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Remove cbioportal and cosmic annotation threshholds in oncoprint controls #4227

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merged 2 commits into from
Apr 12, 2022
Merged

Remove cbioportal and cosmic annotation threshholds in oncoprint controls #4227

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b9b0959
Remove cbioportal and cosmic annotation threshholds in oncoprint cont…
alisman Apr 11, 2022
a4bb0e4
Fix some e2e tests after elimination of annotation settings
alisman Apr 11, 2022
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57 changes: 0 additions & 57 deletions end-to-end-test/remote/specs/core/oncoprint.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -296,63 +296,6 @@ describe('oncoprint', function() {
resultsPageSettingsDropdown +
' input[data-test="annotateCOSMICCount"]';
});
it('annotates all types of mutations with cbioportal count and cosmic', () => {
setSettingsMenuOpen(true);
// select only mutation coloring by cbioportal count
$(cbioportalCheckbox).click();
waitForOncoprint(ONCOPRINT_TIMEOUT);
$(oncoKbCheckbox).click();
waitForOncoprint(ONCOPRINT_TIMEOUT);
$(hotspotsCheckbox).click();
waitForOncoprint(ONCOPRINT_TIMEOUT);
// set threshold 1
browser.execute(function() {
resultsViewOncoprint.setAnnotateCBioPortalInputValue('1');
});
browser.pause(100); // give time to take effect
waitForOncoprint(ONCOPRINT_TIMEOUT);
let legendText = getTextInOncoprintLegend();
assert(
legendText.indexOf('Inframe Mutation (putative driver)') > -1,
'cbio count annotates inframe mutations'
);
assert(
legendText.indexOf('Missense Mutation (putative driver)') > -1,
'cbio count annotates missense mutations'
);
assert(
legendText.indexOf('Truncating Mutation (putative driver)') >
-1,
'cbio count annotates truncating mutations'
);

// select only mutation coloring by cosmic count
setSettingsMenuOpen(true);
$(cosmicCheckbox).click();
waitForOncoprint(ONCOPRINT_TIMEOUT);
$(cbioportalCheckbox).click();
waitForOncoprint(ONCOPRINT_TIMEOUT);
// set threshold 1
browser.execute(function() {
resultsViewOncoprint.setAnnotateCOSMICInputValue('1');
});
browser.pause(100); // give time to take effect
waitForOncoprint(ONCOPRINT_TIMEOUT);
legendText = getTextInOncoprintLegend();
assert(
legendText.indexOf('Inframe Mutation (putative driver)') > -1,
'cosmic count annotates inframe mutations'
);
assert(
legendText.indexOf('Missense Mutation (putative driver)') > -1,
'cosmic count annotates missense mutations'
);
assert(
legendText.indexOf('Truncating Mutation (putative driver)') >
-1,
'cosmic count annotates truncating mutations'
);
});
});

describe('germline mutation', () => {
Expand Down
3 changes: 0 additions & 3 deletions end-to-end-test/remote/specs/core/oncoprinter.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,6 @@ describe('oncoprinter tests', function() {

setOncoprintMutationsMenuOpen(true);
assert(!$('input[data-test="annotateOncoKb"]').isSelected());
assert(
!$('input[data-test="annotateCBioPortalCount"]').isSelected()
);
assert($('input[data-test="annotateCustomBinary"]').isSelected());
}

Expand Down
20 changes: 0 additions & 20 deletions src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -158,12 +158,6 @@ export default class Oncoprinter extends React.Component<
this.mouseInsideBounds = false;
}

@action
public setAnnotateCBioPortalInputValue(value: string) {
this.controlsHandlers.onChangeAnnotateCBioPortalInputValue &&
this.controlsHandlers.onChangeAnnotateCBioPortalInputValue(value);
}

private buildControlsHandlers() {
return {
onSelectShowUnalteredColumns: (show: boolean) => {
Expand Down Expand Up @@ -205,20 +199,6 @@ export default class Oncoprinter extends React.Component<
onSelectAnnotateOncoKb: action((s: boolean) => {
this.props.store.driverAnnotationSettings.oncoKb = s;
}),
onSelectAnnotateCBioPortal: action((s: boolean) => {
this.props.store.driverAnnotationSettings.cbioportalCount = s;
}),
/*onSelectAnnotateHotspots:action((s:boolean)=>{
this.props.store.driverAnnotationSettings.hotspots = s;
}),*/
onChangeAnnotateCBioPortalInputValue: action((s: string) => {
this.props.store.driverAnnotationSettings.cbioportalCountThreshold = parseInt(
s,
10
);
this.controlsHandlers.onSelectAnnotateCBioPortal &&
this.controlsHandlers.onSelectAnnotateCBioPortal(true);
}),
onSelectCustomDriverAnnotationBinary: action((s: boolean) => {
this.props.store.driverAnnotationSettings.customBinary = s;
}),
Expand Down
32 changes: 0 additions & 32 deletions src/shared/alterationFiltering/AnnotationFilteringSettings.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -48,12 +48,6 @@ export interface IDriverAnnotationControlsState {
annotateDriversHotspotsError?: boolean;
annotateDriversHotspots?: boolean;

