@gen-epix/ui-client-casedb 4.0.0

package/dist/components/ui/TreeDescription/TreeDescription.d.ts

@@ -0,0 +1,5 @@
+import { TreeConfiguration } from '../../../models/dashboard';
+export type TreeDescriptionProps = {
+    readonly treeConfiguration: TreeConfiguration;
+};
+export declare const TreeDescription: ({ treeConfiguration, }: TreeDescriptionProps) => import("react").JSX.Element;

package/dist/components/ui/TreeDescription/index.d.ts

@@ -0,0 +1 @@
+export * from './TreeDescription';

package/dist/components/ui/TreeDescription/index.js

@@ -0,0 +1,40 @@
+import { Box as e, useTheme as t } from "@mui/material";
+import { useTranslation as n } from "react-i18next";
+import { jsx as r, jsxs as i } from "react/jsx-runtime";
+//#region src/components/ui/TreeDescription/TreeDescription.tsx
+var a = ({ treeConfiguration: a }) => {
+	let o = t(), { t: s } = n();
+	return /* @__PURE__ */ i(e, {
+		sx: {
+			"& dd": { marginLeft: o.spacing(2) },
+			"& dl": { margin: 0 }
+		},
+		children: [/* @__PURE__ */ i(e, {
+			sx: { marginY: 1 },
+			children: [/* @__PURE__ */ r("strong", {
+				style: { fontSize: "1rem" },
+				children: s`Genetic distance protocol`
+			}), /* @__PURE__ */ i("dl", { children: [
+				/* @__PURE__ */ r("dt", { children: s`Name` }),
+				/* @__PURE__ */ r("dd", { children: a.geneticDistanceProtocol.name }),
+				/* @__PURE__ */ r("dt", { children: s`Description` }),
+				/* @__PURE__ */ r("dd", { children: a.geneticDistanceProtocol.description })
+			] })]
+		}), /* @__PURE__ */ i(e, {
+			sx: { marginY: 1 },
+			children: [/* @__PURE__ */ r("strong", {
+				style: { fontSize: "1rem" },
+				children: s`Tree algorithm`
+			}), /* @__PURE__ */ i("dl", { children: [
+				/* @__PURE__ */ r("dt", { children: s`Name` }),
+				/* @__PURE__ */ r("dd", { children: a.treeAlgorithm.name }),
+				/* @__PURE__ */ r("dt", { children: s`Description` }),
+				/* @__PURE__ */ r("dd", { children: a.treeAlgorithm.description })
+			] })]
+		})]
+	});
+};
+//#endregion
+export { a as TreeDescription };
+
+//# sourceMappingURL=index.js.map

package/dist/components/ui/TreeDescription/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../../src/components/ui/TreeDescription/TreeDescription.tsx"],"sourcesContent":["import {\n  Box,\n  useTheme,\n} from '@mui/material';\nimport { useTranslation } from 'react-i18next';\n\nimport type { TreeConfiguration } from '../../../models/dashboard';\n\nexport type TreeDescriptionProps = {\n  readonly treeConfiguration: TreeConfiguration;\n};\n\nexport const TreeDescription = ({\n  treeConfiguration,\n}: TreeDescriptionProps) => {\n  const theme = useTheme();\n  const { t } = useTranslation();\n\n  return (\n    <Box\n      sx={{\n        '& dd': {\n          marginLeft: theme.spacing(2),\n        },\n        '& dl': {\n          margin: 0,\n        },\n      }}\n    >\n      <Box\n        sx={{\n          marginY: 1,\n        }}\n      >\n        <strong style={{ fontSize: '1rem' }}>\n          {t`Genetic distance protocol`}\n        </strong>\n        <dl>\n          <dt>\n            {t`Name`}\n          </dt>\n          <dd>\n            {treeConfiguration.geneticDistanceProtocol.name}\n          </dd>\n          <dt>\n            {t`Description`}\n          </dt>\n          <dd>\n            {treeConfiguration.geneticDistanceProtocol.description}\n          </dd>\n        </dl>\n      </Box>\n      <Box\n        sx={{\n          marginY: 1,\n        }}\n      >\n        <strong style={{ fontSize: '1rem' }}>\n          {t`Tree algorithm`}\n        </strong>\n        <dl>\n          <dt>\n            {t`Name`}\n          </dt>\n          <dd>\n            {treeConfiguration.treeAlgorithm.name}\n          </dd>\n          <dt>\n            {t`Description`}\n          </dt>\n          <dd>\n            {treeConfiguration.treeAlgorithm.description}\n          </dd>\n        </dl>\n      </Box>\n\n    </Box>\n  );\n};\n"],"mappings":";;;;AAYA,IAAa,KAAmB,EAC9B,2BAC0B;CAC1B,IAAM,IAAQ,EAAS,GACjB,EAAE,SAAM,EAAe;CAE7B,OACE,kBAAC,GAAD;EACE,IAAI;GACF,QAAQ,EACN,YAAY,EAAM,QAAQ,CAAC,EAC7B;GACA,QAAQ,EACN,QAAQ,EACV;EACF;YARF,CAUE,kBAAC,GAAD;GACE,IAAI,EACF,SAAS,EACX;aAHF,CAKE,kBAAC,UAAD;IAAQ,OAAO,EAAE,UAAU,OAAO;cAC/B,CAAC;GACI,CAAA,GACR,kBAAC,MAAD,EAAA,UAAA;IACE,kBAAC,MAAD,EAAA,UACG,CAAC,OACA,CAAA;IACJ,kBAAC,MAAD,EAAA,UACG,EAAkB,wBAAwB,KACzC,CAAA;IACJ,kBAAC,MAAD,EAAA,UACG,CAAC,cACA,CAAA;IACJ,kBAAC,MAAD,EAAA,UACG,EAAkB,wBAAwB,YACzC,CAAA;GACF,EAAA,CAAA,CACD;MACL,kBAAC,GAAD;GACE,IAAI,EACF,SAAS,EACX;aAHF,CAKE,kBAAC,UAAD;IAAQ,OAAO,EAAE,UAAU,OAAO;cAC/B,CAAC;GACI,CAAA,GACR,kBAAC,MAAD,EAAA,UAAA;IACE,kBAAC,MAAD,EAAA,UACG,CAAC,OACA,CAAA;IACJ,kBAAC,MAAD,EAAA,UACG,EAAkB,cAAc,KAC/B,CAAA;IACJ,kBAAC,MAAD,EAAA,UACG,CAAC,cACA,CAAA;IACJ,kBAAC,MAAD,EAAA,UACG,EAAkB,cAAc,YAC/B,CAAA;GACF,EAAA,CAAA,CACD;IAEF;;AAET"}

package/dist/components/ui/TreeWidget/TreeWidget.d.ts

@@ -0,0 +1 @@
+export declare const TreeWidget: () => import("react").JSX.Element;

package/dist/components/ui/TreeWidget/index.d.ts

@@ -0,0 +1 @@
+export * from './TreeWidget';

package/dist/components/ui/TreeWidget/index.js

@@ -0,0 +1,404 @@
+import { n as e } from "../../../_chunks/FilterUtil.js";
+import { SELECTION_FILTER_GROUP as t } from "../../../utils/CaseTypeUtil/index.js";
+import { CASEDB_QUERY_KEY as n } from "../../../constants/query.js";
+import { TreeWidgetUtil as r } from "../../../utils/TreeWidgetUtil/index.js";
+import { DASHBOARD_COMPONENT_NAME as i } from "../../../constants/dashboard.js";
+import { t as a } from "../../../_chunks/react.js";
+import { t as ee } from "../../../_chunks/dashboardStore.js";
+import { ContextMenu as te } from "../ContextMenu/index.js";
+import { WidgetUnavailable as ne } from "../WidgetUnavailable/index.js";
+import { EventBusService as o } from "../../../classes/services/EventBusService/index.js";
+import { t as s } from "../../../_chunks/CaseDbDownloadUtil.js";
+import { TreeDescription as re } from "../TreeDescription/index.js";
+import { n as ie } from "../../../_chunks/LegendaItem.js";
+import { t as ae } from "../../../_chunks/Dashboard.js";
+import { t as oe } from "../../../_chunks/userProfileStoreContext.js";
+import { t as se } from "../../../_chunks/index.module.js";
+import { CaseDbCaseApi as ce } from "@gen-epix/api-casedb";
+import { ConfigService as c } from "@gen-epix/ui/classes/services/ConfigService";
+import { Box as le, Button as ue, ListItemIcon as de, ListItemText as l, MenuItem as u, useTheme as fe } from "@mui/material";
+import { use as d, useCallback as f, useEffect as p, useMemo as m, useRef as pe, useState as h } from "react";
