NickAkhmetov/SCFind Genes Query #3737
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… titles/tooltips to expanded graphs
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Pull Request Overview
This PR enables gene queries using the scFind method and cleans up legacy code related to cell types. Key changes include updating query method defaults in the molecular data query form, refactoring autocomplete logic, and introducing new chart components for gene expression and cell type distribution tailored for scFind data.
Reviewed Changes
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Show a summary per file
| File | Description |
|---|---|
| MolecularDataQueryForm.tsx | Updated the default queryMethod to 'scFind' for gene queries and adjusted query method resets. |
| QueryMethod.tsx | Added scFind as an active gene query option and removed a duplicate entry. |
| AutocompleteEntity/hooks.ts | Updated the condition for handling scFind autocomplete to also check the targetEntity value. |
| SCFindGeneCharts.tsx & CellTypesChart.tsx | Introduced new chart components for gene expression level and cell type distributions. |
| Various API hooks (useFindDatasetForGenes.ts, useCellTypeExpression.ts, useCLIDToLabel.ts) | Updated request key construction and parameter handling to support scFind gene queries. |
| DatasetsOverview & FractionGraph/Related Files | Cleaned up outdated components and adjusted layout/documentation components accordingly. |
Comments suppressed due to low confidence (4)
context/app/static/js/components/cells/MolecularDataQueryForm/MolecularDataQueryForm.tsx:24
- Changing the default queryMethod to 'scFind' for gene queries impacts the user experience; please ensure that this update aligns with the intended behavior and communication with stakeholders.
queryMethod: 'scFind',
context/app/static/js/components/cells/MolecularDataQueryForm/AutocompleteEntity/hooks.ts:24
- The additional check on targetEntity being 'cell-type' may limit autocomplete behavior when using scFind; confirm that this condition is intentional and that gene queries using scFind do not require autocomplete.
if (queryMethod === 'scFind' && targetEntity === 'cell-type') {
context/app/static/js/api/scfind/useCellTypeExpression.ts:30
- Usage of String.prototype.replaceAll requires a supported environment; verify that target browsers or polyfills are in place if older environments must be supported.
cell_type: `${datasetName.replaceAll('.', '-')}.${datasetName}`,
context/app/static/js/api/scfind/useCLIDToLabel.ts:20
- Switching the key to 'CLID2CellType' might affect consumers of this hook; please ensure all dependent components are updated accordingly.
return createScFindKey(scFindEndpoint, 'CLID2CellType', {
| // TODO: Update with correct response type once the API is fixed | ||
| return useSWR<GeneExpressionBinsResponse, unknown, GeneExpressionBinKey>(key, (url) => fetcher({ url })); |
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Still pending resolution of this issue; however, since the cell type expression bins endpoint works, it's okay.
…om cell labels in cluster chart
| </Box> | ||
| )} | ||
| </TooltipInPortal> | ||
| )} |
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This could potentially be split into sub-components, particularly the tooltip and legend.
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Agreed, this can be more modular. Since this was already largely an effort to break down the Cell Type Distribution Chart component into smaller subcomponents, I'll break it down further.
| {decimal.format(totalCells)} | ||
| </Typography> | ||
| ); | ||
| } |
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Optional, but these column components are almost identical - could add an additional prop here instead to differentiate between the final return clauses.
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It's tricky to add additional props to these column/cell components since they have to conform to CellContentProps; however, I should be able to reduce repetition via composition instead.
| onMouseLeave: MouseEventHandler<HTMLOrSVGElement>; | ||
| onFocusCapture: FocusEventHandler<HTMLOrSVGElement>; | ||
| onBlurCapture: FocusEventHandler<HTMLOrSVGElement>; | ||
| } |
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This return type could be separated out into an interface to avoid the repetition in the function body
Summary
This PR enables the SCFind method for gene queries on the molecular and biological queries page and applies cleanup for previous work related to cell types based on feedback in that branch.
Design Documentation/Original Tickets
Testing
Manually tested various gene queries, regression tested cell types query to make sure that didn't break.
Screenshots/Video
Checklist
CHANGELOG-your-feature-name-here.mdis present in the root directory, describing the change(s) in full sentences.Additional Notes