diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 4336feab1cbf60c25dcd175fb52e808c33de8f11..078295d82561d31a13aee8d2750ef8ad74c1f094 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -36,7 +36,7 @@ import {downLoadFile, pieChartContextRenderer, removeDuplicateObjectsFromList} f
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';
-import { LoadingScreenService } from 'src/app/services/loading-screen/loading-screen.service';
+import {LoadingScreenService} from 'src/app/services/loading-screen/loading-screen.service';
declare var vis: any;
@@ -166,7 +166,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (this.task && this.task.info.done) {
this.loading = true;
- this.netex.getTaskResult(this.token).then(result => {
+ this.netex.getTaskResult(this.token).then(async result => {
this.drugstoneConfig.set_analysisConfig(result.parameters.config);
this.result = result;
if (this.result.parameters.target === 'drug') {
@@ -183,166 +183,176 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.networkHandler.activeNetwork.networkEl.nativeElement.innerHTML = '';
this.networkHandler.activeNetwork.networkInternal = null;
// Create
- this.createNetwork(this.result).then(nw => {
- 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;
- }
- this.drugstoneConfig.config.physicsOn = !isBig;
- this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
- this.networkHandler.activeNetwork.networkInternal.on('stabilizationIterationsDone', () => {
- if (!this.drugstoneConfig.config.physicsOn) {
- this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
- }
- this.networkHandler.updateAdjacentNodes();
- });
- this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
- this.tableDrugs.forEach((r) => {
- r.rawScore = r.score;
- });
- 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);
- }
- });
+ await this.createNetwork(this.result).then(nw => {
+ return new Promise<any>((resolve, reject) => {
- 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);
+ const nodes = nw.nodes;
+ const edges = nw.edges;
- this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
- this.showDetailsChange.emit(null);
- });
+ 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('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.once('stabilizationIterationsDone', async () => {
+ if (!this.drugstoneConfig.config.physicsOn || this.networkHandler.activeNetwork.isBig()) {
+ this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
}
- const wrapper = getWrapperFromNode(node);
+ 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;
+ });
+ 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.analysis.removeItems([wrapper]);
- this.analysis.getCount();
- } else {
- this.analysis.addItems([wrapper]);
- this.analysis.getCount();
+ this.tableSelectedProteins.push(r);
}
- }
- });
+ });
- this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
- 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;
+ 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);
- 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);
+ 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;
}
- if (!selected && found !== -1 && tableItem) {
- proteinSelection.splice(found, 1);
+ 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.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);
+ });
+
+ this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
+ const selectedNodes = this.nodeData.nodes.get(properties.nodes);
+ if (selectedNodes.length > 0) {
+ this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
+ } else {
+ this.showDetailsChange.emit(null);
+ }
+ });
- const proteinSelection = [];
- for (const item of items) {
- const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
- if (tableItem) {
- proteinSelection.push(tableItem);
+ 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.tableSelectedProteins = [...proteinSelection];
- }
+ });
+ this.emitVisibleItems(true);
});
- this.emitVisibleItems(true);
});
- this.loadingScreen.stateUpdate(false);
-
+ this.loadingScreen.stateUpdate(false);
});
}
}
@@ -433,7 +443,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.proteins = [];
this.effects = [];
- console.log(result.network)
const network = result.network;
network.nodes = [...new Set<string>(network.nodes)];
@@ -532,7 +541,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public toggleFullscreen() {
this.fullscreen = !this.fullscreen;
- this.loadingScreen.fullscreenUpdate(this.fullscreen)
+ this.loadingScreen.fullscreenUpdate(this.fullscreen);
}
public showEULA() {
diff --git a/src/app/components/network/network-menu-left/network-menu-left.component.html b/src/app/components/network/network-menu-left/network-menu-left.component.html
index 7e47a55ee25f95b1c7b3f7df714395b6603248fe..51d62e72757a392195f508862059e17c8c712b65 100644
--- a/src/app/components/network/network-menu-left/network-menu-left.component.html
+++ b/src/app/components/network/network-menu-left/network-menu-left.component.html
@@ -180,7 +180,7 @@
tooltip="Display adjacent drugs."
