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Implement RFC85 Dynamic Virtual Study (#5016)
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* Implement RFC85 Dynamic Virtual Study


---------

Co-authored-by: pieterlukasse <[email protected]>
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@forus @pieterlukasse
forus and pieterlukasse authored Nov 21, 2024
1 parent 69f34fb commit 1f7e44e
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Showing 5 changed files with 205 additions and 75 deletions.
4 changes: 2 additions & 2 deletions src/appShell/App/usageAgreements/StudyAgreement.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,8 @@ export const StudyAgreement: React.FunctionComponent<{}> = function({}) {
href="https://mskcc.sharepoint.com/sites/pub-ResearchDG/SitePages/Home.aspx?ga=1"
target="_blank"
>
MSK-IMPACT Memorial Hospital Research Data Governance publication
guidelines
MSK-IMPACT Memorial Hospital Research Data Governance
publication guidelines
</a>
.
</>,
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8 changes: 8 additions & 0 deletions src/globalStyles/global.scss
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,14 @@ div:active {
}
}

.form-group-inline {
@extend .form-group;

label {
margin-right: 6px;
}
}

.posRelative {
position: relative;
}
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25 changes: 16 additions & 9 deletions src/pages/studyView/StudyViewUtils.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -903,7 +903,8 @@ export function getVirtualStudyDescription(
attributeNamesSet: { [id: string]: string },
molecularProfileNameSet: { [id: string]: string },
caseListNameSet: { [key: string]: string },
user?: string
user?: string,
hideSampleCounts: boolean = false
) {
let descriptionLines: string[] = [];
const createdOnStr = 'Created on';
Expand All @@ -917,18 +918,24 @@ export function getVirtualStudyDescription(
_.flatMap(studyWithSamples, study => study.uniqueSampleKeys)
);
descriptionLines.push(
`${uniqueSampleKeys.length} sample${
uniqueSampleKeys.length > 1 ? 's' : ''
} from ${studyWithSamples.length} ${
studyWithSamples.length > 1 ? 'studies:' : 'study:'
}`
(hideSampleCounts
? 'Samples'
: `${uniqueSampleKeys.length} sample${
uniqueSampleKeys.length > 1 ? 's' : ''
}`) +
` from ${studyWithSamples.length} ${
studyWithSamples.length > 1 ? 'studies:' : 'study:'
}`
);
//add individual studies sample count
studyWithSamples.forEach(studyObj => {
descriptionLines.push(
`- ${studyObj.name} (${
studyObj.uniqueSampleKeys.length
} sample${uniqueSampleKeys.length > 1 ? 's' : ''})`
`- ${studyObj.name}` +
(hideSampleCounts
? ''
: ` (${studyObj.uniqueSampleKeys.length} sample${
uniqueSampleKeys.length > 1 ? 's' : ''
})`)
);
});
//add filters
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135 changes: 122 additions & 13 deletions src/pages/studyView/virtualStudy/VirtualStudy.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,8 @@ export default class VirtualStudy extends React.Component<
{}
> {
@observable.ref private name: string;
@observable.ref private description: string;
@observable.ref private customDescription: string | undefined;
@observable.ref private dynamic: boolean = false;

@observable private saving = false;
@observable private sharing = false;
Expand All @@ -107,17 +108,6 @@ export default class VirtualStudy extends React.Component<
super(props);
makeObservable(this);
this.name = props.name || '';
this.description =
props.description ||
getVirtualStudyDescription(
this.props.description,
this.props.studyWithSamples,
this.props.filter,
this.attributeNamesSet,
this.props.molecularProfileNameSet,
this.props.caseListNameSet,
this.props.user
);
}

@computed get namePlaceHolder() {
Expand Down Expand Up @@ -167,6 +157,7 @@ export default class VirtualStudy extends React.Component<
study => study.studyId
),
studies: studies,
dynamic: this.dynamic,
};
return await sessionServiceClient.saveVirtualStudy(
parameters,
Expand Down Expand Up @@ -231,6 +222,30 @@ export default class VirtualStudy extends React.Component<
);
}

getDefuaultDescriptionByType(dynamic: boolean) {
return getVirtualStudyDescription(
this.props.description,
this.props.studyWithSamples,
this.props.filter,
this.attributeNamesSet,
this.props.molecularProfileNameSet,
this.props.caseListNameSet,
this.props.user,
dynamic
);
}

@computed get description() {
const noCustomDescriptionProvided =
this.customDescription == undefined ||
this.customDescription ===
this.getDefuaultDescriptionByType(!this.dynamic);
if (noCustomDescriptionProvided) {
return this.getDefuaultDescriptionByType(this.dynamic);
}
return this.customDescription || '';
}

render() {
return (
<div
Expand Down Expand Up @@ -292,12 +307,106 @@ export default class VirtualStudy extends React.Component<
placeholder="Virtual study description (Optional)"
value={this.description}
onChange={event =>
(this.description =
(this.customDescription =
event.currentTarget.value)
}
/>
</div>

