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feat: Convert deposition page datasets table to use V2 data #1549

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merged 1 commit into from
Jan 28, 2025
Merged

feat: Convert deposition page datasets table to use V2 data #1549

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149 changes: 76 additions & 73 deletions frontend/packages/data-portal/app/components/Deposition/DatasetsTable.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ import { CellHeaderDirection } from '@czi-sds/components'
import Skeleton from '@mui/material/Skeleton'
import { useNavigate, useSearchParams } from '@remix-run/react'
import { ColumnDef, createColumnHelper } from '@tanstack/react-table'
import { range, sum } from 'lodash-es'
import { range } from 'lodash-es'
import { useCallback, useMemo } from 'react'

import { AnnotatedObjectsList } from 'app/components/AnnotatedObjectsList'
Expand All @@ -23,26 +23,28 @@ import { IdPrefix } from 'app/constants/idPrefixes'
import { ANNOTATED_OBJECTS_MAX, MAX_PER_PAGE } from 'app/constants/pagination'
import { QueryParams } from 'app/constants/query'
import { DepositionPageDatasetTableWidths } from 'app/constants/table'
import { Dataset, useDepositionById } from 'app/hooks/useDepositionById'
import { useDepositionById } from 'app/hooks/useDepositionById'
import { useI18n } from 'app/hooks/useI18n'
import { useIsLoading } from 'app/hooks/useIsLoading'
import { Events, usePlausible } from 'app/hooks/usePlausible'
import { Dataset } from 'app/types/gql/depositionPageTypes'
import { LogLevel } from 'app/types/logging'
import { cnsNoMerge } from 'app/utils/cns'
import { sendLogs } from 'app/utils/logging'
import { isDefined } from 'app/utils/nullish'
import { getErrorMessage } from 'app/utils/string'
import { carryOverFilterParams, createUrl } from 'app/utils/url'

const LOADING_DATASETS: Dataset[] = range(0, MAX_PER_PAGE).map(
(value) =>
({
authors: [],
id: value,
title: `loading-dataset-${value}`,
runs: [],
runs_aggregate: {},
}) as Dataset,
)
const LOADING_DATASETS: Dataset[] = range(0, MAX_PER_PAGE).map(() => ({
authors: {
edges: [],
},
id: 0,
runs: {
edges: [],
},
title: '',
}))

export function DatasetsTable() {
const { t } = useI18n()
Expand Down Expand Up @@ -78,11 +80,11 @@ export function DatasetsTable() {

try {
return [
columnHelper.accessor('key_photo_thumbnail_url', {
columnHelper.accessor('keyPhotoThumbnailUrl', {
// eslint-disable-next-line jsx-a11y/control-has-associated-label
header: () => <td />,

cell({ row: { original: dataset } }) {
cell({ getValue, row: { original: dataset } }) {
const datasetUrl = getDatasetUrl(dataset.id)

return (
Expand All @@ -94,7 +96,7 @@ export function DatasetsTable() {
<KeyPhoto
className="max-w-[134px]"
title={dataset.title}
src={dataset.key_photo_thumbnail_url ?? undefined}
src={getValue() ?? undefined}
loading={isLoadingDebounced}
textOnGroupHover="openDataset"
/>
Expand Down Expand Up @@ -173,7 +175,12 @@ export function DatasetsTable() {
/>
</>
) : (
<AuthorList authors={dataset.authors} compact />
<AuthorList
authors={dataset.authors.edges.map(
(author) => author.node,
)}
compact
/>
)}
</div>
</div>
Expand All @@ -182,7 +189,7 @@ export function DatasetsTable() {
},
}),

columnHelper.accessor('organism_name', {
columnHelper.accessor('organismName', {
header: () => (
<CellHeader width={DepositionPageDatasetTableWidths.organism}>
{t('organism')}
Expand All @@ -198,7 +205,7 @@ export function DatasetsTable() {
}),

columnHelper.accessor(
(dataset) => dataset.runs_aggregate?.aggregate?.count,
(dataset) => dataset.runsCount?.aggregate?.[0]?.count ?? 0,
{
id: 'runs',

