diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index a8c9d3f90761ef5f543f191471e74b12af0c2f5a..59584070065046c76adedb4adc89366f98a1c843 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -197,12 +197,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
- this.tableDrugs = nodes.filter( e => e.netexId && e.netexId.startsWith('d'));
+ this.tableDrugs = nodes.filter( e => e.drugstoneId && e.drugstoneId.startsWith('d'));
this.tableDrugs.forEach((r) => {
r.rawScore = r.score;
});
- this.tableProteins = nodes.filter( e => e.netexId && e.netexId.startsWith('p'));
+ this.tableProteins = nodes.filter( e => e.drugstoneId && e.drugstoneId.startsWith('p'));
this.tableSelectedProteins = [];
this.tableProteins.forEach((r) => {
r.rawScore = r.score;
@@ -233,7 +233,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- if (node.nodeType === 'drug' || node.netexId === undefined || !node.netexId.startsWith('p')) {
+ if (node.nodeType === 'drug' || node.drugstoneId === undefined || !node.drugstoneId.startsWith('p')) {
return;
}
const wrapper = getWrapperFromNode(node);
@@ -306,7 +306,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.nodeData.nodes.forEach((node) => {
// let drugType;
// let drugInTrial;
- // if (node.netexId && node.netexId.startsWith('d')) {
+ // if (node.drugstoneId && node.drugstoneId.startsWith('d')) {
// drugType = node.status;
// drugInTrial = node.inTrial;
// }
@@ -428,7 +428,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// }
// for (const disorder of response.disorders) {
// disorder.group = 'defaultDisorder';
- // disorder.id = disorder.netexId;
+ // disorder.id = disorder.drugstoneId;
// this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.myConfig))
// }
// this.saveAddNodes(this.adjacentProteinDisorderList);
@@ -456,7 +456,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// }
// for (const disorder of response.disorders) {
// disorder.group = 'defaultDisorder';
- // disorder.id = disorder.netexId;
+ // disorder.id = disorder.drugstoneId;
// this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.myConfig));
// }
// this.saveAddNodes(this.adjacentDrugDisorderList);
@@ -495,9 +495,9 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
public inferNodeGroup(wrapper: Wrapper): string {
if (wrapper.data.group !== undefined) {
return wrapper.data.group;
- } else if (wrapper.data.netexId !== undefined && wrapper.data.netexId.startsWith('d')) {
+ } else if (wrapper.data.drugstoneId !== undefined && wrapper.data.drugstoneId.startsWith('d')) {
return 'drug';
- } else if (wrapper.data.netexId !== undefined && wrapper.data.netexId.startsWith('p')) {
+ } else if (wrapper.data.drugstoneId !== undefined && wrapper.data.drugstoneId.startsWith('p')) {
return 'protein';
}
}
@@ -554,14 +554,14 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// convert id to netex Id if exists
const nodeDetails = details[node];
- nodeDetails.id = nodeDetails.id ? nodeDetails.id : nodeDetails.netexId;
- if (nodeDetails.netexId && nodeDetails.netexId.startsWith('p')) {
+ nodeDetails.id = nodeDetails.id ? nodeDetails.id : nodeDetails.drugstoneId;
+ if (nodeDetails.drugstoneId && nodeDetails.drugstoneId.startsWith('p')) {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'foundNode';
nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
this.proteins.push(nodeDetails);
- } else if (nodeDetails.netexId && nodeDetails.netexId.startsWith('d')) {
+ } else if (nodeDetails.drugstoneId && nodeDetails.drugstoneId.startsWith('d')) {
// node is drug, was found during analysis
nodeDetails.type = 'Drug';
nodeDetails.group = 'foundDrug';
@@ -586,7 +586,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// hasDrugsLoaded(): boolean {
// if (this.nodeData == null || this.nodeData.nodes == null)
// return false;
- // return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.netexId.startsWith('dr')).length > 0;
+ // return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.drugstoneId.startsWith('dr')).length > 0;
