@gen-epix/ui-client-casedb 4.0.0

package/dist/_chunks/Upload.js

@@ -0,0 +1,1506 @@
+import { h as e } from "./_MapCache.js";
+import { t } from "./UploadUtil.js";
+import { CaseTypeUtil as n, t as r } from "../utils/CaseTypeUtil/index.js";
+import { CASEDB_QUERY_KEY as i } from "../constants/query.js";
+import { CaseUtil as a, t as o } from "../utils/CaseUtil/index.js";
+import { UploadError as s } from "../classes/errors/index.js";
+import { CaseTypeFormUtil as c } from "../utils/CaseTypeFormUtil/index.js";
+import { t as l } from "./react.js";
+import { t as u } from "./CompletCaseTypeLoader.js";
+import { t as d } from "./shallow.js";
+import { UPLOAD_STEP as f } from "../models/upload.js";
+import { UploadStoreContext as p } from "../stores/uploadStore/index.js";
+import { c as m, o as h } from "./index.esm.js";
+import { t as g } from "./yup.js";
+import { useCaseTypeOptionsQuery as _, useCaseTypesQuery as v } from "../dataHooks/useCaseTypesQuery/index.js";
+import { useDataCollectionOptionsQuery as y } from "../dataHooks/useDataCollectionsQuery/index.js";
+import { useColMapQuery as b, useColsQuery as x } from "../dataHooks/useColsQuery/index.js";
+import { CaseContentFormDialog as S } from "../components/ui/CaseContentFormDialog/index.js";
+import { FileSelector as C } from "../components/ui/FileSelector/index.js";
+import { useSequencingProtocolOptionsQuery as w } from "../dataHooks/useSequencingProtocolsQuery/index.js";
+import { useAssemblyProtocolOptionsQuery as T } from "../dataHooks/useAssemblyProtocolsQuery/index.js";
+import { mixed as E, object as D, string as O } from "yup";
+import { CaseDbCaseApi as k, CaseDbDataIssueType as A, CaseDbEtlStatus as j, CaseDbUploadAction as M } from "@gen-epix/api-casedb";
+import { QueryClientService as ee } from "@gen-epix/ui/classes/services/QueryClientService";
+import { ObjectUtil as N } from "@gen-epix/ui-core/utils/ObjectUtil";
+import { FORM_FIELD_DEFINITION_TYPE as P } from "@gen-epix/ui-form/models/form";
+import { ConfigService as te } from "@gen-epix/ui/classes/services/ConfigService";
+import { Alert as F, AlertTitle as I, Autocomplete as ne, Box as L, Button as R, Container as re, ListItemIcon as z, ListItemText as B, MenuItem as ie, Table as V, TableBody as H, TableCell as U, TableHead as ae, TableRow as oe, TextField as se, Tooltip as ce, Typography as le, useTheme as ue } from "@mui/material";
+import { use as W, useCallback as G, useEffect as K, useId as de, useMemo as q, useRef as J, useState as Y } from "react";
+import { useTranslation as X } from "react-i18next";
+import { TableStoreContextProvider as fe, createTableStore as pe, useTableStoreContext as me } from "@gen-epix/ui/stores/tableStore";
+import { Fragment as Z, jsx as Q, jsxs as $ } from "react/jsx-runtime";
+import { ResponseHandler as he } from "@gen-epix/ui/components/ui/ResponseHandler";
+import { useItemQuery as ge } from "@gen-epix/ui/hooks/useItemQuery";
+import { useArray as _e } from "@gen-epix/ui-core/hooks/useArray";
+import ve from "@mui/material/Box";
+import { Stepper as ye } from "@gen-epix/ui/components/ui/Stepper";
+import { GenericForm as be } from "@gen-epix/ui-form/components/helpers/GenericForm";
+import { useQueryMemo as xe } from "@gen-epix/ui/hooks/useQueryMemo";
+import { useIdentifierIssuerOwnOrganizationOptionsQuery as Se } from "@gen-epix/ui/dataHooks/useIdentifierIssuerOwnOrganizationQuery";
+import { Select as Ce } from "@gen-epix/ui-form/components/fields/Select";
+import { BackdropSpinner as we } from "@gen-epix/ui/components/ui/BackdropSpinner";
+import { Confirmation as Te } from "@gen-epix/ui/components/ui/Confirmation";
+import Ee from "@mui/icons-material/Edit";
+import De from "@mui/icons-material/ErrorOutlined";
+import Oe from "@mui/icons-material/Add";
+import { Table as ke, TableMenu as Ae } from "@gen-epix/ui/components/ui/Table";
+import { TABLE_COLUMN_FROZEN as je } from "@gen-epix/ui/models/table";
+import { TableUtil as Me } from "@gen-epix/ui/utils/TableUtil";
+import { useInitializeTableStore as Ne } from "@gen-epix/ui/hooks/useInitializeTableStore";
+import { withDialog as Pe } from "@gen-epix/ui/hoc/withDialog";
+import { TestIdUtil as Fe } from "@gen-epix/ui-core/utils/TestIdUtil";
+import { FormUtil as Ie } from "@gen-epix/ui-form/utils/FormUtil";
+import { GenericErrorMessage as Le } from "@gen-epix/ui/components/ui/GenericErrorMessage";
+import { InactivityService as Re } from "@gen-epix/ui/classes/services/InactivityService";
+import { LinearProgressWithLabel as ze } from "@gen-epix/ui/components/ui/LinearProgressWithLabel";
+import { RouterService as Be } from "@gen-epix/ui/classes/services/RouterService";
+//#region src/components/ui/Upload/UploadNavigation.tsx
+var Ve = ({ backLabel: e, onGoBackButtonClick: t, onProceedButtonClick: n, proceedDisabled: r, proceedLabel: i }) => {
+	let { t: a } = X(), o = W(p), s = l(o, (e) => e.stepOrder), c = l(o, (e) => e.activeStep), u = l(o, (e) => e.goBackFromFirstStepCallback), d = l(o, (e) => e.goBackFromFirstStepLabel), f = c === s[0], m = f ? u ?? t : t;
+	return /* @__PURE__ */ $(L, {
+		sx: {
+			borderTop: (e) => `1px solid ${e.palette.divider}`,
+			display: "flex",
+			gap: 2,
+			justifyContent: "flex-end",
+			marginTop: 1,
+			paddingTop: 1
+		},
+		children: [m && /* @__PURE__ */ Q(R, {
+			onClick: m,
+			variant: "outlined",
+			children: (f ? d ?? e : e) ?? a`Go back`
+		}), n && /* @__PURE__ */ Q(R, {
+			color: "secondary",
+			disabled: r,
+			onClick: n,
+			variant: "contained",
+			children: i ?? a`Next`
+		})]
+	});
+}, He = () => {
+	let { t: e } = X(), n = v(), r = _(), a = y(), o = x(), s = de(), c = W(p), u = l(c, (e) => e.caseTypeId), d = l(c, (e) => e.fileList), f = l(c, (e) => e.fileName), m = l(c, (e) => e.fileParsingError), b = l(c, (e) => e.goToNextStep), S = l(c, (e) => e.createdInDataCollectionOptions), C = l(c, (e) => e.rawData), w = l(c, (e) => e.setCols), T = l(c, (e) => e.setCaseTypeId), A = l(c, (e) => e.setCompleteCaseType), j = l(c, (e) => e.setCreatedInDataCollectionId), M = l(c, (e) => e.setFileList), ee = l(c, (e) => e.setSheet), N = l(c, (e) => e.setDataCollectionOptions), te = l(c, (e) => e.sheet), ne = l(c, (e) => e.sheetOptions), L = q(() => D().shape({
+		caseTypeId: O().uuid4().required(),
+		createdInDataCollectionId: O().uuid4().required(),
+		fileList: E().required(e`File is required`),
+		sheet: O().required(e`Sheet is required`)
+	}), [e]), R = h({
+		defaultValues: {
+			caseTypeId: null,
+			createdInDataCollectionId: null,
+			fileList: null,
+			sheet: null
+		},
+		resolver: g(L),
+		values: {
+			caseTypeId: c.getState().caseTypeId ?? null,
+			createdInDataCollectionId: c.getState().createdInDataCollectionId ?? null,
+			fileList: c.getState().fileList ?? null,
+			sheet: c.getState().sheet ?? null
+		}
+	}), { handleSubmit: z, setError: B, setValue: ie } = R;
+	K(() => {
+		Array.isArray(o?.data) && w(o.data);
+	}, [o.data, w]), K(() => {
+		a?.options?.length && N(a.options);
+	}, [a?.options, N]);
+	let { data: V, error: H, isLoading: U } = ge({
+		baseQueryKey: i.COMPLETE_CASE_TYPES,