+import { useTranslation as me } from "react-i18next";
+import he from "@mui/icons-material/FilterAlt";
+import { Fragment as ge, jsx as g, jsxs as _ } from "react/jsx-runtime";
+import { useQueryMemo as _e } from "@gen-epix/ui/hooks/useQueryMemo";
+import { Spinner as ve } from "@gen-epix/ui/components/ui/Spinner";
+import { Subject as ye } from "@gen-epix/ui-core/classes/Subject";
+import be from "@mui/icons-material/Link";
+import xe from "@mui/icons-material/Clear";
+import Se from "@mui/icons-material/ArrowUpward";
+import Ce from "@mui/icons-material/InfoOutlined";
+import { PhylogeneticTree as we } from "@gen-epix/ui-phylogenetic-tree/components/PhylogeneticTree";
+//#region src/components/ui/TreeWidget/TreeWidget.tsx
+var v = () => {
+	let v = fe(), { t: y } = me(), b = c.getInstance().config.tree, [x, Te] = h(), [S, C] = h(!0), w = pe(null), T = d(ee), E = d(ie), D = d(oe), O = a(T, (e) => e.setPhylogeneticTreeResponse), k = a(T, (e) => e.baseData), Ee = a(T, (e) => e.sortedData), De = a(T, (e) => e.filteredData[t]), Oe = a(T, (e) => e.setSorting), A = a(T, (e) => e.tree), j = a(T, (e) => e.sortByField), ke = a(T, (e) => e.stratification), M = a(T, (e) => e.completeCaseType), N = a(T, (t) => !t.filters.find((t) => t instanceof e).isInitialFilterValue()), Ae = a(T, (e) => e.addTreeFilter), je = a(T, (e) => e.treeFilterStepOut), Me = a(T, (e) => e.updateWidgetData), P = a(T, (e) => e.updateWidgetDataPersistable), F = a(T, (e) => e.removeTreeFilter), I = a(T, (e) => e.isDataLoading), Ne = a(T, (e) => e.newick), Pe = a(T, (e) => e.resetTreeAddresses), Fe = a(D, (e) => e.dashboardWidgetSettings[i.TREE].isShowDistancesEnabled), Ie = a(D, (e) => e.dashboardWidgetSettings[i.TREE].isShowSupportLinesWhenUnlinkedEnabled), [Le, L] = h(null), [R, z] = h(null), [B, Re] = h(null), [V, H] = h(T.getState().getWidgetDataPersistable(i.TREE).treeConfiguration), U = m(() => new ye({
+		caseIds: [],
+		origin: null
+	}), []), ze = m(() => {
+		let e = T.getState().getWidgetData(i.TREE);
+		return {
+			horizontalScrollPosition: isNaN(e?.horizontalScrollPosition) ? 0 : e.horizontalScrollPosition,
+			verticalScrollPosition: isNaN(e?.verticalScrollPosition) ? 0 : e.verticalScrollPosition,
+			zoomLevel: isNaN(e?.zoomLevel) ? 1 : e.zoomLevel
+		};
+	}, [T]), Be = m(() => Ee.map((e) => e.id), [Ee]), W = m(() => r.getTreeConfigurations(M), [M]), Ve = m(() => {
+		if (!V) return y("Phylogenetic tree visualization");
+		let e = V.col?.label || y("data");
+		return y("Figure of a phylogenetic tree belonging to {{label}}. Generated using {{geneticDistanceProtocol}} and {{treeAlgorithm}}.", {
+			geneticDistanceProtocol: V.geneticDistanceProtocol?.name || y("unknown protocol"),
+			label: e,
+			treeAlgorithm: V.treeAlgorithm?.name || y("unknown algorithm")
+		});
+	}, [V, y]);
+	p(() => {
+		let e = E.highlightSubject.subscribe((e) => {
+			e.origin !== i.TREE && U.next(e);
+		}), t = U.subscribe((e) => {
+			e.origin === i.TREE && E.highlight(e);
+		});
+		return () => {
+			e(), t();
+		};
+	}, [E, U]);
+	let G = m(() => De.map((e) => e.id).sort(), [De]);
+	p(() => {
+		Pe();
+	}, [G, Pe]);
+	let K = m(() => G.length >= 2 && G.every((e) => !!e), [G]), q = m(() => G.length > 0 && M.props.read_max_tree_size > 0 && G.length > M.props.read_max_tree_size, [G, M.props.read_max_tree_size]), He = m(() => ({
