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Created geneset in Genomic node #160

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Created geneset in Genomic node #160

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eabd207
Add pathway in genomic and keep main type and subtype in clinical
victoria34 Aug 8, 2019
0186bf0
Create Geneset for genomic node
victoria34 Sep 6, 2019
5278f5b
Finish geneses
victoria34 Sep 6, 2019
8808870
Validate type of geneset
victoria34 Sep 9, 2019
60c87d9
Change url
victoria34 Sep 9, 2019
32b91fb
Removed genesets in Gene model
victoria34 Sep 9, 2019
af7d50f
Rename sub_type to subtype
victoria34 Sep 9, 2019
8a7a365
Replace id by uuid
victoria34 Sep 20, 2019
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2 changes: 1 addition & 1 deletion package.json
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Expand Up @@ -97,7 +97,7 @@
"uglifyjs-webpack-plugin": "1.1.5",
"web-app-manifest-loader": "0.1.1",
"webpack": "3.10.0",
"webpack-dev-server": "2.9.5",
"webpack-dev-server": "^3.7.2",
"webpack-merge": "4.1.1",
"webpack-notifier": "1.5.1",
"webpack-visualizer-plugin": "0.1.11",
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12 changes: 6 additions & 6 deletions src/main/webapp/app/clinical/clinical.component.html
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Expand Up @@ -21,7 +21,7 @@
</ng-select>
</div>
<div class="subTypeStyle">
<ng-select class="selectStyle" [items]="subTypesOptions[clinicalInput.main_type]" [(ngModel)]="clinicalInput.sub_type"
<ng-select class="selectStyle" [items]="subTypesOptions[clinicalInput.main_type]" [(ngModel)]="clinicalInput.subtype"
[clearable]="true" placeholder="Select Subtype" (change)="onSingleSelected($event)">
</ng-select>
</div>
Expand All @@ -32,10 +32,10 @@
<div class="col-sm-8">
<span id="gender1">
<label for="gender-male1">
<input id="gender-male1" type="radio" value="Male" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Male
<input id="gender-male1" class="gender-radio" type="radio" value="Male" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Male
</label>
<label for="gender-female1">
<input id="gender-female1" type="radio" value="Female" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Female
<input id="gender-female1" class="gender-radio" type="radio" value="Female" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Female
</label>
</span>
</div>
Expand Down Expand Up @@ -69,7 +69,7 @@
</ng-select>
</div>
<div class="subTypeStyle">
<ng-select class="selectStyle" [items]="subTypesOptions[clinicalInput.main_type]" [(ngModel)]="clinicalInput.sub_type"
<ng-select class="selectStyle" [items]="subTypesOptions[clinicalInput.main_type]" [(ngModel)]="clinicalInput.subtype"
[clearable]="true" placeholder="Select Subtype" (change)="onSingleSelected($event)">
</ng-select>
</div>
Expand All @@ -80,10 +80,10 @@
<div class="col-sm-8">
<span id="gender2">
<label for="gender-male2">
<input id="gender-male2" type="radio" value="Male" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Male
<input id="gender-male2" class="gender-radio" type="radio" value="Male" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Male
</label>
<label for="gender-female2">
<input id="gender-female2" type="radio" value="Female" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Female
<input id="gender-female2" class="gender-radio" type="radio" value="Female" name="gender" [(ngModel)]="clinicalInput.gender" (click)="unCheckRadio('gender', $event)">Female
</label>
</span>
</div>
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4 changes: 2 additions & 2 deletions src/main/webapp/app/clinical/clinical.component.ts
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Expand Up @@ -106,13 +106,13 @@ export class ClinicalComponent implements OnInit {
}
onSingleSelected(option) {
if (_.isUndefined(option)) {
this.clinicalInput.sub_type = '';
this.clinicalInput.subtype = '';
} else if (option && this.clinicalInput.main_type !== this.subToMainMapping[option]) {
this.clinicalInput.main_type = this.subToMainMapping[option];
}
}
onSingleDeselectedMaintype() {
this.clinicalInput.sub_type = '';
this.clinicalInput.subtype = '';
this.clinicalInput.main_type = '';
}
getDisplayContent(key: string) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/webapp/app/clinical/clinical.model.ts
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Expand Up @@ -2,7 +2,7 @@ export interface Clinical {
age_numerical?: string,
oncotree_primary_diagnosis?: string,
main_type?: string,
sub_type?: string,
subtype?: string,
gender?: string,
no_oncotree_primary_diagnosis?: boolean
}
3 changes: 3 additions & 0 deletions src/main/webapp/app/clinical/clinical.scss
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Expand Up @@ -25,3 +25,6 @@ label {
.collapse-margin{
margin: 10px 0px 10px 30px;
}
.gender-radio {
margin-right: 5px;
}
22 changes: 22 additions & 0 deletions src/main/webapp/app/genomic/geneset.model.ts
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@@ -0,0 +1,22 @@
export interface Geneset {
name: string,
uuid: number,
genes: Gene[]
}

