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Implement RFC85 Dynamic Virtual Study #5016

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Implement RFC85 Dynamic Virtual Study #5016

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9debc08
Implement RFC85 Dynamic Virtual Study
forus Oct 2, 2024
c7880ae
Rename boolean varialbe name isDynamic -> dynamic
forus Oct 12, 2024
ebbd1b7
Improve help tooltip text of virtual study type
forus Oct 18, 2024
4b49f4f
Update description for dynamic/static VS if blank or default
forus Oct 23, 2024
3287498
Merge branch 'master' into rfc85-dynamic-virtual-study
forus Oct 28, 2024
0fb9260
Merge branch 'master' into rfc85-dynamic-virtual-study
forus Nov 1, 2024
6484e18
Merge branch 'master' into rfc85-dynamic-virtual-study
forus Nov 5, 2024
869cf79
Make VS code Prettier
forus Nov 5, 2024
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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;
}
Expand Down
25 changes: 16 additions & 9 deletions src/pages/studyView/StudyViewUtils.tsx
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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
Expand Down
143 changes: 131 additions & 12 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 description: string = '';
@observable.ref private dynamic: boolean = false;

@observable private saving = false;
@observable private sharing = false;
Expand All @@ -107,17 +108,7 @@ 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
);
this.setDynamicTypeTo(false);
}

@computed get namePlaceHolder() {
Expand Down Expand Up @@ -167,6 +158,7 @@ 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 +223,35 @@ export default class VirtualStudy extends React.Component<
);
}

updateDescriptionIfBlankOrDefault(hideSampleCounts: boolean) {
const getVirtualStudyDescriptionWithCounts = getVirtualStudyDescription.bind(
null,
this.props.description,
this.props.studyWithSamples,
this.props.filter,
this.attributeNamesSet,
this.props.molecularProfileNameSet,
this.props.caseListNameSet,
this.props.user
);
const blankOrDefaultDescription =
!this.description ||
!this.description.trim() ||
this.description ===
getVirtualStudyDescriptionWithCounts(!hideSampleCounts);
if (blankOrDefaultDescription) {
this.description = getVirtualStudyDescriptionWithCounts(
hideSampleCounts
);
}
}

setDynamicTypeTo(dynamic: boolean) {
this.dynamic = dynamic;

this.updateDescriptionIfBlankOrDefault(dynamic);
}

render() {
return (
<div
Expand Down Expand Up @@ -298,6 +319,104 @@ export default class VirtualStudy extends React.Component<
/>
</div>

<div className="form-group-inline">
<label>Type:</label>
<label>
<input
type="radio"
name="option"
value="static"
checked={!this.dynamic}
onChange={_ =>
this.setDynamicTypeTo(
false
)
}
/>{' '}
Static
</label>
<label>
<input
type="radio"
name="option"
value="dynamic"
checked={this.dynamic}
onChange={_ =>
this.setDynamicTypeTo(
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 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
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