annotateDriversCBioPortal: boolean;
annotateCBioPortalInputValue: string;

annotateDriversCOSMIC?: boolean;
annotateCOSMICInputValue?: string;

customDriverAnnotationBinaryMenuLabel?: string;
customDriverAnnotationTiersMenuLabel?: string;
customDriverAnnotationTiers?: string[];
Expand All @@ -66,10 +60,6 @@ export interface IDriverAnnotationControlsHandlers {
onSelectDistinguishDrivers: (distinguish: boolean) => void;
onSelectAnnotateOncoKb: (annotate: boolean) => void;
onSelectAnnotateHotspots?: (annotate: boolean) => void;
onSelectAnnotateCBioPortal: (annotate: boolean) => void;
onSelectAnnotateCOSMIC?: (annotate: boolean) => void;
onChangeAnnotateCBioPortalInputValue?: (value: string) => void;
onChangeAnnotateCOSMICInputValue?: (value: string) => void;
onSelectCustomDriverAnnotationBinary?: (s: boolean) => void;
onSelectCustomDriverAnnotationTier?: (value: string, s: boolean) => void;
}
Expand Down Expand Up @@ -212,22 +202,6 @@ export function buildDriverAnnotationControlsHandlers(
onSelectAnnotateHotspots: action((s: boolean) => {
driverAnnotationSettings.hotspots = s;
}),
onSelectAnnotateCBioPortal: action((s: boolean) => {
driverAnnotationSettings.cbioportalCount = s;
}),
onSelectAnnotateCOSMIC: action((s: boolean) => {
driverAnnotationSettings.cosmicCount = s;
}),
onChangeAnnotateCBioPortalInputValue: action((s: string) => {
driverAnnotationSettings.cbioportalCountThreshold = parseInt(s, 10);
handlers.onSelectAnnotateCBioPortal &&
handlers.onSelectAnnotateCBioPortal(true);
}),
onChangeAnnotateCOSMICInputValue: action((s: string) => {
driverAnnotationSettings.cosmicCountThreshold = parseInt(s, 10);
handlers.onSelectAnnotateCOSMIC &&
handlers.onSelectAnnotateCOSMIC(true);
}),
onSelectCustomDriverAnnotationBinary: action((s: boolean) => {
driverAnnotationSettings.customBinary = s;
}),
Expand Down Expand Up @@ -281,12 +255,6 @@ export function buildDriverAnnotationControlsState(
get annotateDriversHotspotsError() {
return !!didHotspotFailInOncoprint;
},
get annotateDriversCBioPortal() {
return driverAnnotationSettings.cbioportalCount;
},
get annotateDriversCOSMIC() {
return driverAnnotationSettings.cosmicCount;
},
get includePutativeDrivers() {
return driverAnnotationSettings.includeDriver;
},
Expand Down
137 changes: 63 additions & 74 deletions src/shared/components/driverAnnotations/DriverAnnotationControls.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -52,17 +52,6 @@ export default class DriverAnnotationControls extends React.Component<
!this.props.state.annotateDriversHotspots
);
break;
case EVENT_KEY.annotateCBioPortal:
this.props.handlers.onSelectAnnotateCBioPortal(
!this.props.state.annotateDriversCBioPortal
);
break;
case EVENT_KEY.annotateCOSMIC:
this.props.handlers.onSelectAnnotateCOSMIC &&
this.props.handlers.onSelectAnnotateCOSMIC(
!this.props.state.annotateDriversCOSMIC
);
break;
case EVENT_KEY.customDriverBinaryAnnotation:
this.props.handlers.onSelectCustomDriverAnnotationBinary &&
this.props.handlers.onSelectCustomDriverAnnotationBinary(
Expand Down Expand Up @@ -244,69 +233,69 @@ export default class DriverAnnotationControls extends React.Component<
</label>
</div>
)}
{this.props.handlers
.onChangeAnnotateCBioPortalInputValue && (
<div className="checkbox">
<label>
<input
type="checkbox"
value={EVENT_KEY.annotateCBioPortal}
checked={
this.props.state
.annotateDriversCBioPortal
}
onClick={this.onInputClick}
data-test="annotateCBioPortalCount"
/>
cBioPortal {'>'}=
</label>
<EditableSpan
value={
this.props.state
.annotateCBioPortalInputValue ||
''
}
setValue={
this.props.handlers
.onChangeAnnotateCBioPortalInputValue
}
numericOnly={true}
textFieldAppearance={true}
maxChars={10}
/>
</div>
)}
{this.props.handlers
.onChangeAnnotateCOSMICInputValue && (
<div className="checkbox">
<label>
<input
type="checkbox"
value={EVENT_KEY.annotateCOSMIC}
checked={
this.props.state
.annotateDriversCOSMIC
}
onClick={this.onInputClick}
data-test="annotateCOSMICCount"
/>
COSMIC {'>'}=
</label>
<EditableSpan
value={
this.props.state
.annotateCOSMICInputValue || ''
}
setValue={
this.props.handlers
.onChangeAnnotateCOSMICInputValue
}
numericOnly={true}
textFieldAppearance={true}
maxChars={10}
/>
</div>
)}
{/*{this.props.handlers*/}
{/* .onChangeAnnotateCBioPortalInputValue && (*/}
{/* <div className="checkbox">*/}
{/* <label>*/}
{/* <input*/}
{/* type="checkbox"*/}
{/* value={EVENT_KEY.annotateCBioPortal}*/}
{/* checked={*/}
{/* this.props.state*/}
{/* .annotateDriversCBioPortal*/}
{/* }*/}
{/* onClick={this.onInputClick}*/}
{/* data-test="annotateCBioPortalCount"*/}
{/* />*/}
{/* cBioPortal {'>'}=*/}
{/* </label>*/}
{/* <EditableSpan*/}
{/* value={*/}
{/* this.props.state*/}
{/* .annotateCBioPortalInputValue ||*/}
{/* ''*/}
{/* }*/}
{/* setValue={*/}
{/* this.props.handlers*/}
{/* .onChangeAnnotateCBioPortalInputValue*/}
{/* }*/}
{/* numericOnly={true}*/}
{/* textFieldAppearance={true}*/}
{/* maxChars={10}*/}
{/* />*/}
{/* </div>*/}
{/*)}*/}
{/*{this.props.handlers*/}
{/* .onChangeAnnotateCOSMICInputValue && (*/}
{/* <div className="checkbox">*/}
{/* <label>*/}
{/* <input*/}
{/* type="checkbox"*/}
{/* value={EVENT_KEY.annotateCOSMIC}*/}
{/* checked={*/}
{/* this.props.state*/}
{/* .annotateDriversCOSMIC*/}
{/* }*/}
{/* onClick={this.onInputClick}*/}
{/* data-test="annotateCOSMICCount"*/}
{/* />*/}
{/* COSMIC {'>'}=*/}
{/* </label>*/}
{/* <EditableSpan*/}
{/* value={*/}
{/* this.props.state*/}
{/* .annotateCOSMICInputValue || ''*/}
{/* }*/}
{/* setValue={*/}
{/* this.props.handlers*/}
{/* .onChangeAnnotateCOSMICInputValue*/}
{/* }*/}
{/* numericOnly={true}*/}
{/* textFieldAppearance={true}*/}
{/* maxChars={10}*/}
{/* />*/}
{/* </div>*/}
{/*)}*/}
</span>
)}
{!!this.props.state
Expand Down
34 changes: 0 additions & 34 deletions src/shared/components/oncoprint/ResultsViewOncoprint.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -625,18 +625,6 @@ export default class ResultsViewOncoprint extends React.Component<
this.mouseInsideBounds = false;
}

