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Merged
nafiz1001 merged 2 commits into from
Sep 2, 2026
Merged

SampleAndLibrary to SampleAndLibraryAndIdentity #1187

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42bfb13
SampleAndLibrary to SampleAndLibraryAndIdentity
nafiz1001 Aug 31, 2026
2e841e2
npx prettier --write ./src/components/individuals/IndividualAssociate…
nafiz1001 Sep 2, 2026
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163 changes: 83 additions & 80 deletions frontend/src/components/individuals/IndividualAssociatedSamples.tsx
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Original file line number Diff line number Diff line change
@@ -1,94 +1,97 @@
import React, { useMemo, useCallback } from "react"
import { SAMPLE_COLUMN_DEFINITIONS as SAMPLE_COLUMNS, SAMPLE_COLUMN_FILTERS, SampleColumnID } from '../samples/SampleTableColumns';
import { clearFilters, setFilter, setSortBy } from '../../modules/individualDetails/actions'
import { FilterDescription, FilterValue, SortBy } from "../../models/paged_items";
import { useAppDispatch } from "../../hooks";
import { IndividualDetails } from "../../modules/individualDetails/models";
import { SampleAndLibrary } from "../WorkflowSamplesTable/ColumnSets";
import WorkflowSamplesTable from '../WorkflowSamplesTable/WorkflowSamplesTable'
import {
SAMPLE_COLUMN_DEFINITIONS as SAMPLE_COLUMNS,
SAMPLE_COLUMN_FILTERS,
SampleColumnID,
} from "../samples/SampleTableColumns"
import { clearFilters, setFilter, setSortBy } from "../../modules/individualDetails/actions"
import { FilterDescription, FilterValue, SortBy } from "../../models/paged_items"
import { useAppDispatch } from "../../hooks"
import { IndividualDetails } from "../../modules/individualDetails/models"
import { SampleAndLibraryAndIdentity } from "../WorkflowSamplesTable/ColumnSets"
import WorkflowSamplesTable from "../WorkflowSamplesTable/WorkflowSamplesTable"

interface IndividualAssociatedSamplesProps {
samples: SampleAndLibrary[],
individual: IndividualDetails
samples: SampleAndLibraryAndIdentity[]
individual: IndividualDetails
}

const IndividualAssociatedSamples = ({ samples, individual }: IndividualAssociatedSamplesProps) => {
const dispatch = useAppDispatch()

const dispatch = useAppDispatch();
const handleSetFilter = useCallback(
(filterKey: string, value: FilterValue, description: FilterDescription) => {
if (typeof description === "undefined") {
return
}
if (individual.individual) dispatch(setFilter(individual.individual.id, description, value))
},
[dispatch],
)
const handleSetSortBy = useCallback(
(sortBy: SortBy) => {
if (individual.individual) dispatch(setSortBy(individual.individual.id, sortBy))
},
[dispatch],
)
const columnsForSelection = useMemo(() => {
const columns = [
SAMPLE_COLUMNS.ID,
SAMPLE_COLUMNS.KIND,
SAMPLE_COLUMNS.NAME,
SAMPLE_COLUMNS.PROJECT,
SAMPLE_COLUMNS.CONTAINER_BARCODE,
SAMPLE_COLUMNS.COORDINATES,
SAMPLE_COLUMNS.VOLUME,
SAMPLE_COLUMNS.CONCENTRATION,
SAMPLE_COLUMNS.QC_FLAG,
SAMPLE_COLUMNS.CREATION_DATE,
SAMPLE_COLUMNS.DEPLETED,
]
return columns
}, [samples])

const handleSetFilter = useCallback(
(filterKey: string, value: FilterValue, description: FilterDescription) => {
if (typeof description === 'undefined') {
return
}
if (individual.individual)
dispatch(setFilter(individual.individual.id, description, value))
}, [dispatch]
)
const handleSetSortBy = useCallback(
(sortBy: SortBy) => {
if (individual.individual)
dispatch(setSortBy(individual.individual.id, sortBy))
},
[dispatch]
)
const columnsForSelection = useMemo(() => {
const columns = [
SAMPLE_COLUMNS.ID,
SAMPLE_COLUMNS.KIND,
SAMPLE_COLUMNS.NAME,
SAMPLE_COLUMNS.PROJECT,
SAMPLE_COLUMNS.CONTAINER_BARCODE,
SAMPLE_COLUMNS.COORDINATES,
SAMPLE_COLUMNS.VOLUME,
SAMPLE_COLUMNS.CONCENTRATION,
SAMPLE_COLUMNS.QC_FLAG,
SAMPLE_COLUMNS.CREATION_DATE,
SAMPLE_COLUMNS.DEPLETED
]
return columns
}, [samples])