[value]="networkHandler.activeNetwork.adjacentDrugs"
(valueChange)="
- networkHandler.activeNetwork.updateAdjacentDrugs($event)
+ networkHandler.activeNetwork.updateAdjacentDrugs($event, true)
"
></app-toggle-inplace-reversed>
</div>
@@ -199,7 +199,7 @@
tooltip="Show disorders adjacent to all currently displayed proteins/genes."
[value]="networkHandler.activeNetwork.adjacentDisordersProtein"
(valueChange)="
- networkHandler.activeNetwork.updateAdjacentProteinDisorders($event)
+ networkHandler.activeNetwork.updateAdjacentProteinDisorders($event, true)
"
icon="head-side-mask"
></app-toggle-inplace-reversed>
@@ -219,7 +219,7 @@
[value]="networkHandler.activeNetwork.adjacentDisordersDrug"
[disabled]="!networkHandler.activeNetwork.hasDrugsLoaded()"
(valueChange)="
- networkHandler.activeNetwork.updateAdjacentDrugDisorders($event)
+ networkHandler.activeNetwork.updateAdjacentDrugDisorders($event, true)
"
icon="biohazard"
></app-toggle-inplace-reversed>
diff --git a/src/app/components/network/network-menu/network-menu.component.html b/src/app/components/network/network-menu/network-menu.component.html
index f0ed1fa9664c6d1ec798d0c1bb0ea972e77c29c2..4da926a76c46b5b28c91aef0686145fb9bf42074 100644
--- a/src/app/components/network/network-menu/network-menu.component.html
+++ b/src/app/components/network/network-menu/network-menu.component.html
@@ -177,7 +177,7 @@
tooltip="Display adjacent drugs."
[value]="networkHandler.activeNetwork.adjacentDrugs"
(valueChange)="
- networkHandler.activeNetwork.updateAdjacentDrugs($event)
+ networkHandler.activeNetwork.updateAdjacentDrugs($event, true)
"
></app-toggle-inplace>
</div>
@@ -196,7 +196,7 @@
tooltip="Show disorders adjacent to all currently displayed proteins/genes."
[value]="networkHandler.activeNetwork.adjacentDisordersProtein"
(valueChange)="
- networkHandler.activeNetwork.updateAdjacentProteinDisorders($event)
+ networkHandler.activeNetwork.updateAdjacentProteinDisorders($event, true)
"
icon="head-side-mask"
></app-toggle-inplace>
@@ -216,7 +216,7 @@
[value]="networkHandler.activeNetwork.adjacentDisordersDrug"
[disabled]="!networkHandler.activeNetwork.hasDrugsLoaded()"
(valueChange)="
- networkHandler.activeNetwork.updateAdjacentDrugDisorders($event)
+ networkHandler.activeNetwork.updateAdjacentDrugDisorders($event, true)
"
icon="biohazard"
></app-toggle-inplace>
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 4f4ab1d2b4268c86c67e95ce4d98cd8e6dc12285..cdcee9ae5ff828862459bb395868f63a316c76c4 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -99,6 +99,10 @@ export class NetworkComponent implements OnInit {
this.networkHandler.networks[this.networkType] = this;
}
+ isBig(): boolean {
+ return this.nodeData.nodes.length > 100 || this.nodeData.edges.length > 100;
+ }
+
setLoading(bool: boolean): void {
this.loading = bool;
}
@@ -129,90 +133,128 @@ export class NetworkComponent implements OnInit {
this.nodeData.nodes.add(toAdd);
}
- public updateAdjacentProteinDisorders(bool: boolean) {
- this.loadingScreen.stateUpdate(true);
- this.adjacentDisordersProtein = bool;
- if (this.adjacentDisordersProtein) {
- this.adjacentProteinDisorderList = [];
- this.adjacentProteinDisorderEdgesList = [];
- this.legendService.add_to_context('adjacentDisorders');
- this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'proteins', this.drugstoneConfig.config.associatedProteinDisorder, this.drugstoneConfig.config.licensedDatasets).subscribe(response => {
- const proteinMap = this.getProteinMap();
- const addedEdge = {};
- for (const interaction of response.edges) {
- const edge = mapCustomEdge({