// }
// public updateAdjacentDrugs(bool: boolean) {
@@ -684,7 +684,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// this.selectedTissue = null;
// const updatedNodes = [];
// for (const item of this.proteins) {
- // if (item.netexId === undefined) {
+ // if (item.drugstoneId === undefined) {
// // nodes that are not mapped to backend remain untouched
// continue;
// }
@@ -718,7 +718,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// // filter out non-proteins, e.g. drugs
// const proteinNodes = [];
// this.nodeData.nodes.forEach(element => {
- // if (element.id.startsWith('p') && element.netexId !== undefined) {
+ // if (element.id.startsWith('p') && element.drugstoneId !== undefined) {
// proteinNodes.push(element);
// }
// });
@@ -728,17 +728,17 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// // mapping from netex IDs to network IDs, TODO check if this step is necessary
// const networkIdMappping = {}
// this.nodeData.nodes.forEach(element => {
- // networkIdMappping[element.netexId] = element.id
+ // networkIdMappping[element.drugstoneId] = element.id
// });
// const maxExpr = Math.max(...Object.values(this.expressionMap));
- // for (const [netexId, expressionlvl] of Object.entries(this.expressionMap)) {
- // const networkId = networkIdMappping[netexId]
+ // for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
+ // const networkId = networkIdMappping[drugstoneId]
// const node = this.nodeData.nodes.get(networkId);
// if (node === null) {
// continue;
// }
// const wrapper = getWrapperFromNode(node)
- // this.gradientMap[netexId] = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
+ // this.gradientMap[drugstoneId] = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
// const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([networkId]);
// node.x = pos[networkId].x;
// node.y = pos[networkId].y;
@@ -749,7 +749,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// this.myConfig,
// isSeed,
// this.analysis.inSelection(wrapper),
- // this.gradientMap[netexId]));
+ // this.gradientMap[drugstoneId]));
// node.shape = 'custom';
// node.ctxRenderer = pieChartContextRenderer;
// updatedNodes.push(node);
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 744580ef4303ca5e218da8271e9b1c894b7d0d49..dc8f22f3986e645db3a150e1550e54ca41cedc59 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -101,7 +101,7 @@
</div>
<app-toggle
- *ngIf="wrapper.data.netexId && wrapper.data.netexId.startsWith('p')"
+ *ngIf="wrapper.data.drugstoneId && wrapper.data.drugstoneId.startsWith('p')"
[value]="analysis.inSelection(wrapper)"
(valueChange)="
$event ? analysis.addItems([wrapper]) : analysis.removeItems([wrapper])
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 c251083c4e2e7f682a275259049c664f3ecbee94..16d614924e923c166611266c9b961ea70be4a8e2 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
@@ -151,8 +151,8 @@
(click)="networkHandler.activeNetwork.selectTissue(tissue)"
[class.is-active]="
networkHandler.activeNetwork.selectedTissue &&
- tissue.netexId ===
- networkHandler.activeNetwork.selectedTissue.netexId
+ tissue.drugstoneId ===
+ networkHandler.activeNetwork.selectedTissue.drugstoneId
"
class="dropdown-item"
>
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 5fe50c46f26a47fe6853b1c19cdb4eeaf961d99f..4a80fc1d0c0ad392ad463c891dfe58bfe9608707 100644
--- a/src/app/components/network/network-menu/network-menu.component.html
+++ b/src/app/components/network/network-menu/network-menu.component.html
@@ -38,194 +38,203 @@
<app-center-view></app-center-view>
</div>
</div>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="drugstoneConfig.config.showNetworkMenuButtonScreenshot"
- >
- <div class="network-footer-toolbar-element">
- <button
- (click)="networkHandler.activeNetwork.toImage()"
- class="button is-primary is-rounded has-tooltip"
- pTooltip="Take a screenshot of the current network."
