galaxyproject · NoopDog · Aug 18, 2025 · Aug 18, 2025 · Aug 18, 2025 · Aug 18, 2025
diff --git a/...ncingStep/components/ENASequencingData/components/AccessionSelector/accessionSelector.tsx b/...ncingStep/components/ENASequencingData/components/AccessionSelector/accessionSelector.tsx
@@ -24,6 +24,7 @@ export const AccessionSelector = ({
   onRequestData,
   open,
   status,
+  table,
 }: Props): JSX.Element => {
   return (
     <StyledDialog
@@ -36,6 +37,7 @@ export const AccessionSelector = ({
           onSubmit: (event: FormEvent<HTMLFormElement>) =>
             onRequestData(event, {
               onSuccess: () => {
+                table.resetColumnFilters(); // Clear column filters from previous query.
                 onContinue();
                 onClose();
               },

diff --git a/...ts/Step/SequencingStep/components/ENASequencingData/components/AccessionSelector/types.ts b/...ts/Step/SequencingStep/components/ENASequencingData/components/AccessionSelector/types.ts
@@ -1,4 +1,6 @@
-import { OnRequestData, Status } from "../../hooks/UseENA/types";
+import { OnRequestData, Status } from "../../hooks/UseENADataByAccession/types";
+import { Table } from "@tanstack/react-table";
+import { ReadRun } from "../../types";
 
 export interface Props {
   clearErrors: () => void;
@@ -7,4 +9,5 @@ export interface Props {
   onRequestData: OnRequestData;
   open: boolean;
   status: Status;
+  table: Table<ReadRun>;
 }
diff --git a/...ingStep/components/ENASequencingData/components/CollectionSelector/collectionSelector.tsx b/...ingStep/components/ENASequencingData/components/CollectionSelector/collectionSelector.tsx
@@ -8,6 +8,7 @@ import { Table } from "./components/Table/table";
 import { RowSelectionState } from "@tanstack/table-core";
 import { buildEnaSequencingReads } from "../../utils";
 import { ColumnFilters } from "./components/ColumnFilters/columnFilters";
+import { preSelectColumnFilters } from "./utils";
 
 export const CollectionSelector = ({
   onClose,
@@ -20,7 +21,12 @@ export const CollectionSelector = ({
   const [rowSelection, setRowSelection] = useState<RowSelectionState>({});
   return (
     <StyledDialog
-      onTransitionEnter={() => setRowSelection(table.getState().rowSelection)}
+      onTransitionEnter={() => {
+        setRowSelection(table.getState().rowSelection);
+        if (selectedCount > 0) return;
+        preSelectColumnFilters(table, stepKey);
+      }}
+      onClose={onClose}
       open={open}
     >
       <DialogTitle onClose={onClose} title="Select Sequencing Runs" />
@@ -46,10 +52,19 @@ export const CollectionSelector = ({
             onClose();
           }}
         >
-          Add {selectedCount ? selectedCount : ""} Sequencing Run
-          {selectedCount > 1 ? "s" : ""}
+          {renderButtonText(selectedCount)}
         </Button>
       </DialogActions>
     </StyledDialog>
   );
 };
+
+/**
+ * Renders the button text based on the selected count.
+ * @param selectedCount - The number of selected rows.
+ * @returns The button text.
+ */
+function renderButtonText(selectedCount: number): string {
+  if (selectedCount === 1) return "Add 1 Sequencing Run";
+  return `Add ${selectedCount} Sequencing Runs`;
+}
diff --git a/...ep/SequencingStep/components/ENASequencingData/components/CollectionSelector/constants.ts b/...ep/SequencingStep/components/ENASequencingData/components/CollectionSelector/constants.ts
@@ -0,0 +1,16 @@
+import { SEQUENCING_DATA_TYPE } from "../../../../types";
+import { CATEGORY_CONFIGS } from "./hooks/UseTable/categoryConfigs";
+
+export const PRESELECTED_COLUMN_FILTERS: Record<
+  SEQUENCING_DATA_TYPE,
+  Record<string, string[]>
+> = {
+  [SEQUENCING_DATA_TYPE.READ_RUNS_PAIRED]: {
+    [CATEGORY_CONFIGS.LIBRARY_LAYOUT.key]: ["PAIRED"],
+    [CATEGORY_CONFIGS.LIBRARY_STRATEGY.key]: ["WGS"],
+  },
+  [SEQUENCING_DATA_TYPE.READ_RUNS_SINGLE]: {
+    [CATEGORY_CONFIGS.LIBRARY_LAYOUT.key]: ["SINGLE"],
+    [CATEGORY_CONFIGS.LIBRARY_STRATEGY.key]: ["WGS"],
+  },
+};
diff --git a/...ponents/ENASequencingData/components/CollectionSelector/hooks/UseTable/categoryConfigs.ts b/...ponents/ENASequencingData/components/CollectionSelector/hooks/UseTable/categoryConfigs.ts
@@ -10,6 +10,7 @@ export const CATEGORY_CONFIGS: Record<string, CategoryConfig> = {
     label: "Experiment Accession",
   },
   FASTQ_FTP: { key: "fastq_ftp", label: "Fastq FTP" },
+  FIRST_PUBLIC: { key: "first_public", label: "First Public" },
   INSTRUMENT_MODEL: { key: "instrument_model", label: "Instrument Model" },
   INSTRUMENT_PLATFORM: {
     key: "instrument_platform",

diff --git a/...ep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/columnDef.ts b/...ep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/columnDef.ts
@@ -35,6 +35,13 @@ const FASTQ_FTP: ColumnDef<ReadRun> = {
   meta: { width: { max: "1.8fr", min: "200px" } },
 };
 