+		case_ids: G,
+		case_type_id: M.id,
+		genetic_distance_col_id: V?.col.id,
+		tree_algorithm_code: V?.treeAlgorithm.code
+	}), [
+		G,
+		M.id,
+		V
+	]), { data: J, error: Ue, isLoading: We } = _e({
+		enabled: K && !!V && !q,
+		queryFn: async ({ signal: e }) => (await ce.getInstance().retrievePhylogeneticTree(He, { signal: e })).data,
+		queryKey: [n.PHYLOGENETIC_TREE, JSON.stringify(He)],
+		retry: !1,
+		staleTime: Infinity
+	}), Ge = f(() => {
+		o.getInstance().emit("openFiltersMenu");
+	}, []), Y = !!V && (I || K && We), X = q || !I && (!Y && !!Ue || !K || A?.maxBranchLength?.toNumber() === 0 || A?.size === 0 || !V || !Y && A === null), Z = !q && !!V && !I && !Ue && !We && A?.size > 0 && K, Ke = m(() => {
+		if (!X) return null;
+		if (!K) return y`The phylogenetic tree cannot be displayed because there are not enough sequences available for the shown cases. A minimum of 2 sequences is required to generate a phylogenetic tree.`;
+		if (K && !A) return y`The phylogenetic tree cannot be displayed because the tree could not be generated. Either there are no sequences available for the shown cases or the selected tree configuration does not yield a valid tree.`;
+		if (q) return /* @__PURE__ */ _(ge, { children: [/* @__PURE__ */ g(le, {
+			sx: { marginBottom: 2 },
+			children: y("The phylogenetic tree cannot be displayed because the number of cases ({{caseCount}}) exceeds the maximum allowed number of cases ({{maxSize}}) to display a phylogenetic tree. Refine your filters to reduce the number of results.", {
+				caseCount: G.length,
+				maxSize: M.props.read_max_tree_size
+			})
+		}), /* @__PURE__ */ g(ue, {
+			color: "inherit",
+			onClick: Ge,
+			variant: "outlined",
+			children: y`Refine filters`
+		})] });
+	}, [
+		G.length,
+		M.props.read_max_tree_size,
+		K,
+		q,
+		X,
+		Ge,
+		y,
+		A
+	]);
+	p(() => {
+		J && O(J);
+	}, [J, O]), p(() => {
+		if (!W?.length) {
+			H(null), P(i.TREE, { treeConfiguration: null });
+			return;
+		}
+		let e = T.getState().getWidgetDataPersistable(i.TREE)?.treeConfiguration || W[0];
+		H(e), P(i.TREE, { treeConfiguration: e });
+	}, [
+		T,
+		W,
+		P
+	]), p(() => {
+		j && S && Z && w.current?.unlink({
+			positionX: 0,
+			positionY: 0,
+			zoomLevel: c.getInstance().config.tree.INITIAL_UNLINKED_ZOOM_LEVEL
+		});
+	}, [
+		S,
+		Z,
+		j
+	]);
+	let qe = se((e) => {
+		Me(i.TREE, {
+			horizontalScrollPosition: e.horizontalScrollPosition,
+			verticalScrollPosition: e.verticalScrollPosition,
+			zoomLevel: e.zoomLevel
+		});
+	}, 500), Je = f((e) => {
+		qe(e);
+	}, [qe]), Ye = f((e) => {
+		Te(e);
+	}, []), Xe = f(() => {
+		L(null), z(null);
+	}, []), Ze = f(() => {
+		(async () => {
+			await Oe(null, null), w.current?.syncScrollToVisibleTree();
+		})();
+	}, [Oe]), Qe = f(() => {
+		Ze();
+	}, [Ze]), Q = f(() => {
+		w.current?.link(0);
+	}, []), $e = f(async (e) => {
+		await Ae(R.rootId), Q(), e();
+	}, [
+		Ae,
+		R,
+		Q
+	]), et = f(async () => {
+		await F(), Q();
+	}, [F, Q]), tt = f(async () => {
+		await je(), Q();
+	}, [Q, je]), nt = f(({ mouseEvent: e, pathProperties: t }) => {
+		if (z(null), Re(null), t?.treeNode) {
+			let { treeNode: n } = t;
+			L({
+				caseIds: n.subTreeLeaveNames ? n.subTreeLeaveNames : [n.name],
+				mouseEvent: e,