- [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
- tooltipPosition="left"
- [ngClass]="{
- 'is-small': drugstoneConfig.smallStyle
- }"
- >
- <span class="icon">
- <i class="fas fa-camera" aria-hidden="true"></i>
- </span>
- <span
- [ngClass]="{
- 'text-normal': drugstoneConfig.smallStyle
- }"
- >Screenshot</span
- >
- </button>
- </div>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="drugstoneConfig.config.showNetworkMenuButtonExportGraphml"
- >
- <div class="network-footer-toolbar-element">
- <app-download-button
- [nodeData]="networkHandler.activeNetwork.nodeData"
- [buttonId]="'explorer-download'"
- ></app-download-button>
- </div>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="drugstoneConfig.config.showNetworkMenuButtonExpression"
- >
<div
- class="dropdown network-footer-toolbar-element"
- [class.is-active]="networkHandler.activeNetwork.expressionExpanded"
+ class="row is-full m-1"
+ *ngIf="drugstoneConfig.config.showNetworkMenuButtonScreenshot"
>
- <div class="dropdown-trigger">
+ <div class="network-footer-toolbar-element">
<button
- (click)="
- networkHandler.activeNetwork.expressionExpanded =
- !networkHandler.activeNetwork.expressionExpanded
- "
- class="button is-rounded is-primary"
- [class.is-outlined]="!networkHandler.activeNetwork.selectedTissue"
- aria-haspopup="true"
- aria-controls="dropdown-menu"
- pTooltip="Tissue expression data is provided by the GTEx project."
+ (click)="networkHandler.activeNetwork.toImage()"
+ class="button is-primary is-rounded has-tooltip"
+ pTooltip="Take a screenshot of the current network."
[tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
tooltipPosition="left"
[ngClass]="{
'is-small': drugstoneConfig.smallStyle
}"
>
- <span class="icon is-small">
- <i class="fas fa-child"></i>
+ <span class="icon">
+ <i class="fas fa-camera" aria-hidden="true"></i>
</span>
<span
- *ngIf="!networkHandler.activeNetwork.selectedTissue"
[ngClass]="{
- 'text-small': drugstoneConfig.smallStyle
+ 'text-normal': drugstoneConfig.smallStyle
}"
- >Tissue</span
+ >Screenshot</span
>
- <span
- *ngIf="networkHandler.activeNetwork.selectedTissue"
+ </button>
+ </div>
+ </div>
+ <div
+ class="row is-full m-1"
+ *ngIf="drugstoneConfig.config.showNetworkMenuButtonExportGraphml"
+ >
+ <div class="network-footer-toolbar-element">
+ <app-download-button
+ [nodeData]="networkHandler.activeNetwork.nodeData"
+ [buttonId]="'explorer-download'"
+ ></app-download-button>
+ </div>
+ </div>
+ <div
+ class="row is-full m-1"
+ *ngIf="drugstoneConfig.config.showNetworkMenuButtonExpression"
+ >
+ <div
+ class="dropdown network-footer-toolbar-element"
+ [class.is-active]="networkHandler.activeNetwork.expressionExpanded"
+ >
+ <div class="dropdown-trigger">
+ <button
+ (click)="
+ networkHandler.activeNetwork.expressionExpanded =
+ !networkHandler.activeNetwork.expressionExpanded
+ "
+ class="button is-rounded is-primary"
+ [class.is-outlined]="!networkHandler.activeNetwork.selectedTissue"
+ aria-haspopup="true"
+ aria-controls="dropdown-menu"
+ pTooltip="Tissue expression data is provided by the GTEx project."
