="task.info.target === 'drug-target'"-->
-<!-- ></app-fa-solid-icon>-->
-<!-- <app-fa-solid-icon-->
-<!-- icon="capsules"-->
-<!-- *ngIf="task.info.target === 'drug'"-->
-<!-- ></app-fa-solid-icon>-->
-<!-- {{ algorithmNames[task.info.algorithm] }}</span-->
-<!-- >-->
</div>
<div class="column">
<app-fa-solid-icon
@@ -57,9 +26,9 @@
</div>
</div>
<div class="columns mb-0">
-<!-- <div class="column is-8 pt-0 pb-0">-->
-<!-- <small>Created {{ task.info.finishedAt | date: "short" }}</small>-->
-<!-- </div>-->
+ <div class="column is-8 pt-0 pb-0">
+ <small>Created {{ task.createdAt | date: "short" }}</small>
+ </div>
<div class="column pt-0 pb-0">
<a
(click)="analysis.removeTask(task)"
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 9f3269d43300c8d7c3556caeb5ff88b183ed4a8a..f8541ecd93e0094528c3b485c42ccd14048c6a94 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -422,7 +422,16 @@
pTooltip="Add all proteins to the selection."
>
<app-fa-solid-icon icon="plus"></app-fa-solid-icon>
- <span> Add all </span>
+ <span>Add all</span>
+ </a>
+ <a
+ (click)="analysis.addFirstNeighbors()"
+ class="card-footer-item text-primary"
+ tooltipPosition="top"
+ pTooltip="Add first neighbor proteins of selection to selection."
+ >
+ <app-fa-solid-icon icon="plus"></app-fa-solid-icon>
+ <span>Add First neighbors</span>
</a>
</footer>
<footer class="card-footer">
@@ -456,24 +465,27 @@
</a>
<a
*ngIf="analysis.getSelection().length"
- (click)="analysis.resetSelection()"
- class="card-footer-item has-text-danger"
+ (click)="analysis.viewFromSelection()"
+ class="card-footer-item text-primary"
tooltipPosition="top"
- pTooltip="Remove all entries from the selection."
+ pTooltip="Create view from the selection."
>
- <app-fa-solid-icon icon="broom"></app-fa-solid-icon>
- <span> Reset </span>
+ <app-fa-solid-icon icon="check"></app-fa-solid-icon>
+ <span> Save selection </span>
</a>
+ </footer>
+ <footer class="card-footer">
<a
*ngIf="analysis.getSelection().length"
- (click)="analysis.viewFromSelection()"
+ (click)="analysis.resetSelection()"
class="card-footer-item has-text-danger"
tooltipPosition="top"
- pTooltip="Create view from the selection."
+ pTooltip="Remove all entries from the selection."
>
- <app-fa-solid-icon icon="check"></app-fa-solid-icon>
- <span> Save selection </span>
+ <app-fa-solid-icon icon="broom"></app-fa-solid-icon>
+ <span> Reset </span>
</a>
+
</footer>
<!-- </div> -->
@@ -487,7 +499,7 @@
>
<p class="card-header-title">
<app-fa-solid-icon icon="tasks"></app-fa-solid-icon>
- Views ({{ analysis.selectionTokens != null ? analysis.selectionTokens.length : 0 }})
+ Views ({{ analysis.viewTokens != null ? analysis.viewTokens.length : 0 }})
</p>
<a
(click)="collapseViews = !collapseViews"
@@ -508,13 +520,13 @@
<div *ngIf="collapseViews">
<div
class="card-content overflow task-list-container"
- *ngIf="analysis.selectionTokens && analysis.selectionTokens.length > 0"
+ *ngIf="analysis.viewTokens && analysis.viewTokens.length > 0"
>
<app-view-list [(token)]="selectedViewToken"></app-view-list>
</div>
<footer class="card-footer">
<a
- *ngIf="analysis.selectionTokens && analysis.selectionTokens.length > 0"
+ *ngIf="analysis.viewTokens && analysis.viewTokens.length > 0"
(click)="
analysis.removeAllSelections(); selectedViewToken = null
"
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index c316d55e34e10ab401ef494308a9fab1f3c5673f..cbb95cd844cf3ba46f5d00b4c98db60d9b00cd49 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -405,11 +405,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