+		itemId: u,
+		useQueryOptions: {
+			enabled: !!u,
+			queryFn: async ({ signal: e }) => (await k.getInstance().completeCaseTypesGetOne(u, { signal: e })).data
+		}
+	});
+	K(() => {
+		V && A(V);
+	}, [V, A]);
+	let ae = G(async (e) => {
+		await M(e);
+	}, [M]), oe = G(async (e) => {
+		await ee(e);
+	}, [ee]), se = G((e) => {
+		T(e);
+	}, [T]), ce = G((e) => {
+		j(e);
+	}, [j]), ue = q(() => {
+		let n = [{
+			accept: ".csv,.tsv,.txt,.xlsx",
+			definition: P.FILE,
+			label: e`File`,
+			name: "fileList",
+			onChange: ae
+		}];
+		return t.isXlsxFile(f) && n.push({
+			definition: P.SELECT,
+			label: e`Sheet`,
+			name: "sheet",
+			onChange: oe,
+			options: ne
+		}), n.push({
+			definition: P.AUTOCOMPLETE,
+			disabled: !d,
+			label: e`Case type`,
+			loading: r.isLoading,
+			name: "caseTypeId",
+			onChange: se,
+			options: r.options
+		}, {
+			definition: P.SELECT,
+			disabled: !d || !u,
+			label: e`Create in data collection`,
+			loading: a.isLoading || U,
+			name: "createdInDataCollectionId",
+			onChange: ce,
+			options: S
+		}), n;
+	}, [
+		e,
+		ae,
+		f,
+		r.options,
+		r.isLoading,
+		d,
+		se,
+		S,
+		a.isLoading,
+		U,
+		u,
+		ce,
+		ne,
+		oe
+	]);
+	K(() => {
+		m ? B("fileList", {
+			message: m,
+			type: "manual"
+		}) : B("fileList", void 0);
+	}, [
+		m,
+		B,
+		ie
+	]);
+	let J = G(async () => {
+		await b();
+	}, [b]), Y = _e([
+		n,
+		r,
+		a,
+		o
+	]), fe = G(async () => {
+		await z(J)();
+	}, [z, J]), pe = q(() => !(o.isLoading === !1 && o.data?.length === 0 || r.isLoading === !1 && r.options?.length === 0 || a.isLoading === !1 && a.options?.length === 0), [
+		o.data?.length,
+		o.isLoading,
+		r.isLoading,
+		r.options?.length,
+		a.isLoading,
+		a.options?.length
+	]);
+	return /* @__PURE__ */ Q(he, {
+		error: H,
+		inlineSpinner: !0,
+		loadables: Y,
+		children: /* @__PURE__ */ $(re, {
+			maxWidth: "lg",
+			children: [!pe && /* @__PURE__ */ Q(F, {
+				severity: "warning",
+				sx: { mb: 2 },
+				children: e("Upload is disabled because you have insufficient data access to proceed. Contact your organization administrator for assistance.")
+			}), pe && /* @__PURE__ */ $(Z, { children: [
+				C && C.length > 0 && /* @__PURE__ */ $(F, {
+					severity: "info",
+					sx: { mb: 2 },
+					children: [
+						/* @__PURE__ */ Q(I, { children: e("{{fileName}} loaded successfully", { fileName: f }) }),
+						te && /* @__PURE__ */ Q(le, { children: e("Sheet name: {{sheet}}", { sheet: te || "" }) }),
+						/* @__PURE__ */ Q(le, { children: e("Number of columns: {{columnCount}}", { columnCount: C[0].length }) }),
+						/* @__PURE__ */ Q(le, { children: e("Number of data rows: {{rowCount}}", { rowCount: C.length - 1 }) })
+					]
+				}),
+				/* @__PURE__ */ Q(be, {
+					formFieldDefinitions: ue,
+					formId: s,
+					formMethods: R,
+					onSubmit: z(J),
+					schema: L
+				}),
+				/* @__PURE__ */ Q(Ve, { onProceedButtonClick: fe })
+			] })]
+		})
+	});
+}, Ue = /* @__PURE__ */ e(r(), 1), We = /* @__PURE__ */ e(o(), 1), Ge = () => {
+	let { t: e } = X(), n = b(), r = Se(), i = W(p), a = l(i, (e) => e.completeCaseType), o = l(i, (e) => e.rawData), s = l(i, (e) => e.fileName), c = l(i, (e) => e.goToNextStep), u = l(i, (e) => e.goToPreviousStep), d = l(i, (e) => e.setMappedColumns), f = _e([n, r]), _ = de(), v = q(() => t.getColumnMappingSchema(o, a), [a, o]), y = q(() => t.getDefaultColumnMappingFormValues(o[0], i.getState().mappedColumns, r.options), [
+		o,
+		i,
+		r.options
+	]), x = h({
+		defaultValues: { ...y },
+		resolver: g(v),
+		values: { ...y }
+	}), { clearErrors: S, control: C, handleSubmit: w } = x, T = m({ control: C }), E = q(() => t.getColumnMappingFormFieldDefinitions(a, o[0], s).map((e) => ({
+		...e,
+		onChange: () => S()
+	})), [
+		a,
+		o,
+		s,
+		S
+	]);
+	K(() => {
+		(async () => {
+			await d(t.getMappedColumnsFromFormData(T, o, n.map, a));
+		})();
+	}, [
+		d,
+		T,
+		o,
+		n.map,
+		a
+	]);
+	let D = q(() => (0, We.default)(o[0].map((e, t) => t), t.getMappedColumnsFromFormData(T, o, n.map, a).map((e) => e.originalIndex)).map((e) => ({
+		originalIndex: e,
+		originalLabel: o[0][e]
+	})), [
+		n.map,
+		o,
+		T,
+		a
+	]), O = G(async (e) => {
+		await d(t.getMappedColumnsFromFormData(e, o, n.map, a)), await c();
+	}, [
+		o,
+		n.map,
+		c,
+		d,
+		a
+	]), k = q(() => t.getSampleIdColIds(a), [a]), A = G((t, n) => {
+		let i = parseInt(t.name, 10), a = (0, Ue.default)(o.slice(1).map((e) => e[i] ?? "")).filter((e) => !!e).slice(0, 5).join(", ").trim() || e("<no data>"), s = n, c = T[t.name];
+		return k.includes(c) && (s = /* @__PURE__ */ $(Z, { children: [/* @__PURE__ */ Q(L, { children: n }), /* @__PURE__ */ Q(L, {
+			sx: { marginTop: 1 },
+			children: /* @__PURE__ */ Q(Ce, {
+				label: e("{{columnLabel}}: Identifier issuer", { columnLabel: t.label }),
+				loading: r.isLoading,
+				name: c,
+				options: r.options
+			})
+		})] })), /* @__PURE__ */ $(oe, { children: [
+			/* @__PURE__ */ Q(U, { children: t.label }),
+			/* @__PURE__ */ Q(U, { children: s }),
+			/* @__PURE__ */ Q(U, { children: a })
+		] }, t.name);
+	}, [
+		T,
+		r.isLoading,
+		r.options,
+		o,
+		k,
+		e
+	]), j = G((t) => /* @__PURE__ */ $(V, {
+		size: "small",
+		children: [/* @__PURE__ */ Q(ae, {
+			sx: {
+				backgroundColor: (e) => e.palette.background.paper,
+				position: "sticky",
+				top: 0,
+				zIndex: (e) => e.zIndex.appBar - 1
+			},
+			children: /* @__PURE__ */ $(oe, { children: [
+				/* @__PURE__ */ Q(U, {
+					sx: { width: "33%" },
+					children: e`Source`
+				}),
+				/* @__PURE__ */ Q(U, {
+					sx: { width: "33%" },
+					children: te.getInstance().config.applicationName
+				}),
+				/* @__PURE__ */ Q(U, {
+					sx: { width: "34%" },
+					children: e`Data preview (first 5 unique values)`
+				})
+			] })
+		}), /* @__PURE__ */ Q(H, { children: t })]
+	}), [e]), M = G(async () => {
+		await w(O)();
+	}, [w, O]), ee = G(() => {
+		u();
+	}, [u]);
+	return /* @__PURE__ */ Q(he, {
+		loadables: f,
+		children: /* @__PURE__ */ $(L, {
+			sx: {
+				display: "grid",
+				gridTemplateRows: "max-content auto max-content",
+				height: "100%"
+			},
+			children: [
+				/* @__PURE__ */ Q(re, {
+					maxWidth: "lg",
+					sx: { marginBottom: 2 },
+					children: /* @__PURE__ */ $(F, {
+						severity: D.length === 0 ? "info" : "warning",
+						children: [
+							/* @__PURE__ */ Q(I, { children: D.length === 0 ? e("All columns in {{fileName}} have been mapped to known columns in {{applicationName}}", {
+								applicationName: te.getInstance().config.applicationName,
+								fileName: s
+							}) : e("{{numUnmappedColumns}} column(s) in {{fileName}} are not mapped", {
+								fileName: s,
+								numUnmappedColumns: D.length
+							}) }),
+							D.map((t) => /* @__PURE__ */ Q(L, { children: e("The column \"{{columnName}}\" (column {{columnIndex}}) has not been mapped.", {
+								columnIndex: t.originalIndex + 1,
+								columnName: t.originalLabel
+							}) }, t.originalIndex)),
+							D.length === 0 && e("You can proceed to the next step.")