+				position: {
+					left: e.clientX,
+					top: e.clientY
+				}
+			}), n.subTreeNames.length && n.name && n.maxBranchLength.toNumber() && z({
+				caseIds: n.subTreeLeaveNames,
+				rootId: n.name
+			}), n.name && !n.subTreeNames.length && Re(n.name);
+			return;
+		}
+		t?.subTreeLeaveNames?.length && L({
+			caseIds: t.subTreeLeaveNames,
+			mouseEvent: e,
+			position: {
+				left: e.clientX,
+				top: e.clientY
+			}
+		});
+	}, []), rt = f((e) => {
+		o.getInstance().emit("openCaseInfoDialog", {
+			caseId: k.find((e) => e.id === B).id,
+			caseTypeId: M.id
+		}), e();
+	}, [
+		B,
+		k,
+		M.id
+	]), it = f((e) => {
+		if (R) return /* @__PURE__ */ _(u, {
+			divider: !0,
+			onClick: async () => $e(e),
+			children: [/* @__PURE__ */ g(de, { children: /* @__PURE__ */ g(he, { fontSize: "small" }) }), /* @__PURE__ */ g(l, { children: y`Filter (show only this subtree)` })]
+		});
+		if (B) return /* @__PURE__ */ _(u, {
+			divider: !0,
+			onClick: () => rt(e),
+			children: [/* @__PURE__ */ g(de, { children: /* @__PURE__ */ g(Ce, { fontSize: "small" }) }), /* @__PURE__ */ g(l, { children: y`Show details` })]
+		});
+	}, [
+		B,
+		rt,
+		$e,
+		y,
+		R
+	]), at = m(() => W?.length ? {
+		disabled: !V,
+		items: W?.map((e) => ({
+			active: !!V && V.computedId === e.computedId,
+			callback: () => {
+				(async () => {
+					await F(), P(i.TREE, { treeConfiguration: e }), H(e);
+				})();
+			},
+			label: r.getTreeConfigurationLabel(e),
+			tooltip: /* @__PURE__ */ g(re, { treeConfiguration: e })
+		})) ?? [],
+		label: V ? y("Tree: {{algorithm}}", { algorithm: r.getTreeConfigurationLabel(V) }) : y`Tree`,
+		tooltip: V ? /* @__PURE__ */ g(re, { treeConfiguration: V }) : void 0
+	} : y`Tree`, [
+		W,
+		V,
+		y,
+		F,
+		P
+	]), ot = m(() => [
+		{
+			callback: tt,
+			disabled: !N,
+			label: y`Change tree filter to nearest ancestor`,
+			leftIcon: /* @__PURE__ */ g(Se, {})
+		},
+		{
+			callback: et,
+			disabled: !N,
+			label: y`Remove tree filter`,
+			leftIcon: /* @__PURE__ */ g(xe, {})
+		},
+		{
+			callback: Qe,
+			label: y`Link and snap the Line List to the Tree (resets tree zoom level and Line List sorting)`,
+			leftIcon: /* @__PURE__ */ g(be, { sx: { color: S ? void 0 : v.palette.error.main } })
+		}
+	], [
+		N,
+		S,
+		Qe,
+		et,
+		tt,
+		y,
+		v.palette.error.main
+	]);
+	p(() => {
+		let e = () => {
+			let e = y("Phylogenetic Tree - {{geneticDistanceProtocol}} - {{treeAlgorithm}}", {
+				geneticDistanceProtocol: V?.geneticDistanceProtocol.name ?? "",
+				treeAlgorithm: V?.treeAlgorithm.name ?? ""
+			});
+			o.getInstance().emit("onDownloadOptionsChanged", {
+				disabled: X,
+				items: [
+					{
+						callback: () => s.downloadNewick(e, Ne, M, y),
+						label: y`Save as Newick`
+					},
+					{
+						callback: () => s.downloadCanvasImage(e, x, "jpeg", M, y),
+						label: y`Save as JPEG`
+					},
+					{
+						callback: () => s.downloadCanvasImage(e, x, "png", M, y),
+						label: y`Save as PNG`
+					}
+				],
+				zone: i.TREE,
+				zoneLabel: y`Phylogenetic Tree`
+			});
+		};
+		e();
+		let t = o.getInstance();
+		return t.addEventListener("onDownloadOptionsRequested", e), () => {
+			t.emit("onDownloadOptionsChanged", {
+				items: null,
+				zone: i.TREE,
+				zoneLabel: y`Tree`