});
- // if (!this.drugstoneConfig.config.showSidebar) {
- // // skip network options for selecting nodes when there are no options to use it
- // return;
- // }
-
this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
const nodeIds: Array<string> = properties.nodes;
if (nodeIds != null && nodeIds.length > 0) {
@@ -532,6 +527,67 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.drugstoneConfig.smallStyle = this.windowWidth < 1250;
}
+ public initNetworkListeners(resolve){
+ this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
+ const nodeIds: Array<string> = properties.nodes;
+ if (nodeIds != null && nodeIds.length > 0) {
+ const nodeId = nodeIds[0];
+ const node = this.nodeData.nodes.get(nodeId);
+ if (node.drugstoneId === undefined || node.drugstoneType !== 'protein') {
+ this.analysis.unmappedNodeToast();
+ // skip if node is not a protein mapped to backend
+ return;
+ }
+ const wrapper = getWrapperFromNode(node);
+ if (this.analysis.inSelection(node)) {
+ this.analysis.removeItems([wrapper]);
+ } else {
+ this.analysis.addItems([wrapper]);
+ }
+ }
+ });
+
+ this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
+ if (properties.nodes.length === 0 && properties.edges.length === 1) {
+ // clicked on one edge
+ const edgeId = properties.edges[0];
+ this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
+ } else {
+ // clicked not on one edge
+ const nodeIds: Array<string> = properties.nodes;
+ if (nodeIds != null && nodeIds.length > 0) {
+ const nodeId = nodeIds[0];
+ const node = this.nodeData.nodes.get(nodeId);
+ const wrapper = getWrapperFromNode(node);
+ this.openNodeSummary(wrapper, false);
+ } else {
+ this.closeSummary();
+ }
+ }
+ });
+
+ this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
+ this.closeSummary();
+ });
+
+ if (this.networkHandler.activeNetwork.selectedWrapper) {
+ this.zoomToNode(this.networkHandler.activeNetwork.selectedWrapper.id);
+ }
+
+ this.networkHandler.activeNetwork.currentViewNodes = this.nodeData.nodes;
+ this.networkHandler.activeNetwork.currentViewEdges = this.nodeData.edges;
+
+ this.networkHandler.activeNetwork.queryItems = [];
+ this.networkHandler.activeNetwork.updateQueryItems();
+ this.networkHandler.activeNetwork.currentViewProteins = this.networkHandler.activeNetwork.inputNetwork.nodes;
+ // this.fillQueryItems(this.currentViewNodes);
+ if (this.networkHandler.activeNetwork.selectedWrapper) {
+ this.networkHandler.activeNetwork.networkInternal.selectNodes([this.networkHandler.activeNetwork.selectedWrapper.id]);
+ }
+
+ resolve(true);
+ }
+
public async openNodeSummary(item: Wrapper, zoom: boolean) {
// close edge summary if open
this.networkHandler.activeNetwork.activeEdge = null;
diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts
index 81422449af3b923fe79ecc71bb0374ca831aaaf3..d68cc591a3f607366a4975f5d790f058d54cb76f 100644
--- a/src/app/services/analysis/analysis.service.ts
+++ b/src/app/services/analysis/analysis.service.ts
@@ -61,7 +61,8 @@ export class AnalysisService {
private selections = new Map<string, Map<string, Wrapper>>();
public tokens: string[] = [];
- public selectionTokens: string[] = [];
+ public viewTokens: string[] = [];
+ public viewInfos = [];
private tokensCookieKey = `drugstone-tokens-${window.location.host}`;
private selectionsCookieKey = `drugstone-selections-${window.location.host}`;
private tokensFinishedCookieKey = `drugstone-finishedTokens-${window.location.host}`;
@@ -90,8 +91,8 @@ export class AnalysisService {