+						]
+					})
+				}),
+				/* @__PURE__ */ Q(L, {
+					sx: {
+						overflowY: "auto",
+						position: "relative"
+					},
+					children: /* @__PURE__ */ Q(L, {
+						sx: {
+							bottom: 0,
+							left: 0,
+							position: "absolute",
+							right: 0,
+							top: 0
+						},
+						children: /* @__PURE__ */ Q(re, { children: /* @__PURE__ */ Q(be, {
+							formFieldDefinitions: E,
+							formId: _,
+							formMethods: x,
+							onSubmit: w(O),
+							renderField: A,
+							schema: v,
+							wrapForm: j
+						}) })
+					})
+				}),
+				/* @__PURE__ */ Q(L, { children: /* @__PURE__ */ Q(Ve, {
+					onGoBackButtonClick: ee,
+					onProceedButtonClick: M
+				}) })
+			]
+		})
+	});
+}, Ke = (e) => (t) => {
+	let [n, r] = Y(!1), i = G(() => {
+		r(!0);
+	}, []);
+	return /* @__PURE__ */ Q(u, {
+		caseTypeId: t.caseTypeId,
+		onCompleteCaseTypeLoaded: i,
+		children: n && /* @__PURE__ */ Q(e, { ...t })
+	});
+}, qe = Pe(({ onActionsChange: e, onClose: t, onSubmit: n, onTitleChange: r, openProps: i }) => {
+	let { t: a } = X(), o = de(), s = q(() => i.completeCaseType.cols[i.colId], [i.completeCaseType.cols, i.colId]);
+	K(() => {
+		r(a("Edit values for {{colLabel}} (for selected rows)", { colLabel: s.label }));
+	}, [
+		r,
+		s.label,
+		a
+	]);
+	let l = q(() => c.createYupSchema({
+		completeCaseType: i.completeCaseType,
+		includedColIds: [i.colId]
+	}), [i.completeCaseType, i.colId]), u = h({ resolver: g(l) }), { handleSubmit: d } = u, { fieldDefinitions: f } = q(() => c.createFormDefinitions({
+		completeCaseType: i.completeCaseType,
+		includedColIds: [i.colId]
+	}), [i.completeCaseType, i.colId]), p = G((e) => {
+		n(Ie.createStringValuesFromFormValues(f, e)), t();
+	}, [
+		f,
+		t,
+		n
+	]);
+	return K(() => {
+		e([{
+			...Fe.createAttributes("UploadEditColumnValuesDialog-submitButton"),
+			color: "primary",
+			form: o,
+			label: a`Save and revalidate`,
+			type: "submit",
+			variant: "contained"
+		}]);
+	}, [
+		o,
+		e,
+		a
+	]), /* @__PURE__ */ $(L, { children: [i.shouldShowRightsWarning && /* @__PURE__ */ Q(L, {
+		sx: { marginBottom: 2 },
+		children: /* @__PURE__ */ $(F, {
+			severity: "warning",
+			children: [/* @__PURE__ */ Q(I, { children: a`You do not have the necessary rights to edit all rows in this column.` }), a`Only the cases that you have write access to for this column will be updated. Please review the changes carefully before submitting.`]
+		})
+	}), /* @__PURE__ */ Q(be, {
+		formFieldDefinitions: f,
+		formId: o,
+		formMethods: u,
+		onSubmit: d(p),
+		schema: l
+	})] });
+}, {
+	defaultTitle: "",
+	fullWidth: !0,
+	maxWidth: "md",
+	testId: "UploadEditColumnValuesDialog"
+}), Je = ({ caseRightsColMap: e, caseUploadResults: t, completeCaseType: n, getOriginalCellValue: r, onCaseContentEditSubmit: i, onColContentEditSubmit: o, tableStore: s }) => {
+	let c = ue(), { t: l } = X(), u = J(null), d = J(null), f = q(() => [
+		A.UNAUTHORIZED,
+		A.INVALID,
+		A.CONFLICT,
+		A.MISSING,
+		A.DERIVED,
+		A.TRANSFORMED
+	], []), p = q(() => [A.UNAUTHORIZED, A.INVALID], []), m = q(() => [A.MISSING, A.CONFLICT], []), h = G((r) => {
+		d.current?.open({
+			colId: r.column.id,
+			completeCaseType: n,
+			shouldShowRightsWarning: e?.[r.column.id]?.length !== t?.length
+		});
+	}, [
+		n,
+		e,
+		t
+	]), g = G((e, t) => {
+		i(e, t);
+	}, [i]), _ = G((t) => {
+		let n = {};
+		Object.keys(t).forEach((r) => {
+			(e?.[r] ?? []).forEach((e) => {
+				n[e] = {
+					...n[e] ?? {},
+					[r]: t[r]
+				};
+			});
+		}), o(n);
+	}, [o, e]), v = G((e) => {
+		let t = [];
+		return e.forEach((e) => {
+			let r = `${n.cols[e.col_id].label}: ${e.message}`;
+			t.push({
+				key: `${e.col_id}-${e.data_issue_type}-${e.code}`,
+				message: r
+			});
+		}), t;
+	}, [n.cols]), y = G((e) => /* @__PURE__ */ Q(Z, { children: v(e).map(({ key: e, message: t }, n) => /* @__PURE__ */ Q(L, {
+		sx: { marginTop: +(n > 0) },
+		children: t
+	}, e)) }), [v]), b = G((e) => v(e).map((e) => e.message).join(", "), [v]), x = G((e, t, n) => t.filter((t) => !(t.col_id !== e || t.data_issue_type === A.TRANSFORMED && t.original_value === n)).sort((e, t) => f.indexOf(e.data_issue_type) - f.indexOf(t.data_issue_type)), [f]), C = G(() => /* @__PURE__ */ Q(ce, {
+		"aria-hidden": !1,
+		arrow: !0,
+		title: l("Indicates if there are any issues with the case"),
+		children: /* @__PURE__ */ Q(De, { fontSize: "small" })
+	}), [l]), w = G(({ row: e }) => {
+		let t = e.data_issues.filter((e) => e.data_issue_type === A.INVALID || e.data_issue_type === A.UNAUTHORIZED);
+		if (t.length > 0) return /* @__PURE__ */ Q(ce, {
+			"aria-hidden": !1,
+			"aria-label": b(t),
+			arrow: !0,
+			title: y(t),
+			children: /* @__PURE__ */ Q(De, {
+				fontSize: "small",
+				sx: {
+					color: c.palette.error.main,
+					marginTop: "5px"
+				}
+			})
+		});
+	}, [
+		y,
+		b,
+		c.palette.error.main
+	]), T = G(() => /* @__PURE__ */ Q(ce, {
+		"aria-hidden": !1,
+		arrow: !0,
+		title: l("Indicates if case is new (will be created)"),
+		children: /* @__PURE__ */ Q(Oe, { fontSize: "small" })
+	}), [l]), E = G(({ row: e }) => e.id ? null : /* @__PURE__ */ Q(Oe, {
+		"aria-hidden": !1,
+		"aria-label": l`This case does not have an ID and will be created`,
+		fontSize: "small",
+		sx: {
+			marginTop: "5px",
+			position: "absolute"
+		}
+	}), [l]), D = G(({ id: e, row: t }) => {
+		let r = a.getRowValue(t.validated_content, n.cols[e], n).long, i = x(e, t.data_issues, r);
+		if (i.length === 0) return /* @__PURE__ */ Q(Z, { children: r });
+		let o = c.palette.info.main;
+		p.includes(i[0].data_issue_type) ? o = c.palette.error.main : m.includes(i[0].data_issue_type) && (o = c.palette.warning.main);
+		let s = i.find((e) => e.original_value)?.original_value || "", l = /* @__PURE__ */ $(Z, { children: [s && r && s !== r && /* @__PURE__ */ $(Z, { children: [/* @__PURE__ */ Q("s", { children: s }), "\xA0"] }), r && /* @__PURE__ */ Q(Z, { children: r })] });
+		return /* @__PURE__ */ $(L, {
+			sx: {
+				alignItems: "center",
+				display: "flex"
+			},
+			children: [/* @__PURE__ */ Q(L, {
+				sx: {
+					height: c.spacing(2),
+					marginRight: c.spacing(1),
+					minHeight: c.spacing(2),
+					minWidth: c.spacing(2),
+					position: "relative",
+					width: c.spacing(2)
+				},
+				children: /* @__PURE__ */ Q(ce, {
+					arrow: !0,
+					title: y(i),