Expand All @@ -224,71 +231,67 @@ export function DatasetsTable() {

cell: ({ getValue }) => (
<TableCell
primaryText={(getValue() ?? 0).toLocaleString()}
primaryText={getValue().toLocaleString()}
width={DepositionPageDatasetTableWidths.runs}
/>
),
},
),

columnHelper.accessor((dataset) => dataset.runs, {
id: 'annotations',

header: () => (
<CellHeader
width={DepositionPageDatasetTableWidths.annotations}
subHeader={t('depositionOnly')}
>
{t('annotations')}
</CellHeader>
),
columnHelper.accessor(
(dataset) =>
dataset.runs.edges
.flatMap(
(run) =>
run.node.annotationsAggregate?.aggregate?.map(
(aggregate) => aggregate.count ?? 0,
) ?? [],
)
.reduce((prevCount, nextCount) => prevCount + nextCount, 0),
{
id: 'annotations',

cell({ getValue }) {
const runs = getValue()
const annotationCount = sum(
runs.flatMap((run) =>
run.tomogram_voxel_spacings.flatMap(
(voxelSpacing) =>
voxelSpacing.annotations_aggregate.aggregate?.count ?? 0,
),
),
)
header: () => (
<CellHeader
width={DepositionPageDatasetTableWidths.annotations}
subHeader={t('depositionOnly')}
>
{t('annotations')}
</CellHeader>
),

return (
cell: ({ getValue }) => (
<TableCell width={DepositionPageDatasetTableWidths.annotations}>
{annotationCount.toLocaleString()}
{getValue().toLocaleString()}
</TableCell>
)
),
},
}),

columnHelper.accessor((dataset) => dataset.runs, {
id: 'annotatedObjects',

header: () => (
<CellHeader
width={DepositionPageDatasetTableWidths.annotatedObjects}
subHeader={t('depositionOnly')}
>
{t('annotatedObjects')}
</CellHeader>
),
),

cell({ getValue }) {
const runs = getValue()
const annotatedObjects = Array.from(
new Set(
runs.flatMap((run) =>
run.tomogram_voxel_spacings.flatMap((voxelSpacing) =>
voxelSpacing.annotations.flatMap(
(annotation) => annotation.object_name,
),
),
),
columnHelper.accessor(
(dataset) => [
...new Set(
dataset.runs.edges.flatMap(
(run) =>
run.node.annotationsAggregate?.aggregate
?.map((aggregate) => aggregate.groupBy?.objectName)
.filter(isDefined) ?? [],
),
)
),
],
{
id: 'annotatedObjects',

return (
header: () => (
<CellHeader
width={DepositionPageDatasetTableWidths.annotatedObjects}
subHeader={t('depositionOnly')}
>
{t('annotatedObjects')}
</CellHeader>
),

cell: ({ getValue }) => (
<TableCell
width={DepositionPageDatasetTableWidths.annotatedObjects}
renderLoadingSkeleton={() => (
Expand All @@ -299,15 +302,15 @@ export function DatasetsTable() {
</div>
)}
>
{annotatedObjects.length === 0 ? (
{getValue().length === 0 ? (
'--'
) : (
<AnnotatedObjectsList annotatedObjects={annotatedObjects} />
<AnnotatedObjectsList annotatedObjects={getValue()} />
)}
</TableCell>
)
),
},
}),
),
] as ColumnDef<Dataset>[]
} catch (err) {
sendLogs({
Expand Down
2 changes: 1 addition & 1 deletion frontend/packages/data-portal/app/hooks/useDepositionById.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ export function useDepositionById() {

return {
deposition: v1.deposition as Deposition,
datasets: v1.datasets,
datasets: v2.datasets,
annotationMethodCounts,
}
}
3 changes: 3 additions & 0 deletions frontend/packages/data-portal/app/types/gql/depositionPageTypes.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
import { GetDepositionByIdV2Query } from 'app/__generated_v2__/graphql'

export type Dataset = GetDepositionByIdV2Query['datasets'][number]
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