+ [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"
+ tooltipPosition="left"
[ngClass]="{
- 'text-small': drugstoneConfig.smallStyle
+ 'is-small': drugstoneConfig.smallStyle
}"
- >{{ networkHandler.activeNetwork.selectedTissue.name }}</span
- >
- <span
- *ngIf="networkHandler.activeNetwork.expressionExpanded"
- class="icon is-small"
- >
- <i class="fas fa-angle-down" aria-hidden="true"></i>
- </span>
- <span
- *ngIf="!networkHandler.activeNetwork.expressionExpanded"
- class="icon is-small"
>
- <i class="fas fa-angle-left" aria-hidden="true"></i>
- </span>
- </button>
- </div>
- <div class="dropdown-menu" id="dropdown-menu" role="menu">
- <div class="dropdown-content tissue-dropdown">
- <div class="scroll-area">
- <a
- (click)="networkHandler.activeNetwork.selectTissue(null)"
- [class.is-active]="!networkHandler.activeNetwork.selectedTissue"
- class="dropdown-item"
+ <span class="icon is-small">
+ <i class="fas fa-child"></i>
+ </span>
+ <span
+ *ngIf="!networkHandler.activeNetwork.selectedTissue"
+ [ngClass]="{
+ 'text-small': drugstoneConfig.smallStyle
+ }"
+ >Tissue</span
+ >
+ <span
+ *ngIf="networkHandler.activeNetwork.selectedTissue"
+ [ngClass]="{
+ 'text-small': drugstoneConfig.smallStyle
+ }"
+ >{{ networkHandler.activeNetwork.selectedTissue.name }}</span
+ >
+ <span
+ *ngIf="networkHandler.activeNetwork.expressionExpanded"
+ class="icon is-small"
>
- None
- </a>
- <a
- *ngFor="
- let tissue of networkHandler.activeNetwork.analysis.getTissues()
- "
- (click)="networkHandler.activeNetwork.selectTissue(tissue)"
- [class.is-active]="
- networkHandler.activeNetwork.selectedTissue &&
- tissue.netexId ===
- networkHandler.activeNetwork.selectedTissue.netexId
- "
- class="dropdown-item"
+ <i class="fas fa-angle-down" aria-hidden="true"></i>
+ </span>
+ <span
+ *ngIf="!networkHandler.activeNetwork.expressionExpanded"
+ class="icon is-small"
>
- {{ tissue.name }}
- </a>
+ <i class="fas fa-angle-left" aria-hidden="true"></i>
+ </span>
+ </button>
+ </div>
+ <div class="dropdown-menu" id="dropdown-menu" role="menu">
+ <div class="dropdown-content tissue-dropdown">
+ <div class="scroll-area">
+ <a
+ (click)="networkHandler.activeNetwork.selectTissue(null)"
+ [class.is-active]="
+ !networkHandler.activeNetwork.selectedTissue
+ "
+ class="dropdown-item"
+ >
+ None
+ </a>
+ <a
+ *ngFor="
+ let tissue of networkHandler.activeNetwork.analysis.getTissues()
+ "
+ (click)="networkHandler.activeNetwork.selectTissue(tissue)"
+ [class.is-active]="
+ networkHandler.activeNetwork.selectedTissue &&
+ tissue.drugstoneId ===
+ networkHandler.activeNetwork.selectedTissue.drugstoneId
+ "
+ class="dropdown-item"
+ >
+ {{ tissue.name }}
+ </a>
+ </div>
</div>
</div>
</div>
</div>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="drugstoneConfig.config.showNetworkMenuButtonAdjacentDrugs"
- >
- <app-toggle-inplace
- class="network-footer-toolbar-element"
- text="{{ drugstoneConfig.config.networkMenuButtonAdjacentDrugsLabel }}"
- icon="fas fa-capsules"
- tooltip="Display adjacent drugs."
- [value]="networkHandler.activeNetwork.adjacentDrugs"
- (valueChange)="networkHandler.activeNetwork.updateAdjacentDrugs($event)"
- ></app-toggle-inplace>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="
- drugstoneConfig.config.showNetworkMenuButtonAdjacentDisordersProteins
- "
- >
- <app-toggle-inplace
- class="network-footer-toolbar-element"
- text="{{
- drugstoneConfig.config.networkMenuButtonAdjacentDisordersProteinsLabel
- }}"
- tooltip="Show disorders adjacent to all currently displayed proteins/genes."