+const FIRST_PUBLIC: ColumnDef<ReadRun> = {
+  accessorKey: CATEGORY_CONFIGS.FIRST_PUBLIC.key,
+  enableColumnFilter: false,
+  header: CATEGORY_CONFIGS.FIRST_PUBLIC.label,
+  meta: META,
+};
+
 const INSTRUMENT_MODEL: ColumnDef<ReadRun> = {
   accessorKey: CATEGORY_CONFIGS.INSTRUMENT_MODEL.key,
   filterFn: SELECT_FILTER_FN,
@@ -102,6 +109,7 @@ const STUDY_ACCESSION: ColumnDef<ReadRun> = {
 export const columns: ColumnDef<ReadRun>[] = [
   COLUMN_DEF.ROW_SELECTION as ColumnDef<ReadRun>,
   RUN_ACCESSION,
+  FIRST_PUBLIC,
   FASTQ_FTP,
   EXPERIMENT_ACCESSION,
   SAMPLE_ACCESSION,

diff --git a/...ingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/hook.ts b/...ingStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/hook.ts
@@ -1,5 +1,4 @@
 import {
-  functionalUpdate,
   getCoreRowModel,
   getFacetedRowModel,
   getFilteredRowModel,
@@ -14,22 +13,42 @@ import { useCallback, useMemo, useState } from "react";
 import { getFacetedUniqueValuesWithArrayValues } from "@databiosphere/findable-ui/lib/components/Table/common/utils";
 import { arrIncludesSome } from "@databiosphere/findable-ui/lib/components/Table/columnDef/columnFilters/filterFn";
 import { ColumnFiltersState, Updater } from "@tanstack/react-table";
+import { UseENADataByAccession } from "../../../../hooks/UseENADataByAccession/types";
+import { UseENADataByTaxonomyId } from "../../../../hooks/UseENADataByTaxonomyId/types";
+import { ENA_QUERY_METHOD } from "../../../../../../types";
+import { updateColumnFilters } from "./utils";
 
 export const useTable = (
-  readRuns: ReadRun[] | undefined = []
+  enaQueryMethod: ENA_QUERY_METHOD,
+  enaAccession: UseENADataByAccession<ReadRun>,
+  enaTaxonomyId: UseENADataByTaxonomyId<ReadRun>
 ): Table<ReadRun> => {
-  const [columnFilters, setColumnFilters] = useState<ColumnFiltersState>([]);
+  const [columnFiltersByMethod, setColumnFiltersByMethod] = useState<
+    Record<ENA_QUERY_METHOD, ColumnFiltersState>
+  >({
+    [ENA_QUERY_METHOD.ACCESSION]: [],
+    [ENA_QUERY_METHOD.TAXONOMY_ID]: [],
+  });
 
   const onColumnFiltersChange = useCallback(
-    (updaterOrValue: Updater<ColumnFiltersState>): void => {
-      setColumnFilters((old) => functionalUpdate(updaterOrValue, old));
-    },
-    [setColumnFilters]
+    (updaterOrValue: Updater<ColumnFiltersState>): void =>
+      setColumnFiltersByMethod(
+        updateColumnFilters(enaQueryMethod, updaterOrValue)
+      ),
+    [enaQueryMethod]
   );
 
-  const data = useMemo(() => readRuns, [readRuns]);
+  // Get the data for the ENA query method (by accession or by taxonomy ID).
+  const { data: readRuns } =
+    enaQueryMethod === ENA_QUERY_METHOD.ACCESSION
+      ? enaAccession
+      : enaTaxonomyId;
+
+  const data = useMemo(() => readRuns || [], [readRuns]);
+
+  const meta = { enaQueryMethod };
 