const filterKeys = useMemo(() => {
return {
[SampleColumnID.ID]: 'id',
[SampleColumnID.KIND]: 'derived_samples__sample_kind__name',
[SampleColumnID.NAME]: 'name',
[SampleColumnID.INDIVIDUAL]: 'derived_samples__biosample__individual__name',
[SampleColumnID.CONTAINER_NAME]: 'container__name',
[SampleColumnID.CONTAINER_BARCODE]: 'container__barcode',
[SampleColumnID.COORDINATES]: 'coordinate__name',
[SampleColumnID.VOLUME]: 'volume',
[SampleColumnID.CONCENTRATION]: 'concentration',
[SampleColumnID.CREATION_DATE]: 'creation_date',
[SampleColumnID.DEPLETED]: 'depleted',
[SampleColumnID.QC_FLAG]: 'qc_flag',
[SampleColumnID.PROJECT]: 'derived_by_samples__project__name',
}
}, [])
const filterKeys = useMemo(() => {
return {
[SampleColumnID.ID]: "id",
[SampleColumnID.KIND]: "derived_samples__sample_kind__name",
[SampleColumnID.NAME]: "name",
[SampleColumnID.INDIVIDUAL]: "derived_samples__biosample__individual__name",
[SampleColumnID.CONTAINER_NAME]: "container__name",
[SampleColumnID.CONTAINER_BARCODE]: "container__barcode",
[SampleColumnID.COORDINATES]: "coordinate__name",
[SampleColumnID.VOLUME]: "volume",
[SampleColumnID.CONCENTRATION]: "concentration",
[SampleColumnID.CREATION_DATE]: "creation_date",
[SampleColumnID.DEPLETED]: "depleted",
[SampleColumnID.QC_FLAG]: "qc_flag",
[SampleColumnID.PROJECT]: "derived_by_samples__project__name",
}
}, [])

const filterDefinitions = useMemo(() => {
return { ...SAMPLE_COLUMN_FILTERS }
}, [])
const filterDefinitions = useMemo(() => {
return { ...SAMPLE_COLUMN_FILTERS }
}, [])

const localClearFilters = () => {
if (clearFilters && individual.individual)
dispatch(clearFilters(individual.individual.id))
}
const localClearFilters = () => {
if (clearFilters && individual.individual) dispatch(clearFilters(individual.individual.id))
}

return <>
<WorkflowSamplesTable
clearFilters={localClearFilters}
hasFilter={true}
filters={individual.samplesByIndividual.filters}
filterDefinitions={filterDefinitions}
filterKeys={filterKeys}
samples={samples ? samples : []}
setFilter={handleSetFilter}
setSortBy={handleSetSortBy}
columns={columnsForSelection}
/>
return (
<>
<WorkflowSamplesTable
clearFilters={localClearFilters}
hasFilter={true}
filters={individual.samplesByIndividual.filters}
filterDefinitions={filterDefinitions}
filterKeys={filterKeys}
samples={samples ? samples : []}
setFilter={handleSetFilter}
setSortBy={handleSetSortBy}
columns={columnsForSelection}
/>
</>
)
}

export default IndividualAssociatedSamples
export default IndividualAssociatedSamples
138 changes: 69 additions & 69 deletions frontend/src/components/individuals/IndividualsDetailContent.tsx
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@@ -1,78 +1,78 @@
import React, { useEffect, useState } from "react";
import { useParams } from "react-router-dom";
import { Tabs } from 'antd'
import useHashURL from '../../hooks/useHashURL'
import AppPageHeader from "../AppPageHeader";
import PageContent from "../PageContent";
import EditButton from "../EditButton";
import IndividualOverview from "./IndividualOverview";
import { useAppDispatch, useAppSelector } from "../../hooks";
import { selectIndividualsDetailsById } from "../../selectors";
import IndividualAssociatedSamples from "./IndividualAssociatedSamples";
import { flushIndividualDetails, listTable } from "../../modules/individualDetails/actions";
import { IndividualDetails, IndividualDetailsById } from "../../modules/individualDetails/models";
import { Sample } from "../../models/frontend_models";
import { SampleAndLibrary } from "../WorkflowSamplesTable/ColumnSets";
import React, { useEffect, useState } from "react"
import { useParams } from "react-router-dom"
import { Tabs } from "antd"
import useHashURL from "../../hooks/useHashURL"
import AppPageHeader from "../AppPageHeader"
import PageContent from "../PageContent"
import EditButton from "../EditButton"
import IndividualOverview from "./IndividualOverview"
import { useAppDispatch, useAppSelector } from "../../hooks"
import { selectIndividualsDetailsById } from "../../selectors"
import IndividualAssociatedSamples from "./IndividualAssociatedSamples"
import { flushIndividualDetails, listTable } from "../../modules/individualDetails/actions"
import { IndividualDetails, IndividualDetailsById } from "../../modules/individualDetails/models"
import { Sample } from "../../models/frontend_models"
import { SampleAndLibraryAndIdentity } from "../WorkflowSamplesTable/ColumnSets"