- [value]="networkHandler.activeNetwork.adjacentDisordersProtein"
- (valueChange)="
- networkHandler.activeNetwork.updateAdjacentProteinDisorders($event)
- "
- icon="fas fa-head-side-mask"
- ></app-toggle-inplace>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="drugstoneConfig.config.showNetworkMenuButtonAdjacentDisordersDrugs"
- >
- <app-toggle-inplace
- class="network-footer-toolbar-element"
- text="{{
- drugstoneConfig.config.networkMenuButtonAdjacentDisordersDrugsLabel
- }}"
- tooltip="Show disorders adjacent to all currently displayed drugs."
- [value]="networkHandler.activeNetwork.adjacentDisordersDrug"
- [disabled]="!networkHandler.activeNetwork.hasDrugsLoaded()"
- (valueChange)="
- networkHandler.activeNetwork.updateAdjacentDrugDisorders($event)
+ <div
+ class="row is-full m-1"
+ *ngIf="drugstoneConfig.config.showNetworkMenuButtonAdjacentDrugs"
+ >
+ <app-toggle-inplace
+ class="network-footer-toolbar-element"
+ text="{{
+ drugstoneConfig.config.networkMenuButtonAdjacentDrugsLabel
+ }}"
+ icon="fas fa-capsules"
+ tooltip="Display adjacent drugs."
+ [value]="networkHandler.activeNetwork.adjacentDrugs"
+ (valueChange)="
+ networkHandler.activeNetwork.updateAdjacentDrugs($event)
+ "
+ ></app-toggle-inplace>
+ </div>
+ <div
+ class="row is-full m-1"
+ *ngIf="
+ drugstoneConfig.config.showNetworkMenuButtonAdjacentDisordersProteins
"
- icon="fas fa-biohazard"
- ></app-toggle-inplace>
- </div>
- <div
- class="row is-full m-1"
- *ngIf="drugstoneConfig.config.showNetworkMenuButtonAnimation"
- >
- <app-toggle-inplace
- class="network-footer-toolbar-element"
- text="{{ drugstoneConfig.config.networkMenuButtonAnimationLabel }}"
- tooltip="Toggle the network animation."
- [value]="drugstoneConfig.config.physicsOn"
- (valueChange)="
- networkHandler.activeNetwork.updatePhysicsEnabled($event)
+ >
+ <app-toggle-inplace
+ class="network-footer-toolbar-element"
+ text="{{
+ drugstoneConfig.config
+ .networkMenuButtonAdjacentDisordersProteinsLabel
+ }}"
+ tooltip="Show disorders adjacent to all currently displayed proteins/genes."
+ [value]="networkHandler.activeNetwork.adjacentDisordersProtein"
+ (valueChange)="
+ networkHandler.activeNetwork.updateAdjacentProteinDisorders($event)
+ "
+ icon="fas fa-head-side-mask"
+ ></app-toggle-inplace>
+ </div>
+ <div
+ class="row is-full m-1"
+ *ngIf="
+ drugstoneConfig.config.showNetworkMenuButtonAdjacentDisordersDrugs
"
- icon="fas fa-bullseye"
- ></app-toggle-inplace>
+ >
+ <app-toggle-inplace
+ class="network-footer-toolbar-element"
+ text="{{
+ drugstoneConfig.config.networkMenuButtonAdjacentDisordersDrugsLabel
+ }}"
+ tooltip="Show disorders adjacent to all currently displayed drugs."