export interface Gene {
entrezGeneId: number,
hugoSymbol: string,
name: string,
oncogene: boolean,
curatedIsoform: string,
curatedRefSeq: string,
geneAliases: string[],
tsg: boolean
}

export interface GenesetOption {
name: string,
uuid: number,
genes: string[]
}
74 changes: 62 additions & 12 deletions src/main/webapp/app/genomic/genomic.component.html
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@@ -1,12 +1,26 @@
<div *ngIf="type === 'add'; else editPanel">
<div>
<div class="row borderMargin">
<div class="col-sm-4">geneset:</div>
<div class="col-sm-8">
<ng-select class="selectStyle" [items]="genesetOptions" bindLabel="name" bindValue="uuid" [(ngModel)]="genomicInput.geneset_uuid" [clearable]="true"
placeholder="Select Geneset" (change)="changeGeneset()">
</ng-select>
</div>
</div>
<div class="row borderMargin" *ngIf="selectedGenesetOption">
<div class="col-sm-4">hugo_symbol:</div>
<div class="col-sm-8">
<span>{{selectedGenesetOption.genes.join(', ')}}</span>
</div>
</div>
<div class="row borderMargin" *ngIf="!selectedGenesetOption">
<div class="col-sm-3">hugo_symbol:
<span [ngStyle]="getMessageStyle('gene')">{{ validationMessage['gene'] }}</span>
</div>
<div class="col-sm-1">
<label for="no_hugo_symbol1">Not</label>
<input id="no_hugo_symbol1" type="checkbox" class="notLabel" [(ngModel)]="genomicInput.no_hugo_symbol" />
<input id="no_hugo_symbol1" type="checkbox" class="notLabel" [(ngModel)]="genomicInput.no_hugo_symbol"/>
</div>
<div class="col-sm-8">
<input type="text" class="selectStyle" [(ngModel)]="genomicInput.hugo_symbol" size="36" (change)="validateGenomicGene()" />
Expand Down Expand Up @@ -166,12 +180,26 @@
<br/>
<div [ngStyle]="getStyle()" *ngIf="operationPool['relocate'] !== true && operationPool['copy'] !== true && operationPool['currentPath'] === path; else panel">
<div class="row borderMargin">
<div class="col-sm-4">geneset:</div>
<div class="col-sm-8">
<ng-select class="selectStyle" [items]="genesetOptions" bindLabel="name" bindValue="uuid" [(ngModel)]="genomicInput.geneset_uuid" [clearable]="true"
placeholder="Select Geneset" (change)="changeGeneset()" >
</ng-select>
</div>
</div>
<div class="row borderMargin" *ngIf="genomicInput.geneset_uuid">
<div class="col-sm-4">hugo_symbol:</div>
<div class="col-sm-8">
<span>{{selectedGenesetOption.genes.join(', ')}}</span>
</div>
</div>
<div class="row borderMargin" *ngIf="!genomicInput.geneset_uuid">
<div class="col-sm-3">hugo_symbol:
<span [ngStyle]="getMessageStyle('gene')">{{ validationMessage['gene'] }}</span>
</div>
<div class="col-sm-1">
<label for="no_hugo_symbol2">Not</label>
<input id="no_hugo_symbol2" type="checkbox" class="notLabel" [(ngModel)]="genomicInput.no_hugo_symbol" />
<input id="no_hugo_symbol2" type="checkbox" class="notLabel" [(ngModel)]="genomicInput.no_hugo_symbol"/>
</div>
<div class="col-sm-8">
<input class="selectStyle" type="text" [(ngModel)]="genomicInput.hugo_symbol" size="36" (change)="validateGenomicGene()" />
Expand Down Expand Up @@ -324,20 +352,42 @@
</div>
<ng-template #panel>
<div [ngStyle]="getStyle()">
<div class="row">
<div class="col-sm-4">
<label>hugo_symbol: </label>
<div *ngIf="unit.genomic.geneset_uuid">
<div class="row">
<div class="col-sm-4">
<label>geneset: </label>
</div>
<div class="col-sm-8">
<span>{{selectedGenesetOption.name}}</span>
</div>
</div>
<div class="col-sm-8">
<span>{{getDisplayContent('hugo_symbol')}}</span>
<div class="row">
<div class="col-sm-4">
<label>hugo_symbol: </label>
</div>
<div class="col-sm-8">
<span>{{selectedGenesetOption.genes.join(', ')}}</span>
</div>
</div>
</div>
<div class="row">
<div class="col-sm-4">
<label>annotated_variant: </label>
<div *ngIf="!unit.genomic.geneset_uuid && unit.genomic.hugo_symbol">
<div class="row">
<div class="col-sm-4">
<label>hugo_symbol: </label>
</div>
<div class="col-sm-8">
<span>{{getDisplayContent('hugo_symbol')}}</span>
</div>
</div>
<div class="col-sm-8">
<span>{{getDisplayContent('annotated_variant')}}</span>
</div>
<div *ngIf="unit.genomic.annotated_variant">
<div class="row">
<div class="col-sm-4">
<label>annotated_variant: </label>
</div>
<div class="col-sm-8">
<span>{{getDisplayContent('annotated_variant')}}</span>
</div>
</div>
</div>
<div *ngIf="unit.genomic.matching_examples">
Expand Down
19 changes: 18 additions & 1 deletion src/main/webapp/app/genomic/genomic.component.ts
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Expand Up @@ -7,7 +7,8 @@ import 'rxjs/add/operator/distinctUntilChanged';
import { Genomic } from './genomic.model';
import * as _ from 'lodash';
import { ConnectionService } from '../service/connection.service';
import MainUtil from '../service/mainutil';
import { MainutilService } from '../service/mainutil.service';
import { Geneset, GenesetOption } from './geneset.model';