@action
public setAnnotateCBioPortalInputValue(value: string) {
this.controlsHandlers.onChangeAnnotateCBioPortalInputValue &&
this.controlsHandlers.onChangeAnnotateCBioPortalInputValue(value);
}

@action
public setAnnotateCOSMICInputValue(value: string) {
this.controlsHandlers.onChangeAnnotateCOSMICInputValue &&
this.controlsHandlers.onChangeAnnotateCOSMICInputValue(value);
}

private buildControlsHandlers() {
return {
onSelectColumnType: (type: OncoprintAnalysisCaseType) => {
Expand Down Expand Up @@ -714,28 +702,6 @@ export default class ResultsViewOncoprint extends React.Component<
onSelectAnnotateHotspots: action((s: boolean) => {
this.props.store.driverAnnotationSettings.hotspots = s;
}),
onSelectAnnotateCBioPortal: action((s: boolean) => {
this.props.store.driverAnnotationSettings.cbioportalCount = s;
}),
onSelectAnnotateCOSMIC: action((s: boolean) => {
this.props.store.driverAnnotationSettings.cosmicCount = s;
}),
onChangeAnnotateCBioPortalInputValue: action((s: string) => {
this.props.store.driverAnnotationSettings.cbioportalCountThreshold = parseInt(
s,
10
);
this.controlsHandlers.onSelectAnnotateCBioPortal &&
this.controlsHandlers.onSelectAnnotateCBioPortal(true);
}),
onChangeAnnotateCOSMICInputValue: action((s: string) => {
this.props.store.driverAnnotationSettings.cosmicCountThreshold = parseInt(
s,
10
);
this.controlsHandlers.onSelectAnnotateCOSMIC &&
this.controlsHandlers.onSelectAnnotateCOSMIC(true);
}),
onSelectCustomDriverAnnotationBinary: action((s: boolean) => {
this.props.store.driverAnnotationSettings.customBinary = s;
}),
Expand Down
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