+ [value]="networkHandler.activeNetwork.adjacentDisordersDrug"
+ [disabled]="!networkHandler.activeNetwork.hasDrugsLoaded()"
+ (valueChange)="
+ networkHandler.activeNetwork.updateAdjacentDrugDisorders($event)
+ "
+ icon="fas fa-biohazard"
+ ></app-toggle-inplace>
+ </div>
+ <div
+ class="row is-full m-1"
+ *ngIf="drugstoneConfig.config.showNetworkMenuButtonAnimation"
+ >
+ <app-toggle-inplace
+ class="network-footer-toolbar-element"
+ text="{{ drugstoneConfig.config.networkMenuButtonAnimationLabel }}"
+ tooltip="Toggle the network animation."
+ [value]="drugstoneConfig.config.physicsOn"
+ (valueChange)="
+ networkHandler.activeNetwork.updatePhysicsEnabled($event)
+ "
+ icon="fas fa-bullseye"
+ ></app-toggle-inplace>
+ </div>
</div>
</div>
</div>
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 2265d5c9fa641a7e9261acd6fa29ea57225f8d4b..21760f0e010a713a88e268bcebe56b7c1869cdb8 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -73,7 +73,7 @@ export class NetworkComponent implements OnInit {
public highlightSeeds = false;
public seedMap: NodeAttributeMap = {};
- // keys are node netexIds
+ // keys are node drugstoneIds
public expressionMap: NodeAttributeMap = {};
public gradientMap: NodeAttributeMap = {};
@@ -118,7 +118,7 @@ export class NetworkComponent implements OnInit {
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
- disorder.id = disorder.netexId;
+ disorder.id = disorder.drugstoneId;
this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.config))
}
this.saveAddNodes(this.adjacentProteinDisorderList);
@@ -146,7 +146,7 @@ export class NetworkComponent implements OnInit {
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
- disorder.id = disorder.netexId;
+ disorder.id = disorder.drugstoneId;
this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.drugstoneConfig.config));
}
this.saveAddNodes(this.adjacentDrugDisorderList);
@@ -270,7 +270,7 @@ export class NetworkComponent implements OnInit {
const updatedNodes = [];
// for (const item of this.proteins) {
for (const item of this.currentViewProteins) {
- if (item.netexId === undefined) {
+ if (item.drugstoneId === undefined) {
// nodes that are not mapped to backend remain untouched
continue;
}
@@ -302,7 +302,7 @@ export class NetworkComponent implements OnInit {
// filter out non-proteins, e.g. drugs
const proteinNodes = [];
this.nodeData.nodes.forEach(element => {
- if (element.id.startsWith('p') && element.netexId !== undefined) {
+ if (element.id.startsWith('p') && element.drugstoneId !== undefined) {
proteinNodes.push(element);
}
});
@@ -312,11 +312,11 @@ export class NetworkComponent implements OnInit {
// mapping from netex IDs to network IDs, TODO check if this step is necessary
const networkIdMappping = {}
this.nodeData.nodes.forEach(element => {
- networkIdMappping[element.netexId] = element.id
+ networkIdMappping[element.drugstoneId] = element.id
});
const maxExpr = Math.max(...Object.values(this.expressionMap));
- for (const [netexId, expressionlvl] of Object.entries(this.expressionMap)) {
- const networkId = networkIdMappping[netexId]
+ for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
+ const networkId = networkIdMappping[drugstoneId]
const node = this.nodeData.nodes.get(networkId);
if (node === null) {
continue;
@@ -348,7 +348,7 @@ export class NetworkComponent implements OnInit {
public hasDrugsLoaded(): boolean {
if (this.nodeData == null || this.nodeData.nodes == null)
return false;
- return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.netexId.startsWith('dr')).length > 0;
+ return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.drugstoneId.startsWith('dr')).length > 0;
}
public setLegendContext() {
@@ -369,13 +369,13 @@ export class NetworkComponent implements OnInit {
/**
* To highlight the seeds in the analysis network, not used in the browser network
- * @param bool
+ * @param bool
*/
public updateHighlightSeeds(bool: boolean) {
this.highlightSeeds = bool;
const updatedNodes = [];