+					children: /* @__PURE__ */ Q(De, {
+						fontSize: "small",
+						sx: {
+							color: o,
+							marginTop: "-2px",
+							position: "absolute"
+						}
+					})
+				})
+			}), /* @__PURE__ */ Q(L, {
+				sx: {
+					overflow: "hidden",
+					textOverflow: "ellipsis",
+					whiteSpace: "nowrap"
+				},
+				children: l
+			})]
+		});
+	}, [
+		n,
+		p,
+		x,
+		y,
+		c,
+		m
+	]);
+	return Ne({
+		columns: q(() => {
+			let i = [];
+			if (!t?.length) return i;
+			i.push(Me.createReadableIndexColumn()), i.push(Me.createSelectableColumn()), i.push({
+				disableEllipsis: !0,
+				frozen: je.LEFT,
+				headerName: "",
+				hideInFilter: !0,
+				id: "gen-epix-ui-issue",
+				isInitiallyVisible: !0,
+				renderCell: w,
+				renderHeader: C,
+				resizable: !1,
+				type: "text",
+				valueGetter: () => "",
+				widthPx: 38
+			}), i.push({
+				disableEllipsis: !0,
+				frozen: je.LEFT,
+				headerName: "",
+				hideInFilter: !0,
+				id: "gen-epix-ui-id",
+				isInitiallyVisible: !0,
+				renderCell: E,
+				renderHeader: T,
+				resizable: !1,
+				type: "text",
+				valueGetter: () => "",
+				widthPx: 38
+			});
+			let o = /* @__PURE__ */ new Set();
+			return t.forEach((e) => {
+				Object.keys(e.validated_content || {}).forEach((e) => o.add(e)), e.data_issues.forEach((e) => o.add(e.col_id));
+			}), n.ordered_col_ids.forEach((s) => {
+				if (!o.has(s)) return;
+				let c = n.cols[s], u = t.flatMap((e) => e.data_issues.filter((e) => e.col_id === c.id)), d = u.length === 0 || u.some((e) => e.data_issue_type !== A.DERIVED), f = e[c.id]?.length;
+				c && i.push({
+					cellTitleGetter: (e) => {
+						let t = e.row.data_issues.find((e) => e.col_id === c.id);
+						return !t && r ? l("{{value}} (original value: \"{{originalValue}}\")", {
+							originalValue: r(c, e, t) ?? "",
+							value: a.getRowValue(e.row.validated_content, c, n).short
+						}) : "";
+					},
+					customHeaderIcon: f ? {
+						iconElement: /* @__PURE__ */ Q(Ee, { fontSize: "inherit" }),
+						label: l("Edit values for {{colLabel}} (for selected rows)", { colLabel: c.label }),
+						onClick: h
+					} : void 0,
+					headerName: c.code,
+					hideInFilter: !0,
+					id: c.id,
+					isInitiallyVisible: d,
+					renderCell: D,
+					type: "text",
+					valueGetter: (e) => a.getRowValue(e.row.validated_content, c, n).short,
+					widthPx: 250
+				});
+			}), t.some((e) => e.id) && i.push({
+				headerName: l("case_id"),
+				hideInFilter: !0,
+				id: "case_id",
+				isInitiallyVisible: !0,
+				type: "text",
+				valueGetter: (e) => e.row.id || "",
+				widthPx: 250
+			}), i.push(Me.createActionsColumn({
+				getActions: (e) => {
+					let t = [];
+					return t.push(/* @__PURE__ */ $(ie, {
+						onClick: () => {
+							u.current?.open({
+								caseContent: e.row.validated_content,
+								caseId: e.row.id,
+								completeCaseType: n,
+								enabledColIds: n.ordered_col_ids,
+								formId: "edit-case-form"
+							});
+						},
+						children: [/* @__PURE__ */ Q(z, { children: /* @__PURE__ */ Q(Ee, {}) }), /* @__PURE__ */ Q(B, { children: l`Edit` })]
+					}, "editCase")), t;
+				},
+				t: l
+			})), i;
+		}, [
+			t,
+			w,
+			C,
+			E,
+			T,
+			n,
+			l,
+			e,
+			h,
+			D,
+			r
+		]),
+		createFiltersFromColumns: !0,
+		rows: t,
+		store: s
+	}), /* @__PURE__ */ $(Z, { children: [
+		/* @__PURE__ */ Q(L, { children: /* @__PURE__ */ Q(Ae, { ContainerProps: { sx: {
+			display: "inline-block",
+			float: "right"
+		} } }) }),
+		/* @__PURE__ */ Q(ke, { font: c["gen-epix-ui-casedb"].lineList.font }),
+		/* @__PURE__ */ Q(S, {
+			onSubmit: g,
+			ref: u
+		}),
+		/* @__PURE__ */ Q(qe, {
+			onSubmit: _,
+			ref: d
+		})
+	] });
+}, Ye = ({ onGoBackButtonClick: e, onProceedButtonClick: t }) => {
+	let { t: n } = X(), r = me(), i = l(W(p), (e) => e.completeCaseType), a = l(r, (e) => e.selectedIds);
+	return /* @__PURE__ */ Q(Ve, {
+		onGoBackButtonClick: e,
+		onProceedButtonClick: t,
+		proceedDisabled: !a.length || a.length > i.props.create_max_n_cases,
+		proceedLabel: a.length ? n("Proceed with {{count}} selected cases", { count: a.length }) : n("Proceed")
+	});
+}, Xe = Ke(({ caseTypeId: e }) => {
+	let { t } = X(), n = W(p), r = l(n, (e) => e.goToNextStep), i = l(n, (e) => e.goToPreviousStep), o = l(n, (e) => e.completeCaseType), s = l(n, (e) => e.casesForVerificationFromSourceData), c = l(n, (e) => e.createdInDataCollectionId), u = l(n, (e) => e.validateCasesQueryKey), f = l(n, (e) => e.caseRightsColMap), [m, h] = Y(!1), [g, _] = Y(!1), [v, y] = Y(null), b = J([]), x = J(null), S = J(null), C = G((e, t, n) => s[t.rowIndex]?.case?.content[e.id] ?? "", [s]), w = xe({
+		enabled: s.length > 0,
+		gcTime: Infinity,
+		queryFn: async ({ signal: t }) => (await k.getInstance().uploadCases(N.deepNullifyEmptyStrings({
+			case_batch: { cases: s },
+			case_type_id: e,
+			default_created_in_data_collection_id: c ?? void 0,
+			on_exists: M.UPDATE,
+			verify_only: !0
+		}), { signal: t })).data,
+		queryKey: u,
+		select: (e) => e.cases.map((e, t) => ({
+			...e,
+			id: s[t].id
+		})),
+		staleTime: Infinity
+	}), T = _e([w]), E = q(() => pe({ idSelectorCallback: (e) => e.id }), []), D = l(E, d((e) => e.setSelectedIds)), O = G(async (t) => {
+		_(!0);
+		try {
+			let n = (await k.getInstance().uploadCases(N.deepNullifyEmptyStrings({
+				case_batch: { cases: t.map(({ content: e, row: t }, n) => {
+					let r = s.find((e) => e.id === t.id);
+					return { case: {
+						case_type_id: o.id,
+						content: Object.fromEntries(Object.entries(e).map(([t]) => {
+							let n = o.cols[t];
+							if (!n) return [t, e[t]];
+							let r = a.getRowValue(e, n, o);
+							return [t, r.isMissing ? "" : r.long];
+						})),
+						created_in_data_collection_id: r?.case?.created_in_data_collection_id ?? c,
+						id: t.id ?? s[n].id
+					} };
+				}) },
+				case_type_id: e,
+				default_created_in_data_collection_id: c ?? void 0,
+				on_exists: M.UPDATE,
+				verify_only: !0
+			}))).data, r = new Map(t.map(({ row: e }, t) => [e.id, n.cases[t]]));
+			ee.getInstance().queryClient.setQueryData(u, { cases: w.data.map((e) => {
+				let t = r.get(e.id);
+				return t ? {
+					...t,
+					id: e.id
+				} : e;
+			}) });
+			let i = [];
+			if (t.forEach(({ row: e }, t) => {
+				let r = n.cases[t];
+				r.status !== j.SKIPPED && r.status !== j.SUCCESS && r.status !== j.UPDATED && (b.current.includes(e.id) || (b.current.push(e.id), i.push(e.id)));
