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d-calland-callan
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Merge branch 'main' into artic-measles
2 parents dcf40be + f5a0ed0 commit 7002e70

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23 files changed

+327
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‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/components/ColumnFilters/columnFilters.styles.ts‎

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@@ -1,7 +1,13 @@
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import styled from "@emotion/styled";
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import { PALETTE } from "@databiosphere/findable-ui/lib/styles/common/constants/palette";
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import { SearchAllFilters } from "@databiosphere/findable-ui/lib/components/Filter/components/SearchAllFilters/searchAllFilters";
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export const StyledContainer = styled("div")`
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box-shadow: inset -1px 0 ${PALETTE.SMOKE_MAIN};
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overflow: auto;
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`;
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export const StyledSearchAllFilters = styled(SearchAllFilters)`
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margin: 8px 0;
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padding: 0 16px;
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`;

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/components/ColumnFilters/columnFilters.tsx‎

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@@ -4,6 +4,8 @@ import { SurfaceProps } from "@databiosphere/findable-ui/lib/components/Filter/c
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import { Filters } from "@databiosphere/findable-ui/lib/components/Filter/components/Filters/filters";
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import { StyledContainer } from "./columnFilters.styles";
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import { Controls } from "@databiosphere/findable-ui/lib/components/Filter/components/controls/Controls/controls";
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import { StyledSearchAllFilters } from "./columnFilters.styles";
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import { getCategoryViews } from "./utils";
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export const ColumnFilters = ({ table }: Props): JSX.Element => {
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return (
@@ -12,6 +14,10 @@ export const ColumnFilters = ({ table }: Props): JSX.Element => {
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renderSurface={(props: SurfaceProps) => (
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<>
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<Controls onFilter={props.onFilter} />
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<StyledSearchAllFilters
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categoryViews={getCategoryViews(props.categoryFilters)}
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onFilter={props.onFilter}
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/>
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<Filters {...props} />
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</>
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)}

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/components/ColumnFilters/utils.ts‎

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@@ -0,0 +1,15 @@
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import { CategoryFilter } from "@databiosphere/findable-ui/lib/components/Filter/components/Filters/filters";
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import { CategoryView } from "@databiosphere/findable-ui/lib/common/categories/views/types";
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/**
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* Returns all category views from the given category filters.
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* @param categoryFilters - Category filters.
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* @returns Category views.
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*/
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export function getCategoryViews(
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categoryFilters: CategoryFilter[]
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): CategoryView[] {
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return categoryFilters.flatMap(
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(categoryFilter) => categoryFilter.categoryViews
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);
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}

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/categoryConfigs.ts‎

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Original file line numberDiff line numberDiff line change
@@ -1,16 +1,18 @@
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import { CategoryConfig } from "@databiosphere/findable-ui/lib/common/categories/config/types";
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import { VIEW_KIND } from "@databiosphere/findable-ui/lib/common/categories/views/types";
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export const CATEGORY_CONFIGS: Record<string, CategoryConfig> = {
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BASE_COUNT: {
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key: "base_count",
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label: "Base Count",
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viewKind: VIEW_KIND.RANGE,
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},
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EXPERIMENT_ACCESSION: {
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key: "experiment_accession",
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label: "Experiment Accession",
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},
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FASTQ_FTP: { key: "fastq_ftp", label: "Fastq FTP" },
13-
FIRST_PUBLIC: { key: "first_public", label: "First Public" },
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FIRST_CREATED: { key: "first_created", label: "First Created" },
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INSTRUMENT_MODEL: { key: "instrument_model", label: "Instrument Model" },
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INSTRUMENT_PLATFORM: {
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key: "instrument_platform",
@@ -21,6 +23,7 @@ export const CATEGORY_CONFIGS: Record<string, CategoryConfig> = {
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READ_COUNT: {
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key: "read_count",
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label: "Read Count",
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viewKind: VIEW_KIND.RANGE,
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},
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RUN_ACCESSION: { key: "run_accession", label: "Run Accession" },
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SAMPLE_ACCESSION: { key: "sample_accession", label: "Sample Accession" },

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/categoryGroups.ts‎

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import { CategoryGroup } from "@databiosphere/findable-ui/lib/config/entities";
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import { CATEGORY_CONFIGS } from "./categoryConfigs";
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export const CATEGORY_GROUPS: CategoryGroup[] = [
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{
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categoryConfigs: [CATEGORY_CONFIGS.SCIENTIFIC_NAME],
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label: "Organism",
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},
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{
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categoryConfigs: [
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CATEGORY_CONFIGS.SAMPLE_ACCESSION,
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CATEGORY_CONFIGS.STUDY_ACCESSION,
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CATEGORY_CONFIGS.RUN_ACCESSION,
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CATEGORY_CONFIGS.EXPERIMENT_ACCESSION,
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],
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label: "Accession",
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},
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{
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categoryConfigs: [
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CATEGORY_CONFIGS.INSTRUMENT_PLATFORM,
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CATEGORY_CONFIGS.INSTRUMENT_MODEL,
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],
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label: "Instrument",
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},
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{
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categoryConfigs: [
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CATEGORY_CONFIGS.LIBRARY_STRATEGY,
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CATEGORY_CONFIGS.LIBRARY_LAYOUT,
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],
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label: "Library",
31+
},
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{
33+
categoryConfigs: [CATEGORY_CONFIGS.READ_COUNT, CATEGORY_CONFIGS.BASE_COUNT],
34+
label: "Count",
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},
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];