for (const item of this.currentViewProteins) {
- if (item.netexId === undefined) {
+ if (item.drugstoneId === undefined) {
// nodes that are not mapped to backend remain untouched
continue;
}
diff --git a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
index 634873da5fb26e633b2b59b31770da6377942e22..c1e8a59ceb88228e8a45a96243114f24b659b20a 100644
--- a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
+++ b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
@@ -39,7 +39,7 @@ export class AddExpressedProteinsComponent implements OnChanges {
public async addProteins() {
this.loading = true;
const result = await this.http.post<any>(`${environment.backend}query_tissue_proteins/`,
- {tissueId: this.selectedTissue.netexId, threshold: this.threshold}).toPromise();
+ {tissueId: this.selectedTissue.drugstoneId, threshold: this.threshold}).toPromise();
const items = [];
for (const detail of result) {
items.push(getWrapperFromNode(detail));
@@ -59,7 +59,7 @@ export class AddExpressedProteinsComponent implements OnChanges {
if (!this.currentViewProteins || this.expressionMap === undefined) {
return;
}
- this.proteins = this.currentViewProteins.filter(p => this.expressionMap[p.netexId] >= threshold);
+ this.proteins = this.currentViewProteins.filter(p => this.expressionMap[p.drugstoneId] >= threshold);
}
public close() {
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 38ef3ecd0f03eec458368d5dba22a0e63ce6937e..bf4637eb5d15325dc9eeda8800f7053777777491 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -104,8 +104,8 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
}
public async startTask() {
- // all nodes in selection have netexId, hence exist in the backend
- const seeds = this.analysis.getSelection().map((item) => item.data.netexId)
+ // all nodes in selection have drugstoneId, hence exist in the backend
+ const seeds = this.analysis.getSelection().map((item) => item.data.drugstoneId)
const seedsFiltered = seeds.filter(function (el) {
return el != null;
});
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index d84da4c1ec071f23d59027395c383b74a202106f..59daa8bf3c2288312d232a032a9c018e5d70177c 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -5,7 +5,7 @@ export interface Node {
symbol: string;
id: string;
type: string;
- netexId?: string;
+ drugstoneId?: string;
drugId?:string;
uniprotAc?: string;
ensg?: Array<string>;
@@ -28,7 +28,7 @@ export interface Node {
}
export interface Tissue {
- netexId: number;
+ drugstoneId: number;
name: string;
}
@@ -42,7 +42,7 @@ export type NetworkType = 'explorer' | 'analysis'
export type LegendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders' | 'adjacentDrugsAndDisorders';
-/// netexId to expressionlvl
+/// drugstoneId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
export interface NetexInteraction {
@@ -125,21 +125,21 @@ export function getDrugNodeId(drug: Drug) {
/**
* Returns backend_id of Drug object
*/
- return drug.netexId
+ return drug.drugstoneId
}
// export function getDisorderNodeId(disorder: Disorder) {
// /**
// * Returns backend_id of Drug object
// */
-// return disorder.netexId
+// return disorder.drugstoneId
export function getNodeId(node: Node) {
/**
* Returns backend_id of Gene object
*/
- // if ('netexId' in node) {
- // return node['netexId']
+ // if ('drugstoneId' in node) {
+ // return node['drugstoneId']
// } else {
// return node.id
// }
@@ -150,7 +150,7 @@ export function getNetworkId(node: Node) {
/**
* Returns ID of a network node
*/
- return node.netexId
+ return node.drugstoneId
}
export function getId(gene: Node) {
@@ -182,7 +182,7 @@ export interface Wrapper {
label: string;
type?: string;
symbol?: string;
- netexId?: string;
+ drugstoneId?: string;
ensg?: Array<string>;
shape?: string;
color?: string;
@@ -215,7 +215,7 @@ export interface Drug {
inTrial: boolean;
inLiterature: boolean;
trialLinks: string[];
- netexId: string;
+ drugstoneId: string;
group: string;
}