-  const state = { columnFilters };
+  const state = { columnFilters: columnFiltersByMethod[enaQueryMethod] };
 
   return useReactTable<ReadRun>({
     _features: [ROW_POSITION, ROW_PREVIEW],
@@ -44,6 +63,7 @@ export const useTable = (
     getFacetedUniqueValues: getFacetedUniqueValuesWithArrayValues(),
     getFilteredRowModel: getFilteredRowModel(),
     getRowId: (row) => row.run_accession,
+    meta,
     onColumnFiltersChange,
     state,
   });

diff --git a/...ngStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/utils.ts b/...ngStep/components/ENASequencingData/components/CollectionSelector/hooks/UseTable/utils.ts
@@ -0,0 +1,26 @@
+import {
+  ColumnFiltersState,
+  Updater,
+  functionalUpdate,
+} from "@tanstack/react-table";
+import { ENA_QUERY_METHOD } from "../../../../../../types";
+
+/**
+ * Updates the column filters for the specified ENA query method.
+ * @param enaQueryMethod - ENA query method.
+ * @param updaterOrValue - Updater or value.
+ * @returns Updated column filter state for the specified ENA query method.
+ */
+export function updateColumnFilters(
+  enaQueryMethod: ENA_QUERY_METHOD,
+  updaterOrValue: Updater<ColumnFiltersState>
+): (
+  old: Record<ENA_QUERY_METHOD, ColumnFiltersState>
+) => Record<ENA_QUERY_METHOD, ColumnFiltersState> {
+  return (old: Record<ENA_QUERY_METHOD, ColumnFiltersState>) => {
+    return {
+      ...old,
+      [enaQueryMethod]: functionalUpdate(updaterOrValue, old[enaQueryMethod]),
+    };
+  };
+}
diff --git a/...s/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/types.ts b/...s/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/types.ts
@@ -1,12 +1,13 @@
 import { ReadRun } from "../../types";
 import { OnConfigure } from "../../../../../../../../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
 import { Table } from "@tanstack/react-table";
+import { SEQUENCING_DATA_TYPE } from "../../../../types";
 
 export interface Props {
   onClose: () => void;
   onConfigure: OnConfigure;
   open: boolean;
   selectedCount: number;
-  stepKey: "readRunsSingle" | "readRunsPaired";
+  stepKey: SEQUENCING_DATA_TYPE;
   table: Table<ReadRun>;
 }
diff --git a/...s/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/utils.ts b/...s/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/utils.ts
@@ -0,0 +1,70 @@
+import { ENA_QUERY_METHOD, SEQUENCING_DATA_TYPE } from "../../../../types";
+import { ColumnFiltersState, Table } from "@tanstack/react-table";
+import { ReadRun } from "../../types";
+import { PRESELECTED_COLUMN_FILTERS } from "./constants";
+
+/**
+ * Returns true if the table is using data from ENA query method by taxonomy ID.
+ * @param table - The table.
+ * @returns True if the table is using data from ENA query method by taxonomy ID.
+ */
+function isENAQueryMethodByTaxonomyId(table: Table<ReadRun>): boolean {
+  if (!table.options.meta) return false;
+  if (!("enaQueryMethod" in table.options.meta)) return false;
+
+  return table.options.meta.enaQueryMethod === ENA_QUERY_METHOD.TAXONOMY_ID;
+}
+
+/**
+ * Pre-selects column filters based on the given step key for ENA query method by taxonomy ID.
+ * @param table - Table instance.
+ * @param stepKey - Step key.
+ */
+export function preSelectColumnFilters(
+  table: Table<ReadRun>,
+  stepKey: SEQUENCING_DATA_TYPE
+): void {
+  if (isENAQueryMethodByTaxonomyId(table)) {
+    const preselectedFilters = PRESELECTED_COLUMN_FILTERS[stepKey];
+    const columnFiltersState = buildValidatedColumnFilters(
+      table,
+      preselectedFilters
+    );
+    table.setColumnFilters(columnFiltersState);
+  }
+}
+
+/**
+ * Builds validated column filters from preselected filter values.
+ * Filters out columns that don't exist in the table and values that aren't available
+ * in the column's faceted unique values.
+ * @param table - Table instance.
+ * @param preselectedFilters - Record of column IDs to arrays of desired filter values.
+ * @returns Column filters state.
+ */
+function buildValidatedColumnFilters(
+  table: Table<ReadRun>,
+  preselectedFilters: Record<string, string[]>
+): ColumnFiltersState {
+  const columnFiltersState: ColumnFiltersState = [];
+
+  for (const [columnId, desiredValues] of Object.entries(preselectedFilters)) {
+    const column = table.getColumn(columnId);
+    if (!column) continue;
+
+    const availableValues = column.getFacetedUniqueValues();
+    const validValues: string[] = [];
+
+    // Only include values that exist in the column's faceted data.
+    for (const value of desiredValues) {
+      if (!availableValues.has(value)) continue;
+      validValues.push(value);
+    }
+
+    if (validValues.length === 0) continue;
+
+    columnFiltersState.push({ id: columnId, value: validValues });
+  }
+
+  return columnFiltersState;
+}
diff --git a/...nts/Step/SequencingStep/components/ENASequencingData/components/DataSelector/constants.ts b/...nts/Step/SequencingStep/components/ENASequencingData/components/DataSelector/constants.ts
@@ -1,6 +1,10 @@
-import { PaperProps } from "@mui/material";
+import { GridProps, PaperProps } from "@mui/material";
 
-export const MAX_READ_RUNS_FOR_BROWSE_ALL = 200;
+export const GRID_PROPS: GridProps = {
+  alignItems: "center",
+  container: true,
+  gap: 4,
+};
 
 export const PAPER_PROPS: PaperProps = {
   elevation: 0,