- from: interaction.protein,
- to: interaction.disorder
- }, this.drugstoneConfig.config, this.drugstoneConfig);
- if (proteinMap[edge.from]) {
- proteinMap[edge.from].forEach(from => {
- if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
- return;
- }
- const e = JSON.parse(JSON.stringify(edge));
- e.from = from;
- e.to = edge.to;
- this.adjacentProteinDisorderEdgesList.push(e);
- if (!addedEdge[from]) {
- addedEdge[from] = [edge.to];
- } else {
- addedEdge[from].push(edge.to);
- }
+ public async updateAdjacentProteinDisorders(bool: boolean, stabl: boolean) {
+ return new Promise<boolean>((resolve, reject) => {
+ this.loadingScreen.stateUpdate(true);
+ this.adjacentDisordersProtein = bool;
+ if (this.adjacentDisordersProtein) {
+ this.adjacentProteinDisorderList = [];
+ this.adjacentProteinDisorderEdgesList = [];
+ this.legendService.add_to_context('adjacentDisorders');
+ this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'proteins', this.drugstoneConfig.config.associatedProteinDisorder, this.drugstoneConfig.config.licensedDatasets).then(response => {
+ const proteinMap = this.getProteinMap();
+ const addedEdge = {};
+ for (const interaction of response.edges) {
+ const edge = mapCustomEdge({
+ from: interaction.protein,
+ to: interaction.disorder
+ }, this.drugstoneConfig.config, this.drugstoneConfig);
+ if (proteinMap[edge.from]) {
+ proteinMap[edge.from].forEach(from => {
+ if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
+ return;
+ }
+ const e = JSON.parse(JSON.stringify(edge));
+ e.from = from;
+ e.to = edge.to;
+ this.adjacentProteinDisorderEdgesList.push(e);
+ if (!addedEdge[from]) {
+ addedEdge[from] = [edge.to];
+ } else {
+ addedEdge[from].push(edge.to);
+ }
+ });
+ }
+ }
+ for (const disorder of response.disorders) {
+ disorder.group = 'defaultDisorder';
+ disorder.id = disorder.drugstoneId;
+ this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
+ }
+ this.saveAddNodes(this.adjacentProteinDisorderList);
+ this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
+ this.updateQueryItems();
+ }).then(() => {
+ if (stabl) {
+ this.stabilize().then(() => {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
});
+ } else {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
}
+ });
+ } else {
+ if (!this.adjacentDisordersDrug) {
+ this.legendService.remove_from_context('adjacentDisorders');
}
- for (const disorder of response.disorders) {
- disorder.group = 'defaultDisorder';
- disorder.id = disorder.drugstoneId;
- this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
- }
- this.saveAddNodes(this.adjacentProteinDisorderList);
- this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
+ this.saveRemoveDisorders(this.adjacentProteinDisorderList);
+ this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
this.updateQueryItems();
- this.loadingScreen.stateUpdate(false);
- });
- } else {
- if (!this.adjacentDisordersDrug) {
- this.legendService.remove_from_context('adjacentDisorders');
+ if (stabl) {
+ this.stabilize().then(() => {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ });
+ } else {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ }
}
- this.saveRemoveDisorders(this.adjacentProteinDisorderList);
- this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
- this.updateQueryItems();
- this.loadingScreen.stateUpdate(false);
- }
+ });
}
- public updateAdjacentDrugDisorders(bool: boolean) {
- this.loadingScreen.stateUpdate(true);
- this.adjacentDisordersDrug = bool;
- if (this.adjacentDisordersDrug) {
- this.adjacentDrugDisorderList = [];