+			}), t.removeEventListener("onDownloadOptionsRequested", e);
+		};
+	}, [
+		M,
+		S,
+		X,
+		Ne,
+		y,
+		x,
+		V?.geneticDistanceProtocol.name,
+		V?.treeAlgorithm.name
+	]), p(() => {
+		let e = o.getInstance().addEventListener("onLinkLineListAndTree", () => w.current?.link());
+		return () => {
+			e();
+		};
+	}, []);
+	let st = f((e) => {
+		C(e);
+	}, [C]), $ = m(() => new ye({ highlightedNodeNames: E.highlightSubject.data.caseIds }), [E.highlightSubject.data.caseIds]);
+	return p(() => {
+		let e = $.subscribe((e) => {
+			E.highlight({
+				caseIds: e.highlightedNodeNames,
+				origin: i.TREE
+			});
+		});
+		return () => {
+			e();
+		};
+	}, [$, E]), p(() => {
+		let e = E.highlightSubject.subscribe((e) => {
+			e.origin !== i.TREE && $.next({ highlightedNodeNames: e.caseIds });
+		});
+		return () => {
+			e();
+		};
+	}, [E.highlightSubject, $]), /* @__PURE__ */ _(ae, {
+		expandDisabled: X,
+		primaryMenu: ot,
+		title: at,
+		widgetName: i.TREE,
+		children: [/* @__PURE__ */ _(le, {
+			sx: {
+				height: "100%",
+				overflow: "clip",
+				position: "relative",
+				width: "100%"
+			},
+			children: [
+				X && /* @__PURE__ */ g(ge, { children: /* @__PURE__ */ g(ne, {
+					reason: Ke,
+					widgetLabel: y`phylogenetic tree`
+				}) }),
+				Y && !X && /* @__PURE__ */ g(ve, {
+					label: y`Loading`,
+					takingLongerTimeoutMs: c.getInstance().config.tree.TAKING_LONGER_TIMEOUT_MS
+				}),
+				!X && Z && /* @__PURE__ */ g(we, {
+					ancestorDotRadius: b.ANCESTOR_DOT_RADIUS,
+					ariaLabel: Ve,
+					backgroundColor: v.palette.background.paper,
+					dimFn: v["gen-epix-ui-casedb"].tree.dimFn,
+					fontFamily: v.typography.fontFamily,
+					headerHeight: b.HEADER_HEIGHT,
+					highlightedNodeNamesSubject: $,
+					initialViewState: ze,
+					itemHeight: c.getInstance().config.lineList.TABLE_ROW_HEIGHT,
+					leafDotRadius: b.LEAF_DOT_RADIUS,
+					linkedScrollDebounceDelayMs: b.LINKED_SCROLL_DEBOUNCE_DELAY_MS,
+					maxScaleWidthPx: b.MAX_SCALE_WIDTH_PX,
+					maxZoomLevel: b.MAX_ZOOM_LEVEL,
+					maxZoomSpeed: b.MAX_ZOOM_SPEED,
+					minimumDistancePercentageToShowLabel: b.MINIMUM_DISTANCE_PERCENTAGE_TO_SHOW_LABEL,
+					minScaleWidthPx: b.MIN_SCALE_WIDTH_PX,
+					minZoomLevel: b.MIN_ZOOM_LEVEL,
+					minZoomSpeed: b.MIN_ZOOM_SPEED,
+					nodeNameColors: ke?.caseIdColors,
+					onCanvasChange: Ye,
+					onLinkStateChange: st,
+					onPathClick: nt,
+					onViewStateChange: Je,
+					panningThreshold: b.PANNING_THRESHOLD,
+					ref: w,
+					regularFillColorSupportLine: b.REGULAR_FILL_COLOR_SUPPORT_LINE,
+					scaleColor: v.palette.text.primary,
+					scaleIncrements: b.SCALE_INCREMENTS,
+					scrollSubject: E.linkedScrollSubject,
+					shouldShowDistances: Fe,
+					shouldShowSupportLinesWhenUnlinked: Ie,
+					sortedLeafNames: Be,
+					supportLineColorLinked: v["gen-epix-ui-casedb"].tree.supportLineColorLinked,
+					supportLineColorUnlinked: v["gen-epix-ui-casedb"].tree.supportLineColorUnlinked,
+					tree: A,
+					treeColor: v["gen-epix-ui-casedb"].tree.color,
+					treeFont: v["gen-epix-ui-casedb"].tree.font,
+					treePadding: b.TREE_PADDING,
+					visibleRangeSubject: E.lineListRangeSubject
+				})
+			]
+		}), /* @__PURE__ */ g(te, {
+			config: Le,
+			getExtraItems: it,
+			onMenuClose: Xe
+		})]
+	});
+};
+//#endregion