+			}), i.length > 0) {
+				let e = E.getState().selectedIds, t = i.filter((t) => !e.includes(t));
+				t.length > 0 && D([...e, ...t]);
+			}
+		} catch (e) {
+			y(e);
+		} finally {
+			_(!1);
+		}
+	}, [
+		e,
+		w.data,
+		s,
+		o,
+		c,
+		D,
+		E,
+		u
+	]), P = G(async (e) => {
+		let t = E.getState().selectedIds;
+		await O(w.data.filter((e) => t.includes(e.id)).map((t) => ({
+			content: {
+				...t.validated_content,
+				...e[t.id]
+			},
+			row: t
+		})));
+	}, [
+		w.data,
+		O,
+		E
+	]), te = G(async (e, t) => {
+		await O([{
+			content: t,
+			row: w.data.find((t) => t.id === e)
+		}]);
+	}, [w.data, O]);
+	K(() => {
+		let e = E.subscribe((e, t) => {
+			e.selectedIds !== t.selectedIds && (b.current = e.selectedIds, h(e.selectedIds.length > o.props.create_max_n_cases));
+		});
+		return () => {
+			e();
+		};
+	}, [o.props.create_max_n_cases, E]), K(() => {
+		D((w.data ?? []).filter((e) => !e.data_issues.some((e) => e.data_issue_type === A.INVALID || e.data_issue_type === A.UNAUTHORIZED)).map((e) => e.id));
+	}, [w.data, D]);
+	let ne = G(async () => {
+		let e = E.getState().selectedIds, t = w.data.filter((t) => e.includes(t.id) && !t.data_issues.some((e) => e.data_issue_type === A.INVALID));
+		n.setState((e) => ({
+			...e,
+			selectedIdsForUpload: t.map((e) => e.id),
+			validatedCases: w.data
+		})), await r();
+	}, [
+		w.data,
+		r,
+		n,
+		E
+	]), R = G(async () => {
+		n.setState((e) => ({
+			...e,
+			selectedIdsForUpload: b.current,
+			validatedCases: w.data
+		})), await r();
+	}, [
+		r,
+		w.data,
+		n
+	]), re = G(async () => {
+		if (w.data.some((e) => E.getState().selectedIds.includes(e.id) && (e.data_issues.some((e) => e.data_issue_type === A.INVALID) || e.status === j.FAILED))) {
+			x.current?.open();
+			return;
+		}
+		if (w.data.some((e) => !E.getState().selectedIds.includes(e.id) && !e.data_issues.some((e) => e.data_issue_type === A.INVALID))) {
+			S.current?.open();
+			return;
+		}
+		await R();
+	}, [
+		w.data,
+		R,
+		E
+	]), z = G(() => {
+		i();
+	}, [i]);
+	return /* @__PURE__ */ $(L, {
+		sx: {
+			display: "grid",
+			gridTemplateRows: `${m ? "max-content" : ""} max-content auto max-content`,
+			height: "100%",
+			position: "relative",
+			width: "100%"
+		},
+		children: [
+			/* @__PURE__ */ Q(fe, {
+				store: E,
+				children: /* @__PURE__ */ $(he, {
+					error: v,
+					inlineSpinner: !0,
+					loadables: T,
+					loadingMessage: t("Validating cases"),
+					takingLongerTimeoutMs: 1e4,
+					children: [
+						m && /* @__PURE__ */ Q(L, {
+							sx: { marginY: 2 },
+							children: /* @__PURE__ */ Q(F, {
+								severity: "error",
+								children: /* @__PURE__ */ Q(I, { children: t("You have exceeded the maximum number of {{maxCases}} cases for this case type. Please reduce the number of selected cases before proceeding.", { maxCases: o.props.create_max_n_cases }) })
+							})
+						}),
+						/* @__PURE__ */ Q(Je, {
+							caseRightsColMap: f,
+							caseUploadResults: w.data || [],
+							completeCaseType: o,
+							getOriginalCellValue: C,
+							onCaseContentEditSubmit: te,
+							onColContentEditSubmit: P,
+							tableStore: E
+						}),
+						/* @__PURE__ */ Q(Ye, {
+							onGoBackButtonClick: z,
+							onProceedButtonClick: re
+						})
+					]
+				})
+			}),
+			/* @__PURE__ */ Q(we, {
+				label: t("Revalidating cases"),
+				open: g
+			}),
+			/* @__PURE__ */ Q(Te, {
+				body: t`Some of the selected cases contain issues. If you proceed, these cases will be excluded. Are you sure you want to proceed without them?`,
+				cancelLabel: t`Cancel`,
+				confirmLabel: t`Proceed`,
+				onConfirm: ne,
+				ref: x,
+				title: t`Issues found with selected cases`
+			}),
+			/* @__PURE__ */ Q(Te, {
+				body: t`Not all cases are selected. Do you want to proceed without them?`,
+				cancelLabel: t`Cancel`,
+				confirmLabel: t`Proceed`,
+				onConfirm: R,
+				ref: S,
+				title: t`Not all cases are selected.`
+			})
+		]
+	});
+}), Ze = () => {
+	let { t: e } = X(), r = W(p), i = l(r, (e) => e.reset), a = l(r, (e) => e.goToPreviousStep), o = l(r, (e) => e.sequenceMapping), c = l(r, (e) => e.sequenceFilesDataTransfer), u = l(r, (e) => e.validatedCases), d = l(r, (e) => e.selectedIdsForUpload), f = l(r, (e) => e.casesForVerificationFromSourceData), m = l(r, (e) => e.uploadCompleteButtonCallback), h = l(r, (e) => e.uploadCompleteButtonLabel), g = l(r, (e) => e.onUploadComplete), _ = l(r, (e) => e.completeCaseType), [v, y] = Y(0), [b, x] = Y(""), [S, C] = Y(!1), [w, T] = Y(!1), [E, D] = Y(void 0), O = q(() => t.getSequenceMappingStats(o, c), [c, o]), k = q(() => u.filter((e) => d.includes(e.id)), [u, d]);
+	K(() => {
+		let e = new AbortController(), { signal: n } = e, i = () => {
+			e.abort(), Re.getInstance().resume();
+		};
+		return S ? (Re.getInstance().pause(), (async () => {
+			let e = await t.createCasesAndUploadFiles({
+				assemblyProtocolId: r.getState().assemblyProtocolId,
+				casesForVerificationFromSourceData: f,
+				completeCaseType: r.getState().completeCaseType,
+				createdInDataCollectionId: r.getState().createdInDataCollectionId,
+				mappedColumns: r.getState().mappedColumns,
+				onComplete: () => {
+					T(!0);
+				},
+				onError: (e) => {
+					D(e);
+				},
+				onProgress: (e, t) => {
+					y(e), x(t);
+				},
+				sampleIdColId: r.getState().sampleIdColId,
+				selectedValidatedCases: k,
+				sequenceFilesDataTransfer: c,
+				sequenceMapping: o,
+				sequencingProtocolId: r.getState().sequencingProtocolId,
+				signal: n
+			});
+			g && await g(e);
+		})().catch((e) => {
+			n.aborted || D(e);
+		}), i) : i;
+	}, [
+		S,
+		c,
+		o,
+		r,
+		e,
+		k,
+		f,
+		g
+	]);
+	let A = G(async () => {
+		await i();
+	}, [i]), j = G(() => {
+		C(!0);
+	}, []), M = G(() => {
+		a();
+	}, [a]), ee = G(async () => {
+		let e = n.createCaseTypeLink(_);
+		await Be.getInstance().router.navigate(e);
+	}, [_]), N;
+	return N = E ? /* @__PURE__ */ $(L, { children: [E instanceof s && /* @__PURE__ */ $(F, {
+		severity: "error",
+		children: [/* @__PURE__ */ Q(I, { children: e("Failed to create cases during upload.") }), e("An error occurred while creating cases. Please try again or contact support if the issue persists. Cases may have been partially created. No files were uploaded.")]