<div className="form-group-inline">
<label>Type:</label>
<label>
<input
type="radio"
name="option"
value="static"
checked={!this.dynamic}
onChange={_ =>
(this.dynamic = false)
}
/>{' '}
Static
</label>
<label>
<input
type="radio"
name="option"
value="dynamic"
checked={this.dynamic}
onChange={_ =>
(this.dynamic = true)
}
/>{' '}
Dynamic
</label>
<DefaultTooltip
mouseEnterDelay={0}
placement="right"
overlay={
<div>
<p>
<strong>
Type of Virtual
Study:
</strong>
</p>
<p>
This Virtual Study
will contain the set
of sample IDs
currently selected.
Furthermore, you can
define this Virtual
Study to be either
static or dynamic:
</p>
<ul>
<li>
<strong>
Static
</strong>{' '}
– Sample IDs are
the ones
currently
selected and no
new samples are
added to this
Virtual Study
set, even if the
database gets
updated with new
samples that
match the same
filtering/selection
criteria as the
samples in the
current set.
</li>
<li>
<strong>
Dynamic
</strong>{' '}
– Unlike the
Static option,
any new samples
added to the
database that
match the
criteria of this
Virtual Study
will
automatically be
included in its
sample set.
</li>
</ul>
</div>
}
>
<FontAwesome name="question-circle" />
</DefaultTooltip>
</div>

<div>
{this.showSaveButton && (
<button
Expand Down
108 changes: 57 additions & 51 deletions src/pages/studyView/virtualStudy/VirtualStudyModal.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -13,54 +13,60 @@ export interface IVirtualStudyModalProps {
onHide: () => void;
}

export const VirtualStudyModal: React.FunctionComponent<IVirtualStudyModalProps> = observer(({
appStore,
pageStore,
message,
onHide,
}) => {
const isLoading = [
pageStore.filteredVirtualStudies,
pageStore.studyWithSamples,
pageStore.filteredVirtualStudies,
pageStore.molecularProfileNameSet,
pageStore.molecularProfileNameSet,
].some(result => result.isPending);
return (
<Modal onHide={onHide} show={true}>
<Modal.Header closeButton>
<Modal.Title>Create a Virtual Study</Modal.Title>
</Modal.Header>
<Modal.Body>
{isLoading ?
<LoadingIndicator isLoading={true}/>
: <>
{message || null}
<VirtualStudy
user={appStore.userName}
name={
pageStore.isSingleVirtualStudyPageWithoutFilter
? pageStore.filteredVirtualStudies.result[0].data
.name
: undefined
}
description={
pageStore.isSingleVirtualStudyPageWithoutFilter
? pageStore.filteredVirtualStudies.result[0].data
.description
: undefined
}
studyWithSamples={pageStore.studyWithSamples.result}
selectedSamples={pageStore.selectedSamples.result}
filter={pageStore.userSelections}
attributesMetaSet={pageStore.chartMetaSet}
molecularProfileNameSet={
pageStore.molecularProfileNameSet.result || {}
}
caseListNameSet={pageStore.caseListNameSet.result || {}}
/>
</>}
</Modal.Body>
</Modal>
);
});
export const VirtualStudyModal: React.FunctionComponent<IVirtualStudyModalProps> = observer(
({ appStore, pageStore, message, onHide }) => {
const isLoading = [
pageStore.filteredVirtualStudies,
pageStore.studyWithSamples,
pageStore.filteredVirtualStudies,
pageStore.molecularProfileNameSet,
pageStore.molecularProfileNameSet,
].some(result => result.isPending);
return (
<Modal onHide={onHide} show={true}>
<Modal.Header closeButton>
<Modal.Title>Create a Virtual Study</Modal.Title>
</Modal.Header>
<Modal.Body>
{isLoading ? (
<LoadingIndicator isLoading={true} />
) : (
<>
{message || null}
<VirtualStudy
user={appStore.userName}
name={
pageStore.isSingleVirtualStudyPageWithoutFilter
? pageStore.filteredVirtualStudies
.result[0].data.name
: undefined
}
description={
pageStore.isSingleVirtualStudyPageWithoutFilter
? pageStore.filteredVirtualStudies
.result[0].data.description
: undefined
}
studyWithSamples={
pageStore.studyWithSamples.result
}
selectedSamples={
pageStore.selectedSamples.result
}
filter={pageStore.userSelections}
attributesMetaSet={pageStore.chartMetaSet}
molecularProfileNameSet={
pageStore.molecularProfileNameSet.result ||
{}
}
caseListNameSet={
pageStore.caseListNameSet.result || {}
}
/>
</>
)}
</Modal.Body>
</Modal>
);
}
);

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