const IndividualsDetailContent = () => {
const { id } = useParams();
const dispatch = useAppDispatch()
const individualDetailsById: IndividualDetailsById = useAppSelector(selectIndividualsDetailsById)
const { id } = useParams()
const dispatch = useAppDispatch()
const individualDetailsById: IndividualDetailsById = useAppSelector(selectIndividualsDetailsById)

const [activeKey, setActiveKey] = useHashURL('overview')
const [individual, setIndividual] = useState<IndividualDetails>()
const [activeKey, setActiveKey] = useHashURL("overview")
const [individual, setIndividual] = useState<IndividualDetails>()

useEffect(() => {
dispatch(listTable(Number(id)));
}, [id, dispatch])
useEffect(() => {
dispatch(listTable(Number(id)))
}, [id, dispatch])

useEffect(() => {
// Flush the labwork state when the user navigates away from the
// the labwork section.
return () => {
dispatch(flushIndividualDetails(Number(id)))
}
}, [dispatch, id])
useEffect(() => {
if (individualDetailsById[Number(id)]) {
const individualInstance: IndividualDetails = {
...individualDetailsById[Number(id)]
}
if (individualInstance) {
setIndividual(individualInstance)
}
}
}, [individualDetailsById, id])
useEffect(() => {
// Flush the labwork state when the user navigates away from the
// the labwork section.
return () => {
dispatch(flushIndividualDetails(Number(id)))
}
}, [dispatch, id])
useEffect(() => {
if (individualDetailsById[Number(id)]) {
const individualInstance: IndividualDetails = {
...individualDetailsById[Number(id)],
}
if (individualInstance) {
setIndividual(individualInstance)
}
}
}, [individualDetailsById, id])

const samples = individual?.samplesByIndividual.items.reduce((acc, sampleID) => {
const sample = individual?.samplesByIndividual.itemsByID[sampleID]
if (sample) {
acc.push({ sample: sample as Sample })
}
return acc
}, [] as SampleAndLibrary[])
const samples = individual?.samplesByIndividual.items.reduce((acc, sampleID) => {
const sample = individual?.samplesByIndividual.itemsByID[sampleID]
if (sample) {
acc.push({ sample: sample as Sample })
}
return acc
}, [] as SampleAndLibraryAndIdentity[])

const title =
`Individual ${[id, (individual && individual.individual) ? individual.individual.name : undefined].filter(Boolean).join(' - ')}`;
const title = `Individual ${[id, individual && individual.individual ? individual.individual.name : undefined].filter(Boolean).join(" - ")}`

return <>
<AppPageHeader title={title} extra={<EditButton url={`/individuals/${id}/update`} />} />
<PageContent loading={(individual && individual.individual?.isFetching)}>
<Tabs activeKey={activeKey} onChange={setActiveKey} size="large" type="card">
<Tabs.TabPane tab="Overview" key="overview">
<IndividualOverview individual={(individual && individual) ? individual.individual : {}} />
</Tabs.TabPane>
<Tabs.TabPane tab="Associated Samples" key="samples">
{
individual && individual.individual.id &&
< IndividualAssociatedSamples samples={samples ?? []} individual={individual} />
}
</Tabs.TabPane>
</Tabs>
</PageContent>
</>;
return (
<>
<AppPageHeader title={title} extra={<EditButton url={`/individuals/${id}/update`} />} />
<PageContent loading={individual && individual.individual?.isFetching}>
<Tabs activeKey={activeKey} onChange={setActiveKey} size="large" type="card">
<Tabs.TabPane tab="Overview" key="overview">
<IndividualOverview
individual={individual && individual ? individual.individual : {}}
/>
</Tabs.TabPane>
<Tabs.TabPane tab="Associated Samples" key="samples">
{individual && individual.individual.id && (
<IndividualAssociatedSamples samples={samples ?? []} individual={individual} />
)}
</Tabs.TabPane>
</Tabs>
</PageContent>
</>
)
}


};

export default IndividualsDetailContent;
export default IndividualsDetailContent
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