- this.adjacentDrugDisorderEdgesList = [];
- this.legendService.add_to_context('adjacentDisorders');
- this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'drugs', this.drugstoneConfig.config.indicationDrugDisorder, this.drugstoneConfig.config.licensedDatasets).subscribe(response => {
- for (const interaction of response.edges) {
- const edge = {from: interaction.drug, to: interaction.disorder};
- this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
- }
- for (const disorder of response.disorders) {
- disorder.group = 'defaultDisorder';
- disorder.id = disorder.drugstoneId;
- this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
+ public async updateAdjacentDrugDisorders(bool: boolean, stabl: boolean): Promise<any> {
+ return new Promise<boolean>((resolve, reject) => {
+ this.loadingScreen.stateUpdate(true);
+ this.adjacentDisordersDrug = bool;
+ if (this.adjacentDisordersDrug) {
+ this.adjacentDrugDisorderList = [];
+ this.adjacentDrugDisorderEdgesList = [];
+ this.legendService.add_to_context('adjacentDisorders');
+ this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'drugs', this.drugstoneConfig.config.indicationDrugDisorder, this.drugstoneConfig.config.licensedDatasets).then(response => {
+ for (const interaction of response.edges) {
+ const edge = {from: interaction.drug, to: interaction.disorder};
+ this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
+ }
+ for (const disorder of response.disorders) {
+ disorder.group = 'defaultDisorder';
+ disorder.id = disorder.drugstoneId;
+ this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
+ }
+ this.saveAddNodes(this.adjacentDrugDisorderList);
+ this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
+ this.updateQueryItems();
+ }).then(() => {
+ if (stabl) {
+ this.stabilize().then(() => {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ });
+ } else {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ }
+ });
+ } else {
+ if (!this.adjacentDisordersProtein) {
+ this.legendService.remove_from_context('adjacentDisorders');
}
- this.saveAddNodes(this.adjacentDrugDisorderList);
- this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
+ this.saveRemoveDisorders(this.adjacentDrugDisorderList);
+ this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
this.updateQueryItems();
- this.loadingScreen.stateUpdate(false);
- });
- } else {
- if (!this.adjacentDisordersProtein) {
- this.legendService.remove_from_context('adjacentDisorders');
+ if (stabl) {
+ this.stabilize().then(() => {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ });
+ } else {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ }
}
- this.saveRemoveDisorders(this.adjacentDrugDisorderList);
- this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
- this.updateQueryItems();
- this.loadingScreen.stateUpdate(false);
- }
+ });
}
public getProteinMap() {
@@ -241,69 +283,101 @@ export class NetworkComponent implements OnInit {
return proteinMap;
}
- public updateAdjacentDrugs(bool: boolean) {
- this.loadingScreen.stateUpdate(true);
- this.adjacentDrugs = bool;
- if (this.adjacentDrugs) {
- this.adjacentDrugList = [];
- this.adjacentDrugEdgesList = [];
- this.legendService.add_to_context('adjacentDrugs');
- const addedEdge = {};
- const proteinMap = this.getProteinMap();
- this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.drugstoneConfig.config.licensedDatasets, this.nodeData.nodes.get()).subscribe(response => {
- const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'drug').map(n => n.drugstoneId);
- for (const interaction of response.pdis) {
- const edge = mapCustomEdge({