this.tokens = JSON.parse(tokens);
}
if (selections) {
- this.selectionTokens = JSON.parse(selections);
- console.log(this.selectionTokens);
+ this.viewTokens = JSON.parse(selections);
+ this.setViewInfos();
}
if (finishedTokens) {
this.finishedTokens = JSON.parse(finishedTokens);
@@ -103,6 +104,21 @@ export class AnalysisService {
});
}
+ setViewInfos(): void {
+ this.netex.getViewInfos(this.viewTokens).then(res => {
+ // @ts-ignore
+ this.viewInfos = res.reverse();
+ });
+ }
+
+ removeAnalysis(token, type) {
+ if (type !== 'view') {
+ this.removeTask(token);
+ } else {
+ this.removeView(token);
+ }
+ }
+
removeTask(token) {
this.tokens = this.tokens.filter((item) => item !== token);
this.finishedTokens = this.finishedTokens.filter((item) => item !== token);
@@ -110,9 +126,10 @@ export class AnalysisService {
localStorage.setItem(this.tokensCookieKey, JSON.stringify(this.tokens));
}
- removeSelection(token) {
- this.selectionTokens = this.selectionTokens.filter((item) => item !== token);
- localStorage.setItem(this.selectionsCookieKey, JSON.stringify(this.selectionTokens));
+ removeView(token) {
+ this.viewTokens = this.viewTokens.filter((item) => item !== token);
+ localStorage.setItem(this.selectionsCookieKey, JSON.stringify(this.viewTokens));
+ this.setViewInfos();
}
removeAllTasks() {
@@ -123,7 +140,8 @@ export class AnalysisService {
}
removeAllSelections() {
- this.selectionTokens = [];
+ this.viewTokens = [];
+ this.viewInfos = [];
localStorage.removeItem(this.selectionsCookieKey);
}
@@ -195,6 +213,33 @@ export class AnalysisService {
}
}
+
+ // Adds first neighbors of selected nodes to selection
+ public addFirstNeighbors() {
+ const wrappers: Wrapper[] = [];
+ const mappedNodes = {};
+ this.networkHandler.activeNetwork.currentViewNodes.forEach((node) => {
+ if (node.drugstoneType === 'protein' && node.drugstoneId) {
+ mappedNodes[node.label] = node;
+ }
+ });
+ const selectedNodes = new Set(this.selectedItems.keys());
+ const firstNeighborNodes: Set<string> = new Set();
+ this.networkHandler.activeNetwork.currentViewEdges.forEach(edge => {
+ if (selectedNodes.has(edge.from)) {
+ firstNeighborNodes.add(edge.to);
+ }
+ if (selectedNodes.has(edge.to)) {
+ firstNeighborNodes.add(edge.from);
+ }
+ });
+
+ firstNeighborNodes.forEach(n => {
+ wrappers.push(getWrapperFromNode(mappedNodes[n]));
+ });
+ this.addItems(wrappers);
+ }
+
public addAllToSelection() {
const wrappers: Wrapper[] = [];
const unmappedNodes = [];
@@ -281,10 +326,9 @@ export class AnalysisService {
};
const resp = await this.http.post<any>(`${this.netex.getBackend()}save_selection`, payload).toPromise();
// @ts-ignore
- console.log(resp.token);
- // @ts-ignore
- this.selectionTokens.push(resp.token);
- localStorage.setItem(this.selectionsCookieKey, JSON.stringify(this.selectionTokens));
+ this.viewTokens.push(resp.token);
+ this.setViewInfos();
+ localStorage.setItem(this.selectionsCookieKey, JSON.stringify(this.viewTokens));
this.toast.setNewToast({
message: 'Analysis task started. This may take a while. ' +
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index f87da76ae1993f376147871372adae7a7cc330de..4d8364d7d0a1138340f5fb0ed67bb5cdf8e5d206 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -132,4 +132,9 @@ export class NetexControllerService {
*/
return this.http.get(`${this.getBackend()}get_license`).toPromise();
}
+
+ public async getViewInfos(tokens) {
+ return await this.http.post(`${this.getBackend()}view_infos`, {tokens}).toPromise();
+ }
+
}