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/columnDef.ts‎

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Original file line numberDiff line numberDiff line change
@@ -4,18 +4,19 @@ import { buildFastqFTP } from "./viewBuilders";
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import { COLUMN_DEF } from "@databiosphere/findable-ui/lib/components/Table/common/columnDef";
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import { BasicCell } from "../../components/Table/components/TableCell/components/BasicCell/basicCell";
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import { CATEGORY_CONFIGS } from "./categoryConfigs";
7+
import { formatNumber } from "../../../../../../../../../../../../../../../../../viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders";
78

8-
// const RANGE_FILTER_FN = "inNumberRange";
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const RANGE_FILTER_FN = "inNumberRange";
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const SELECT_FILTER_FN = "arrIncludesSome";
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const META: ColumnMeta<ReadRun, unknown> = {
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width: { max: "1.2fr", min: "120px" },
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width: { max: "1.2fr", min: "140px" },
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};
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const BASE_COUNT: ColumnDef<ReadRun> = {
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accessorKey: CATEGORY_CONFIGS.BASE_COUNT.key,
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// filterFn: RANGE_FILTER_FN,
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filterFn: SELECT_FILTER_FN,
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cell: (ctx) => formatNumber(Number(ctx.getValue())),
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filterFn: RANGE_FILTER_FN,
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header: CATEGORY_CONFIGS.BASE_COUNT.label,
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meta: META,
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};
@@ -35,10 +36,10 @@ const FASTQ_FTP: ColumnDef<ReadRun> = {
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meta: { width: { max: "1.8fr", min: "200px" } },
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};
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38-
const FIRST_PUBLIC: ColumnDef<ReadRun> = {
39-
accessorKey: CATEGORY_CONFIGS.FIRST_PUBLIC.key,
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const FIRST_CREATED: ColumnDef<ReadRun> = {
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accessorKey: CATEGORY_CONFIGS.FIRST_CREATED.key,
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enableColumnFilter: false,
41-
header: CATEGORY_CONFIGS.FIRST_PUBLIC.label,
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header: CATEGORY_CONFIGS.FIRST_CREATED.label,
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meta: META,
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};
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@@ -72,8 +73,8 @@ const LIBRARY_STRATEGY: ColumnDef<ReadRun> = {
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const READ_COUNT: ColumnDef<ReadRun> = {
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accessorKey: CATEGORY_CONFIGS.READ_COUNT.key,
75-
// filterFn: RANGE_FILTER_FN,
76-
filterFn: SELECT_FILTER_FN,
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cell: (ctx) => formatNumber(Number(ctx.getValue())),
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filterFn: RANGE_FILTER_FN,
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header: CATEGORY_CONFIGS.READ_COUNT.label,
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meta: META,
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};
@@ -109,7 +110,7 @@ const STUDY_ACCESSION: ColumnDef<ReadRun> = {
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export const columns: ColumnDef<ReadRun>[] = [
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COLUMN_DEF.ROW_SELECTION as ColumnDef<ReadRun>,
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RUN_ACCESSION,
112-
FIRST_PUBLIC,
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FIRST_CREATED,
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FASTQ_FTP,
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EXPERIMENT_ACCESSION,
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SAMPLE_ACCESSION,

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/constants.ts‎

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@@ -4,6 +4,6 @@ import { CATEGORY_CONFIGS } from "./categoryConfigs";
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export const SORTING: SortingState = [
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{
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desc: true,
7-
id: CATEGORY_CONFIGS.FIRST_PUBLIC.key,
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id: CATEGORY_CONFIGS.FIRST_CREATED.key,
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},
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];

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/hook.ts‎

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@@ -19,6 +19,8 @@ import { ENA_QUERY_METHOD } from "../../../../../../types";
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import { updateColumnFilters } from "./utils";
2020
import { SORTING } from "./constants";
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import { getSortedRowModel } from "@tanstack/react-table";
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import { CATEGORY_GROUPS } from "./categoryGroups";
23+
import { getFacetedMinMaxValues } from "@databiosphere/findable-ui/lib/components/Table/featureOptions/facetedColumn/getFacetedMinMaxValues";
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2325
export const useTable = (
2426
enaQueryMethod: ENA_QUERY_METHOD,
@@ -50,7 +52,7 @@ export const useTable = (
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5153
const initialState = { sorting: SORTING };
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53-
const meta = { enaQueryMethod };
55+
const meta = { categoryGroups: CATEGORY_GROUPS, enaQueryMethod };
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5557
const state = { columnFilters: columnFiltersByMethod[enaQueryMethod] };
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@@ -64,6 +66,7 @@ export const useTable = (
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enableSorting: true,
6567
filterFns: { arrIncludesSome },
6668
getCoreRowModel: getCoreRowModel(),
69+
getFacetedMinMaxValues: getFacetedMinMaxValues(),
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getFacetedRowModel: getFacetedRowModel(),
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getFacetedUniqueValues: getFacetedUniqueValuesWithArrayValues(),
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getFilteredRowModel: getFilteredRowModel(),

‎app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/hooks/UseENADataByAccession/constants.ts‎

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@@ -13,7 +13,7 @@ export const ENA_FIELDS = [
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"fastq_ftp",
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"fastq_md5",
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"fastq_aspera",
16-
"first_public",
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"first_created",
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"instrument_model",
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"instrument_platform",
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"library_layout",

‎app/components/index.ts‎

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@@ -15,6 +15,7 @@ export { FluidPaper } from "@databiosphere/findable-ui/lib/components/common/Pap
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export { SectionTitle } from "@databiosphere/findable-ui/lib/components/common/Section/components/SectionTitle/sectionTitle";
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export { Stack } from "@databiosphere/findable-ui/lib/components/common/Stack/stack";
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export { StaticImage } from "@databiosphere/findable-ui/lib/components/common/StaticImage/staticImage";
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export { ChipCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/ChipCell/chipCell";
1819
export {
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BackPageContentMainColumn,
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BackPageContentSideColumn,

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