- from: interaction.protein,
- to: interaction.drug
- }, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
-
- if (proteinMap[edge.from]) {
- proteinMap[edge.from].forEach(from => {
- if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
- return;
- }
- const e = JSON.parse(JSON.stringify(edge));
- e.from = from;
- e.to = edge.to;
- this.adjacentDrugEdgesList.push(e);
- if (!addedEdge[from]) {
- addedEdge[from] = [edge.to];
- } else {
- addedEdge[from].push(edge.to);
- }
- });
+ public stabilize(): Promise<any> {
+ return new Promise<boolean>((resolve, reject) => {
+ this.networkInternal.once('stabilizationIterationsDone', () => {
+ this.updatePhysicsEnabled(this.drugstoneConfig.config.physicsOn);
+ this.networkInternal.fit();
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ });
+ this.loadingScreen.stateUpdate(true);
+ this.networkInternal.stabilize(1000);
+ });
+ }
+
+ public updateAdjacentDrugs(bool: boolean, stabl: boolean): Promise<any> {
+ return new Promise<boolean>(async (resolve, reject) => {
+ this.loadingScreen.stateUpdate(true);
+ this.adjacentDrugs = bool;
+ if (this.adjacentDrugs) {
+ this.adjacentDrugList = [];
+ this.adjacentDrugEdgesList = [];
+ this.legendService.add_to_context('adjacentDrugs');
+ const addedEdge = {};
+ const proteinMap = this.getProteinMap();
+ this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.drugstoneConfig.config.licensedDatasets, this.nodeData.nodes.get()).then(response => {
+ const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'drug').map(n => n.drugstoneId);
+ for (const interaction of response.pdis) {
+ const edge = mapCustomEdge({
+ from: interaction.protein,
+ to: interaction.drug
+ }, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
+
+ if (proteinMap[edge.from]) {
+ proteinMap[edge.from].forEach(from => {
+ if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
+ return;
+ }
+ const e = JSON.parse(JSON.stringify(edge));
+ e.from = from;
+ e.to = edge.to;
+ this.adjacentDrugEdgesList.push(e);
+ if (!addedEdge[from]) {
+ addedEdge[from] = [edge.to];
+ } else {
+ addedEdge[from].push(edge.to);
+ }
+ });
+ }
}
- }
- for (const drug of response.drugs) {
- drug.group = 'foundDrug';
- drug.id = getDrugNodeId(drug);
- if (!existingDrugIDs.includes(drug.drugstoneId)) {
- existingDrugIDs.push(drug.drugstoneId);
- this.adjacentDrugList.push(mapCustomNode(drug, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
+ for (const drug of response.drugs) {
+ drug.group = 'foundDrug';
+ drug.id = getDrugNodeId(drug);
+ if (!existingDrugIDs.includes(drug.drugstoneId)) {
+ existingDrugIDs.push(drug.drugstoneId);
+ this.adjacentDrugList.push(mapCustomNode(drug, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
+ }
+ }
+ this.nodeData.nodes.add(this.adjacentDrugList);
+ this.nodeData.edges.add(this.adjacentDrugEdgesList);
+ this.updateQueryItems();
+ }).then(() => {
+ if (stabl) {
+ this.stabilize().then(() => {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ });
+ } else {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
}
+ });
+ } else {
+ // remove adjacent drugs, make sure that also drug associated disorders are removed
+ if (this.adjacentDisordersDrug) {
+ await this.updateAdjacentDrugDisorders(false, true);
}
- this.nodeData.nodes.add(this.adjacentDrugList);
- this.nodeData.edges.add(this.adjacentDrugEdgesList);
+ this.legendService.remove_from_context('adjacentDrugs');
+ // if (!this.adjacentDisordersProtein)
+ // this.legendService.remove_from_context('adjacentDisorders')
+ this.nodeData.nodes.remove(this.adjacentDrugList);