+	}), /* @__PURE__ */ Q(Le, { error: E })] }) : w ? /* @__PURE__ */ $(L, { children: [/* @__PURE__ */ Q(L, { children: /* @__PURE__ */ Q(F, {
+		severity: "success",
+		children: /* @__PURE__ */ Q(I, { children: e("Upload completed.") })
+	}) }), /* @__PURE__ */ Q(L, {
+		sx: {
+			display: "flex",
+			gap: 2,
+			justifyContent: "flex-end",
+			marginBottom: 1,
+			marginTop: 2
+		},
+		children: m && h ? /* @__PURE__ */ Q(R, {
+			onClick: m,
+			variant: "contained",
+			children: h
+		}) : /* @__PURE__ */ $(Z, { children: [/* @__PURE__ */ Q(R, {
+			onClick: A,
+			variant: "outlined",
+			children: e("Upload more cases")
+		}), /* @__PURE__ */ Q(R, {
+			onClick: ee,
+			variant: "contained",
+			children: e("View uploaded cases")
+		})] })
+	})] }) : S ? /* @__PURE__ */ $(L, { children: [
+		/* @__PURE__ */ Q(L, {
+			sx: { marginBottom: 4 },
+			children: /* @__PURE__ */ $(F, {
+				severity: "info",
+				children: [/* @__PURE__ */ Q(I, { children: e("Uploading cases and files.") }), e("Please wait while the cases and associated files are being uploaded. This may take a while depending on the number and size of the files being uploaded.")]
+			})
+		}),
+		/* @__PURE__ */ Q(L, {
+			sx: {
+				marginBottom: 2,
+				marginTop: 4
+			},
+			children: /* @__PURE__ */ Q(ze, { value: v })
+		}),
+		/* @__PURE__ */ Q(L, {
+			sx: { fontWeight: 700 },
+			children: b
+		})
+	] }) : /* @__PURE__ */ $(L, { children: [/* @__PURE__ */ $(L, { children: [
+		/* @__PURE__ */ Q(L, {
+			sx: { marginY: 2 },
+			children: /* @__PURE__ */ Q(F, {
+				severity: "info",
+				children: /* @__PURE__ */ Q(I, { children: e("{{numCases}} cases are ready to be uploaded.", { numCases: k.length }) })
+			})
+		}),
+		O.mappedSequenceFiles.length > 0 && /* @__PURE__ */ Q(L, {
+			sx: { marginY: 2 },
+			children: /* @__PURE__ */ Q(F, {
+				severity: "info",
+				children: /* @__PURE__ */ Q(I, { children: e("{{numSequenceFiles}} genome files are ready to be uploaded.", { numSequenceFiles: O.mappedSequenceFiles.length }) })
+			})
+		}),
+		O.mappedReadsFiles.length > 0 && /* @__PURE__ */ Q(L, {
+			sx: { marginY: 2 },
+			children: /* @__PURE__ */ Q(F, {
+				severity: "info",
+				children: /* @__PURE__ */ Q(I, { children: e("{{numReadsFiles}} reads files are ready to be uploaded.", { numReadsFiles: O.mappedReadsFiles.length }) })
+			})
+		}),
+		u.length - k.length > 0 && /* @__PURE__ */ Q(L, {
+			sx: { marginY: 2 },
+			children: /* @__PURE__ */ Q(F, {
+				severity: "warning",
+				children: /* @__PURE__ */ Q(I, { children: e("{{numCases}} cases were not selected and will not be uploaded.", { numCases: u.length - k.length }) })
+			})
+		}),
+		O.unmappedSequenceFiles.length > 0 && /* @__PURE__ */ Q(L, {
+			sx: { marginY: 2 },
+			children: /* @__PURE__ */ Q(F, {
+				severity: "warning",
+				children: /* @__PURE__ */ Q(I, { children: e("{{unmappedSequenceFiles}} unmapped genome files will not be uploaded.", { unmappedSequenceFiles: O.unmappedSequenceFiles.length }) })
+			})
+		}),
+		O.unmappedReadsFiles.length > 0 && /* @__PURE__ */ Q(L, {
+			sx: { marginY: 2 },
+			children: /* @__PURE__ */ Q(F, {
+				severity: "warning",
+				children: /* @__PURE__ */ Q(I, { children: e("{{unmappedReadsFiles}} unmapped reads files will not be uploaded.", { unmappedReadsFiles: O.unmappedReadsFiles.length }) })
+			})
+		})
+	] }), /* @__PURE__ */ Q(Ve, {
+		onGoBackButtonClick: M,
+		onProceedButtonClick: j,
+		proceedLabel: "Start upload"
+	})] }), /* @__PURE__ */ Q(re, {
+		maxWidth: "xl",
+		sx: { height: "100%" },
+		children: N
+	});
+}, Qe = (e) => Array.from(e?.files ?? []), $e = ({ hasGenomeFiles: e, hasReadsFiles: t, hasSelectedFiles: n }) => D().shape({
+	assemblyProtocolId: e ? O().uuid4().required() : O().nullable().notRequired(),
+	sampleIdColId: n ? O().uuid4().required() : O().nullable().notRequired(),
+	sequencingProtocolId: t ? O().uuid4().required() : O().nullable().notRequired()
+}), et = () => {
+	let { t: e } = X(), n = ue(), r = W(p), i = l(r, (e) => e.completeCaseType), a = l(r, (e) => e.mappedColumns), o = l(r, (e) => e.validatedCases), s = l(r, (e) => e.goToNextStep), c = l(r, (e) => e.goToPreviousStep), u = l(r, (e) => e.setSequenceFilesDataTransfer), d = l(r, (e) => e.sampleIdColId), f = l(r, (e) => e.sequenceFilesDataTransfer), [m, _] = Y(f), v = de(), y = w(), b = T(), x = _e([y, b]), S = q(() => a.filter((e) => e.isSampleIdColumn).map((e) => ({
+		label: e.col.label,
+		value: e.col.id
+	})), [a]), E = q(() => Qe(m), [m]), D = E.length > 0, O = q(() => E.some((e) => t.isGenomeFile(e.name)), [E]), k = q(() => E.some((e) => t.isReadsFile(e.name)), [E]), A = q(() => $e({
+		hasGenomeFiles: O,
+		hasReadsFiles: k,
+		hasSelectedFiles: D
+	}), [
+		O,
+		k,
+		D
+	]), j = q(() => ({
+		assemblyProtocolId: r.getState().assemblyProtocolId ?? null,
+		sampleIdColId: r.getState().sampleIdColId ?? null,
+		sequencingProtocolId: r.getState().sequencingProtocolId ?? null
+	}), [r]), M = h({
+		defaultValues: j,
+		resolver: g(A),
+		values: j
+	}), { handleSubmit: ee, setValue: N } = M;
+	K(() => {
+		y.isLoading || b.isLoading || (r.getState().sequencingProtocolId || (N("sequencingProtocolId", y.options[0]?.value || null), r.setState({ sequencingProtocolId: y.options[0]?.value || null })), r.getState().assemblyProtocolId || (N("assemblyProtocolId", b.options[0]?.value || null), r.setState({ assemblyProtocolId: b.options[0]?.value || null })), r.getState().sampleIdColId || (N("sampleIdColId", S[0]?.value || null), r.setState({ sampleIdColId: S[0]?.value || null })));
+	}, [
+		b.isLoading,
+		b.options,
+		y.isLoading,
+		y.options,
+		N,
+		r,
+		S
+	]);
+	let te = G((e) => {
+		r.setState({ sequencingProtocolId: e });
+	}, [r]), ne = G((e) => {
+		r.setState({ assemblyProtocolId: e });
+	}, [r]), R = G((e) => {
+		r.setState({ sampleIdColId: e });
+	}, [r]), re = q(() => [
+		{
+			definition: P.SELECT,
+			label: e`Genome files: assembly protocol`,
+			loading: b.isLoading,
+			name: "assemblyProtocolId",
+			onChange: ne,
+			options: b.options