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 32cfb47803ab002427e084ff99d2df1e45516245..cf615e665f1d39e2c77a73dbc360f3b40f72689a 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -275,7 +275,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (nodeIds != null && nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- if (node.netexId === undefined || !node.netexId.startsWith('p')) {
+ if (node.drugstoneId === undefined || !node.drugstoneId.startsWith('p')) {
// skip if node is not a protein mapped to backend
return;
}
@@ -345,17 +345,17 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (this.drugstoneConfig.config.identifier === 'ensg') {
// remove possible duplicate IDs
- network.nodes = removeDuplicateObjectsFromList(network.nodes, 'netexId');
+ network.nodes = removeDuplicateObjectsFromList(network.nodes, 'drugstoneId');
}
// at this point, we have nodes synched with the backend
- // use netexIds where posssible, but use original id as node name if no label given
+ // use drugstoneIds where posssible, but use original id as node name if no label given
const nodeIdMap = {};
network.nodes.forEach((node) => {
// set node label to original id before node id will be set to netex id
node.label = node.label ? node.label : node.id;
- nodeIdMap[node.id] = node.netexId ? node.netexId : node.id;
+ nodeIdMap[node.id] = node.drugstoneId ? node.drugstoneId : node.id;
node.id = nodeIdMap[node.id];
});
@@ -494,9 +494,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
gProfilerLink(): string {
- // nodes in selection have netexId
+ // nodes in selection have drugstoneId
const queryString = this.analysis.getSelection()
- .filter(wrapper => wrapper.data.netexId.startsWith('p'))
+ .filter(wrapper => wrapper.data.drugstoneId.startsWith('p'))
.map(wrapper => wrapper.data.uniprotAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index baa8a5881e96bacf420bf786364b0eb8f5413dd0..bce39cb133098d227fc03de62e4b62722dfe842f 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -89,9 +89,9 @@ export class NetexControllerService {
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
// slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map((node: Node) => node.netexId ? node.netexId.slice(1) : undefined);
+ const genesBackendIds = nodes.map((node: Node) => node.drugstoneId ? node.drugstoneId.slice(1) : undefined);
const params = new HttpParams()
- .set('tissue', tissue.netexId)
+ .set('tissue', tissue.drugstoneId)
.set('proteins', JSON.stringify(genesBackendIds));
return this.http.get(`${environment.backend}tissue_expression/`, {params});
}
@@ -101,10 +101,10 @@ export class NetexControllerService {
const params = {};
if (nodeType === 'proteins') {
// @ts-ignore
- params.proteins = nodes.map((node: Node) => node.netexId && node.netexId.startsWith('p') ? node.netexId.slice(1) : undefined).filter(id => id != null);
+ params.proteins = nodes.map((node: Node) => node.drugstoneId && node.drugstoneId.startsWith('p') ? node.drugstoneId.slice(1) : undefined).filter(id => id != null);
} else if (nodeType === 'drugs') {
// @ts-ignore
- params.drugs = nodes.map((node: Node) => node.drugId && node.netexId.startsWith('dr') ? node.netexId.slice(2) : undefined).filter(id => id != null);
+ params.drugs = nodes.map((node: Node) => node.drugId && node.drugstoneId.startsWith('dr') ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
}
return this.http.post<any>(`${environment.backend}adjacent_disorders/`, params);
}
@@ -114,7 +114,7 @@ export class NetexControllerService {
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
// slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map((node: Node) => node.netexId && node.netexId.startsWith('p') ? node.netexId.slice(1) : undefined).filter(id => id != null);
+ const genesBackendIds = nodes.map((node: Node) => node.drugstoneId && node.drugstoneId.startsWith('p') ? node.drugstoneId.slice(1) : undefined).filter(id => id != null);
const params = {
pdi_dataset: pdiDataset,
proteins: genesBackendIds