+ this.nodeData.edges.remove(this.adjacentDrugEdgesList);
+ this.adjacentDrugList = [];
+ this.adjacentDrugEdgesList = [];
+
this.updateQueryItems();
- this.loadingScreen.stateUpdate(false);
- });
- } else {
- // remove adjacent drugs, make sure that also drug associated disorders are removed
- if (this.adjacentDisordersDrug) {
- this.updateAdjacentDrugDisorders(false);
+ if (stabl) {
+ this.stabilize().then(() => {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ });
+ } else {
+ this.loadingScreen.stateUpdate(false);
+ resolve(true);
+ }
}
- this.legendService.remove_from_context('adjacentDrugs');
- // if (!this.adjacentDisordersProtein)
- // this.legendService.remove_from_context('adjacentDisorders')
- this.nodeData.nodes.remove(this.adjacentDrugList);
- this.nodeData.edges.remove(this.adjacentDrugEdgesList);
- this.adjacentDrugList = [];
- this.adjacentDrugEdgesList = [];
-
- this.updateQueryItems();
- this.loadingScreen.stateUpdate(false);
- }
+ });
}
public saveRemoveDisorders(nodeList: Node[]) {
@@ -337,10 +411,10 @@ export class NetworkComponent implements OnInit {
}
public updatePhysicsEnabled(bool: boolean) {
- this.drugstoneConfig.config.physicsOn = bool;
+ // this.drugstoneConfig.config.physicsOn = bool;
this.networkInternal.setOptions({
physics: {
- enabled: this.drugstoneConfig.config.physicsOn,
+ enabled: bool,
stabilization: {
enabled: false,
},
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 54781ccfdd3db617bfae696a07258bb38769dd65..7b13ff0cbd538954f5fc2348c99547222bc6c78d 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -260,12 +260,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (this.drugstoneConfig.config.physicsOn) {
this.networkHandler.activeNetwork.updatePhysicsEnabled(true);
}
- this.networkHandler.updateAdjacentNodes().catch(e => {
- console.log('also error');
+ this.networkHandler.updateAdjacentNodes(!this.networkHandler.activeNetwork.isBig()).then((updated) => {
+ }).catch(e => {
console.error(e);
});
}).catch(e => {
- console.log('Error');
console.error(e);
});
}
@@ -358,7 +357,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
- this.networkHandler.activeNetwork.networkInternal.on('stabilizationIterationsDone', () => {
+ this.networkHandler.activeNetwork.networkInternal.once('stabilizationIterationsDone', () => {
if (!this.drugstoneConfig.config.physicsOn) {
this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
}
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index 8aa281b9a8e343dda0afb29fdc41602fb854cadb..1b8f3a0f1d0eb5ae6216edbe4c275af4081966f3 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -72,17 +72,17 @@ export class NetexControllerService {
return this.http.post(`${this.getBackend()}tissue_expression/`, payload);
}
- public adjacentDisorders(nodes: Node[], nodeType: string, dataset: string, licenced: boolean): Observable<any> {
+ public adjacentDisorders(nodes: Node[], nodeType: string, dataset: string, licenced: boolean): Promise<any> {
const params = {dataset: dataset, licenced: licenced};
if (nodeType === 'proteins') {
params['proteins'] = nodes.filter((node: Node) => node.drugstoneId && node.drugstoneType === 'protein').flatMap((node: Node) => node.drugstoneId).map(id => id.slice(1));
} else if (nodeType === 'drugs') {
params['drugs'] = nodes.map((node: Node) => node.drugId && node.drugstoneType === 'drug' ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
}
- return this.http.post<any>(`${this.getBackend()}adjacent_disorders/`, params);
+ return this.http.post<any>(`${this.getBackend()}adjacent_disorders/`, params).toPromise();
}