+		},
+		{
+			definition: P.SELECT,
+			label: e`Reads files: sequencing protocol`,
+			loading: y.isLoading,
+			name: "sequencingProtocolId",
+			onChange: te,
+			options: y.options
+		},
+		{
+			definition: P.SELECT,
+			label: e`Sample ID column`,
+			name: "sampleIdColId",
+			onChange: R,
+			options: S
+		}
+	], [
+		b.isLoading,
+		b.options,
+		ne,
+		R,
+		te,
+		S,
+		y.isLoading,
+		y.options,
+		e
+	]), z = q(() => a.some((e) => e.isSampleIdColumn && e.sampleIdentifierIssuerId), [a]), B = q(() => d ? o.some((e) => e.validated_content[d]?.trim().length > 0) : !1, [d, o]), ie = q(() => t.getCompleteCaseTypeColStats(i), [i]), V = q(() => ie.sequenceColumns.length > 0, [ie]), H = q(() => ie.readsColumns.length > 0, [ie]), U = q(() => z && B && (V || H), [
+		z,
+		B,
+		V,
+		H
+	]), ae = q(() => {
+		let e = "";
+		return V && (e += ".fa,.fasta,.fa.gz,.fasta.gz,"), H && (e += ".fq,.fastq,.fq.gz,.fastq.gz,"), e;
+	}, [H, V]), oe = G(async () => {
+		u(U ? m : new DataTransfer()), await ee(async () => {
+			await s();
+		})();
+	}, [
+		U,
+		m,
+		s,
+		ee,
+		u
+	]), se = G(() => {
+		c();
+	}, [c]), ce = G((e) => {
+		_(e), u(e);
+	}, [u]), le = G((e) => /* @__PURE__ */ Q(L, {
+		sx: {
+			display: "grid",
+			gap: n.spacing(1),
+			gridTemplateColumns: "1fr 1fr 1fr"
+		},
+		children: e
+	}), [n]), J = q(() => z ? B ? H ? V ? null : {
+		message: e`The selected case type does not support uploading sequence files.`,
+		title: e("Uploading of sequence files is disabled.")
+	} : {
+		message: e`The selected case type does not support uploading read files.`,
+		title: e("Uploading of read files is disabled.")
+	} : {
+		message: e`No rows have a sample ID filled for the selected sample ID column.`,
+		title: e("Uploading of files is disabled.")
+	} : {
+		message: e`No columns have been mapped as writable sample ID column with selected identifier issuer provider.`,
+		title: e("Uploading of files is disabled.")
+	}, [
+		H,
+		V,
+		B,
+		z,
+		e
+	]), fe = G(() => {}, []);
+	return /* @__PURE__ */ Q(he, {
+		loadables: x,
+		children: /* @__PURE__ */ $(L, {
+			sx: {
+				display: "grid",
+				gridTemplateRows: `${U ? "" : "max-content "}max-content auto max-content`,
+				height: "100%",
+				position: "relative"
+			},
+			children: [
+				!U && /* @__PURE__ */ Q(L, {
+					sx: { marginBottom: 2 },
+					children: /* @__PURE__ */ $(F, {
+						severity: "error",
+						children: [/* @__PURE__ */ Q(I, { children: J.title }), J.message]
+					})
+				}),
+				/* @__PURE__ */ $(L, {
+					sx: { borderBottom: `1px solid ${n.palette.divider}` },
+					children: [
+						/* @__PURE__ */ Q(L, {
+							sx: { maxWidth: n.spacing(128) },
+							children: /* @__PURE__ */ Q(be, {
+								formFieldDefinitions: re,
+								formId: v,
+								formMethods: M,
+								onSubmit: fe,
+								schema: A,
+								wrapForm: le
+							})
+						}),
+						!V && /* @__PURE__ */ Q(L, {
+							sx: { marginY: 1 },
+							children: /* @__PURE__ */ $(F, {
+								severity: "info",
+								children: [/* @__PURE__ */ Q(I, { children: e("Uploading of sequences has been disabled.") }), /* @__PURE__ */ Q(L, { children: e("Uploading of sequences is not supported for the selected case type.") })]
+							})
+						}),
+						!H && /* @__PURE__ */ Q(L, {
+							sx: { marginY: 1 },
+							children: /* @__PURE__ */ $(F, {
+								severity: "info",
+								children: [/* @__PURE__ */ Q(I, { children: e("Uploading of read files has been disabled.") }), /* @__PURE__ */ Q(L, { children: e("Uploading of read files is not supported for the selected case type.") })]
+							})
+						})
+					]
+				}),
+				/* @__PURE__ */ Q(L, {
+					sx: { position: "relative" },
+					children: /* @__PURE__ */ Q(L, {
+						sx: {
+							bottom: 0,
+							height: "100%",
+							left: 0,
+							position: "absolute",
+							right: 0,
+							top: 0
+						},
+						children: U && /* @__PURE__ */ Q(C, {
+							accept: ae,
+							initialDataTransfer: f,
+							numFilesAllowed: Infinity,
+							onDataTransferChange: ce
+						})
+					})
+				}),
+				/* @__PURE__ */ Q(Ve, {
+					onGoBackButtonClick: se,
+					onProceedButtonClick: oe,
+					proceedLabel: U ? void 0 : e`Proceed`
+				})
+			]
+		})
+	});
+}, tt = () => {
+	let { t: e } = X(), n = ue(), r = W(p), i = l(r, (e) => e.goToNextStep), o = l(r, (e) => e.goToPreviousStep), s = l(r, (e) => e.completeCaseType), c = l(r, (e) => e.sampleIdColId), u = l(r, (e) => e.sequenceFilesDataTransfer), f = l(r, d((e) => {
+		let t = e.selectedIdsForUpload;
+		return e.validatedCases.filter((e) => t.includes(e.id));
+	})), m = l(r, (e) => e.setSequenceMapping), h = q(() => t.getCompleteCaseTypeColStats(s), [s]), g = de(), _ = de(), v = J(r.getState().sequenceMapping), y = G(async () => {
+		m(v.current), await i();
+	}, [m, i]), b = G(() => {
+		o();
+	}, [o]), x = G(() => {
+		let n = document.getElementById(g), r = document.getElementById(_);
+		if (!n || !r) return;
+		let { mappedFiles: i, numberOfFilesToMap: a, unmappedFileNames: o } = t.getSequenceMappingStats(v.current, u);
+		n.innerHTML = a === i.length ? e("All {{numberOfFilesToMap}} files are mapped", { numberOfFilesToMap: a }) : e("{{mappedFilesLength}} of {{numberOfFilesToMap}} files mapped", {
+			mappedFilesLength: i.length,
+			numberOfFilesToMap: a
+		}), r.innerHTML = a === i.length ? "" : e("Unmapped files: {{unmappedFileNames}}", { unmappedFileNames: o.join(", ") });
+	}, [
+		_,
+		g,
+		u,
+		e
+	]);
+	K(() => {
+		x();
+	}, [x]);
+	let S = q(() => pe({ idSelectorCallback: (e) => e.id }), []), C = G((e, t) => e.some((e) => {
+		let n = a.getRowValue(e.validated_content, t, s);
+		return n && !n?.isMissing;
+	}), [s]), w = q(() => Array.from(u.files).map((e) => e.name).filter((e) => e.endsWith(".fasta") || e.endsWith(".fa") || e.endsWith(".fa.gz") || e.endsWith(".fasta.gz")), [u.files]), T = q(() => Array.from(u.files).map((e) => e.name).filter((e) => e.endsWith(".fastq") || e.endsWith(".fq") || e.endsWith(".fq.gz") || e.endsWith(".fastaq.gz")), [u.files]), E = G((e) => {