@Component({
selector: 'jhi-genomic',
Expand Down Expand Up @@ -38,6 +39,8 @@ export class GenomicComponent implements OnInit {
};
geneValidation = false;
exampleValidation = false;
genesetOptions = this.trialService.getGenesetsOptions();
selectedGenesetOption: GenesetOption;

search = (text$: Observable<string>) =>
text$
Expand All @@ -59,6 +62,9 @@ export class GenomicComponent implements OnInit {
constructor(private trialService: TrialService, public connectionService: ConnectionService) {}

ngOnInit() {
if (!_.isUndefined(this.unit['genomic']) && !_.isUndefined(this.unit['genomic']['geneset_uuid'])) {
this.selectedGenesetOption = _.find(this.genesetOptions, { uuid: this.unit['genomic']['geneset_uuid'] });
}
this.trialService.genomicInputObs.subscribe((message) => {
this.genomicInput = message;
});
Expand Down Expand Up @@ -116,4 +122,15 @@ export class GenomicComponent implements OnInit {
unCheckRadio(key, event) {
this.genomicInput[key] = MainUtil.uncheckRadio(this.genomicInput[key], event.target.value);
}
changeGeneset() {
if (this.genomicInput.geneset_uuid) {
this.selectedGenesetOption = _.find(this.genesetOptions, { uuid: this.genomicInput.geneset_uuid });
if (_.isEmpty(this.genomicInput.annotated_variant)) {
this.genomicInput.annotated_variant = 'Oncogenic Mutations';
}
} else {
this.selectedGenesetOption = null;
this.genomicInput.annotated_variant = '';
}
}
}
2 changes: 2 additions & 0 deletions src/main/webapp/app/genomic/genomic.model.ts
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@@ -1,5 +1,7 @@
export interface Genomic {
hugo_symbol?: string,
geneset?: string,
geneset_uuid?: number,
annotated_variant?: string,
matching_examples?: string,
germline?: string,
Expand Down
8 changes: 7 additions & 1 deletion src/main/webapp/app/genomic/genomic.scss
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@@ -1,6 +1,9 @@
label {
min-width:180px;
}
input:disabled {
background-color: #cccccc;
}
.selectStyle {
max-width:300px;
}
Expand All @@ -12,6 +15,9 @@ label {
margin-top: -25px;
margin-left: 30px;
}
.icon-margin{
.icon-margin {
margin-left: 20px;
}
.germline-radio {
margin-right: 5px;
}
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