- public adjacentDrugs(pdiDataset: InteractionDrugProteinDB, licenced: boolean, nodes: Node[]): Observable<any> {
+ public adjacentDrugs(pdiDataset: InteractionDrugProteinDB, licenced: boolean, nodes: Node[]): Promise<any> {
/**
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
@@ -93,7 +93,7 @@ export class NetexControllerService {
proteins: genesBackendIds,
licenced: licenced
};
- return this.http.post<any>(`${this.getBackend()}adjacent_drugs/`, params);
+ return this.http.post<any>(`${this.getBackend()}adjacent_drugs/`, params).toPromise();
}
public graphExport(graph_data: { edges: EdgeType[], nodes: Node[] }) {
diff --git a/src/app/services/network-handler/network-handler.service.ts b/src/app/services/network-handler/network-handler.service.ts
index e0f862365d3c49414f0abda19e452b58ca3825d3..981a50bfa2054e94652b6f78e8527c201879e1c4 100644
--- a/src/app/services/network-handler/network-handler.service.ts
+++ b/src/app/services/network-handler/network-handler.service.ts
@@ -35,21 +35,30 @@ export class NetworkHandlerService {
return this.change.asObservable();
}
- async updateAdjacentNodes(): Promise<any> {
+
+ async updateAdjacentNodes(layout: boolean): Promise<any> {
return new Promise<any>(async (resolve, reject) => {
+ let updated = false;
if (this.drugstoneConfig.config.activateNetworkMenuButtonAdjacentDrugs) {
this.activeNetwork.adjacentDrugs = true;
- await this.activeNetwork.updateAdjacentDrugs(true);
+ updated = true;
+ await this.activeNetwork.updateAdjacentDrugs(true, false);
}
if (this.drugstoneConfig.config.activateNetworkMenuButtonAdjacentDisorders) {
this.activeNetwork.adjacentDisordersProtein = true;
- await this.activeNetwork.updateAdjacentProteinDisorders(true);
+ updated = true;
+ await this.activeNetwork.updateAdjacentProteinDisorders(true, false);
}
if (this.drugstoneConfig.config.activateNetworkMenuButtonAdjacentDisordersDrugs) {
this.activeNetwork.adjacentDisordersDrug = true;
- await this.activeNetwork.updateAdjacentDrugDisorders(true);
+ updated = true;
+ await this.activeNetwork.updateAdjacentDrugDisorders(true, false);
+ }
+ resolve(updated);
+ }).then((updated) => {
+ if (layout) {
+ return this.activeNetwork.stabilize();
}
- resolve(true);
});
}
}
diff --git a/src/index.html b/src/index.html
index 238f900747275bf56985f1e7ae90a5f2732f6537..1f7d2bca1343049c9dce429e78b756d0f9a009de 100644
--- a/src/index.html
+++ b/src/index.html
@@ -113,7 +113,7 @@ menu<br>
<div style="max-width: 80vw; width: 1276px; height: 500px">
<drugst-one id="netexp1"
- config="{}"
+ config="{'activateNetworkMenuButtonAdjacentDisorders':false,'activateNetworkMenuButtonAdjacentDrugs':true, 'activateNetworkMenuButtonAdjacentDisordersDrugs': true, 'licensedDatasets':true}"
groups='{"nodeGroups":{"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"default":{"color":"#000000","groupName":"default edge"}}}'
network='{"nodes":[{"id":"CFTR","group":"gene","label":"CFTR"},{"id":"TGFB1","group":"gene","label":"TGFB1"},{"id":"TNFRSF1A","group":"gene","label":"TNFRSF1A"},{"id":"FCGR2A","group":"gene","label":"FCGR2A"},{"id":"ENG","group":"gene","label":"ENG"},{"id":"DCTN4","group":"gene","label":"DCTN4"},{"id":"CLCA4","group":"gene","label":"CLCA4"},{"id":"STX1A","group":"gene","label":"STX1A"},{"id":"SCNN1G","group":"gene","label":"SCNN1G"},{"id":"SCNN1A","group":"gene","label":"SCNN1A"},{"id":"SCNN1B","group":"gene","label":"SCNN1B"}],"edges":[{"from":"DCTN4","to":"CFTR"},{"from":"STX1A","to":"SCNN1B","group":"default"},{"from":"SCNN1A","to":"SCNN1G","group":"default"},{"from":"SCNN1B","to":"SCNN1G","group":"default"}]}'>
></drugst-one>