+		let { dropDownOptions: t, dropDownValue: n, label: r, onChange: i } = e;
+		return /* @__PURE__ */ Q(ne, {
+			freeSolo: !0,
+			fullWidth: !0,
+			onChange: (e, t) => {
+				i(t), m(v.current), x();
+			},
+			options: t,
+			renderInput: (e) => /* @__PURE__ */ Q(se, {
+				...e,
+				label: r,
+				size: "small"
+			}),
+			sx: { lineHeight: "initial" },
+			value: n
+		});
+	}, [m, x]), D = G((e) => {
+		let t = s.cols[e.id], n = e.row.id;
+		return /* @__PURE__ */ Q(L, {
+			sx: {
+				alignItems: "center",
+				display: "flex",
+				flexDirection: "column",
+				height: "100%",
+				justifyContent: "center"
+			},
+			children: E({
+				dropDownOptions: w,
+				dropDownValue: v.current?.[e.row.id]?.sequenceFileNames[t.id] || "",
+				label: t.label,
+				onChange: (e) => {
+					e ? v.current[n].sequenceFileNames[t.id] = e : delete v.current?.[n]?.sequenceFileNames[t.id];
+				}
+			})
+		});
+	}, [
+		s,
+		E,
+		w
+	]), O = G((e) => {
+		let t = s.cols[e.id], n = h.sequenceColumns.includes(t), r = e.row.id, i = v.current?.[r]?.readsFileNames?.[t.id]?.fwd || "", a = v.current?.[r]?.readsFileNames?.[t.id]?.rev || "";
+		return /* @__PURE__ */ $(L, {
+			sx: {
+				alignItems: "center",
+				display: "flex",
+				flexDirection: "row",
+				gap: 1,
+				height: "100%",
+				justifyContent: "center"
+			},
+			children: [E({
+				dropDownOptions: n ? w : T,
+				dropDownValue: i,
+				label: `${t.label} FWD`,
+				onChange: (e) => {
+					e ? v.current[r].readsFileNames[t.id].fwd = e : delete v.current?.[r]?.readsFileNames?.[t.id]?.fwd;
+				}
+			}), E({
+				dropDownOptions: n ? w : T,
+				dropDownValue: a,
+				label: `${t.label} REV`,
+				onChange: (e) => {
+					e ? v.current[r].readsFileNames[t.id].rev = e : delete v.current?.[r]?.readsFileNames?.[t.id]?.rev;
+				}
+			})]
+		});
+	}, [
+		s,
+		h.sequenceColumns,
+		E,
+		w,
+		T
+	]);
+	return Ne({
+		columns: q(() => {
+			let e = [];
+			e.push(Me.createReadableIndexColumn());
+			let t = [
+				...h.sampleIdColumns,
+				...h.sequenceColumns,
+				...h.readsColumns
+			], n = h.sampleIdColumns.find((e) => e.id === c);
+			n && C(f, n) && e.push({
+				headerName: n.label,
+				hideInFilter: !0,
+				id: n.id,
+				isInitiallyVisible: !0,
+				type: "text",
+				valueGetter: (e) => a.getRowValue(e.row.validated_content, n, s).short,
+				widthPx: 300
+			}), h.sequenceColumns.forEach((t) => {
+				e.push({
+					cellTitleGetter: () => null,
+					headerName: t.label,
+					hideInFilter: !0,
+					id: t.id,
+					isInitiallyVisible: !0,
+					renderCell: D,
+					type: "text",
+					valueGetter: (e) => a.getRowValue(e.row.validated_content, t, s).short,
+					widthPx: 400
+				});
+			}), h.readsColumns.forEach((t) => {
+				e.push({
+					cellTitleGetter: () => null,
+					headerName: t.label,
+					hideInFilter: !0,
+					id: t.id,
+					isInitiallyVisible: !0,
+					renderCell: O,
+					type: "text",
+					valueGetter: (e) => a.getRowValue(e.row.validated_content, t, s).short,
+					widthPx: 800
+				});
+			});
+			let r = /* @__PURE__ */ new Set();
+			f.forEach((e) => {
+				Object.keys(e.validated_content || {}).forEach((e) => r.add(e));
+			});
+			let i = [
+				...h.sequenceColumns.map((e) => e.id),
+				...h.readsColumns.map((e) => e.id),
+				n?.id
+			];
+			return s.ordered_col_ids.forEach((n) => {
+				if (i.includes(n) || !r.has(n) || t.find((e) => e.id === n)) return;
+				let o = s.cols[n];
+				o && e.push({
+					headerName: o.code,
+					hideInFilter: !0,
+					id: o.id,
+					isInitiallyVisible: !0,
+					type: "text",
+					valueGetter: (e) => a.getRowValue(e.row.validated_content, o, s).short,
+					widthPx: 250
+				});
+			}), e;
+		}, [
+			C,
+			s,
+			h.readsColumns,
+			h.sampleIdColumns,
+			h.sequenceColumns,
+			O,
+			D,
+			c,
+			f
+		]),
+		createFiltersFromColumns: !0,
+		rows: f,
+		store: S
+	}), /* @__PURE__ */ $(L, {
+		sx: {
+			display: "grid",
+			gridTemplateRows: "max-content auto max-content",
+			height: "100%"
+		},
+		children: [/* @__PURE__ */ Q(L, {
+			sx: { paddingBottom: 1 },
+			children: /* @__PURE__ */ $(F, {
+				severity: "info",
+				children: [/* @__PURE__ */ Q(I, { id: g }), /* @__PURE__ */ Q(L, { id: _ })]
+			})
+		}), /* @__PURE__ */ $(fe, {
+			store: S,
+			children: [/* @__PURE__ */ Q(ke, {
+				font: n["gen-epix-ui-casedb"].lineList.font,
+				rowHeight: 7
+			}), /* @__PURE__ */ Q(Ve, {
+				onGoBackButtonClick: b,
+				onProceedButtonClick: y
+			})]
+		})]
+	});
+}, nt = () => {
+	let { t: e } = X(), t = ue(), n = W(p), r = l(n, (e) => e.completeCaseType), i = l(n, (e) => e.activeStep), a = l(n, (e) => e.stepOrder), o = q(() => ({
+		[f.CREATE_CASES]: e`Submit`,
+		[f.MAP_COLUMNS]: e`Map columns`,
+		[f.MAP_SEQUENCES]: e`Map sequences`,
+		[f.PREVIEW]: e`Preview`,
+		[f.SELECT_FILE]: e`Select file`,
+		[f.SELECT_SEQUENCE_FILES]: e`Select sequence files`
+	}), [e]), s = q(() => [f.SELECT_SEQUENCE_FILES, f.MAP_SEQUENCES], []), c = q(() => a.map((e) => ({
+		key: String(e),
+		label: o[e],
+		optional: s.includes(e)
+	})), [
+		s,
+		o,
+		a
+	]);
+	return /* @__PURE__ */ $(ve, {
+		sx: {
+			display: "grid",
+			gridTemplateRows: "max-content auto",
+			height: "100%",
+			position: "relative",
+			width: "100%"
+		},
+		children: [/* @__PURE__ */ Q(re, { children: /* @__PURE__ */ Q(ye, {
+			activeStep: String(i),
+			steps: c,
+			sx: { marginY: 2 }
+		}) }), /* @__PURE__ */ $(ve, {
+			sx: {
+				height: `calc(100% - ${t.spacing(4)})`,
+				marginBottom: 2,
+				marginTop: 2,
+				position: "relative"
+			},
+			children: [
+				i === f.SELECT_FILE && /* @__PURE__ */ Q(He, {}),
+				i === f.MAP_COLUMNS && /* @__PURE__ */ Q(Ge, {}),
+				i === f.PREVIEW && /* @__PURE__ */ Q(Xe, { caseTypeId: r.id }),
+				i === f.SELECT_SEQUENCE_FILES && /* @__PURE__ */ Q(et, {}),
+				i === f.MAP_SEQUENCES && /* @__PURE__ */ Q(tt, {}),
+				i === f.CREATE_CASES && /* @__PURE__ */ Q(Ze, {})
+			]
+		})]
+	});
+};
+//#endregion
+export { nt as t };
+
+//# sourceMappingURL=Upload.js.map