+export { v as TreeWidget };
+
+//# sourceMappingURL=index.js.map

package/dist/components/ui/TreeWidget/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../../src/components/ui/TreeWidget/TreeWidget.tsx"],"sourcesContent":["import {\n  Box,\n  Button,\n  ListItemIcon,\n  ListItemText,\n  MenuItem,\n  useTheme,\n} from '@mui/material';\nimport ClearIcon from '@mui/icons-material/Clear';\nimport ArrowUpwardIcon from '@mui/icons-material/ArrowUpward';\nimport FilterAltIcon from '@mui/icons-material/FilterAlt';\nimport InfoOutlinedIcon from '@mui/icons-material/InfoOutlined';\nimport LinkIcon from '@mui/icons-material/Link';\nimport type { ReactElement } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useMemo,\n  useRef,\n  useState,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport { useDebouncedCallback } from 'use-debounce';\nimport type { CaseDbRetrievePhylogeneticTreeRequestBody } from '@gen-epix/api-casedb';\nimport { CaseDbCaseApi } from '@gen-epix/api-casedb';\nimport type { MenuItemData } from '@gen-epix/ui/models/nestedMenu';\nimport { ConfigService } from '@gen-epix/ui/classes/services/ConfigService';\nimport { Spinner } from '@gen-epix/ui/components/ui/Spinner';\nimport { useQueryMemo } from '@gen-epix/ui/hooks/useQueryMemo';\nimport { Subject } from '@gen-epix/ui-core/classes/Subject';\nimport { PhylogeneticTree } from '@gen-epix/ui-phylogenetic-tree/components/PhylogeneticTree';\nimport type {\n  PhylogeneticTreeHighlightedNodeNamesSubjectValue,\n  PhylogeneticTreePathClickEvent,\n  PhylogeneticTreeRef,\n  PhylogeneticTreeViewState,\n} from '@gen-epix/ui-phylogenetic-tree/components/PhylogeneticTree';\n\nimport { EventBusService } from '../../../classes/services/EventBusService';\nimport type {\n  DashboardTreeSettings,\n  TreeConfiguration,\n  TreeWidgetData,\n  TreeWidgetDataPersistable,\n} from '../../../models/dashboard';\nimport type { Highlighting } from '../../../models/caseDb';\nimport { DashboardStoreContext } from '../../../stores/dashboardStore';\nimport { SELECTION_FILTER_GROUP } from '../../../utils/CaseTypeUtil';\nimport { CaseDbDownloadUtil } from '../../../utils/CaseDbDownloadUtil';\nimport { TreeWidgetUtil } from '../../../utils/TreeWidgetUtil';\nimport type { ContextMenuConfigWithPosition } from '../ContextMenu';\nimport { ContextMenu } from '../ContextMenu';\nimport { TreeDescription } from '../TreeDescription';\nimport { WidgetUnavailable } from '../WidgetUnavailable';\nimport { CASEDB_QUERY_KEY } from '../../../constants/query';\nimport type { CaseDbConfig } from '../../../models/config';\nimport { TreeFilter } from '../../../classes/filters/TreeFilter';\nimport { DashboardWidget } from '../Dashboard';\nimport { DASHBOARD_COMPONENT_NAME } from '../../../constants/dashboard';\nimport { DashboardContext } from '../Dashboard/context/DashboardContext';\nimport { UserProfileStoreContext } from '../../../stores/userProfileStore/userProfileStoreContext';\n\ntype ZoomInMenuItemConfig = {\n  caseIds?: string[];\n  rootId?: string;\n};\n\nexport const TreeWidget = () => {\n  const theme = useTheme();\n  const { t } = useTranslation();\n  const treeConfig = ConfigService.getInstance<CaseDbConfig>().config.tree;\n  const [treeCanvas, setTreeCanvas] = useState<HTMLCanvasElement>();\n  const [isTreeLinked, setIsTreeLinked] = useState(true);\n  const treeRef = useRef<PhylogeneticTreeRef>(null);\n  const dashboardStore = use(DashboardStoreContext);\n  const dashboardContext = use(DashboardContext);\n  const userProfileStore = use(UserProfileStoreContext);\n  const setPhylogeneticTreeResponse = useStore(dashboardStore, (state) => state.setPhylogeneticTreeResponse);\n  const baseData = useStore(dashboardStore, (state) => state.baseData);\n  const sortedData = useStore(dashboardStore, (state) => state.sortedData);\n  const filteredCases = useStore(dashboardStore, (state) => state.filteredData[SELECTION_FILTER_GROUP]);\n  const setSorting = useStore(dashboardStore, (state) => state.setSorting);\n  const tree = useStore(dashboardStore, (state) => state.tree);\n  const sortByField = useStore(dashboardStore, (state) => state.sortByField);\n  const stratification = useStore(dashboardStore, (state) => state.stratification);\n  const completeCaseType = useStore(dashboardStore, (state) => state.completeCaseType);\n  const hasActiveTreeFilter = useStore(dashboardStore, (state) => !state.filters.find(filter => filter instanceof TreeFilter).isInitialFilterValue());\n  const addTreeFilter = useStore(dashboardStore, (state) => state.addTreeFilter);\n  const treeFilterStepOut = useStore(dashboardStore, (state) => state.treeFilterStepOut);\n  const updateWidgetData = useStore(dashboardStore, (state) => state.updateWidgetData);\n  const updateWidgetDataPersistable = useStore(dashboardStore, (state) => state.updateWidgetDataPersistable);\n  const removeTreeFilter = useStore(dashboardStore, (state) => state.removeTreeFilter);\n  const isCaseDataLoading = useStore(dashboardStore, (state) => state.isDataLoading);\n  const newick = useStore(dashboardStore, (state) => state.newick);\n  const resetTreeAddresses = useStore(dashboardStore, (state) => state.resetTreeAddresses);\n  const isShowDistancesEnabled = useStore(userProfileStore, (state) => (state.dashboardWidgetSettings[DASHBOARD_COMPONENT_NAME.TREE] as DashboardTreeSettings).isShowDistancesEnabled);\n  const isShowSupportLinesWhenUnlinkedEnabled = useStore(userProfileStore, (state) => (state.dashboardWidgetSettings[DASHBOARD_COMPONENT_NAME.TREE] as DashboardTreeSettings).isShowSupportLinesWhenUnlinkedEnabled);\n  const [contextMenuConfig, setContextMenuConfig] = useState<ContextMenuConfigWithPosition | null>(null);\n  const [zoomInMenuItemConfig, setZoomInMenuItemConfig] = useState<ZoomInMenuItemConfig>(null);\n  const [extraLeafInfoId, setExtraLeafInfoId] = useState<string>(null);\n  const [treeConfiguration, setTreeConfiguration] = useState<TreeConfiguration>(dashboardStore.getState().getWidgetDataPersistable<TreeWidgetDataPersistable>(DASHBOARD_COMPONENT_NAME.TREE).treeConfiguration);\n  const treeHighlightingSubject = useMemo(() => new Subject<Highlighting>({\n    caseIds: [],\n    origin: null,\n  }), []);\n  const initialTreeViewState = useMemo<PhylogeneticTreeViewState>(() => {\n    const widgetData = dashboardStore.getState().getWidgetData<TreeWidgetData>(DASHBOARD_COMPONENT_NAME.TREE);\n    return {\n      horizontalScrollPosition: !isNaN(widgetData?.horizontalScrollPosition) ? widgetData.horizontalScrollPosition : 0,\n      verticalScrollPosition: !isNaN(widgetData?.verticalScrollPosition) ? widgetData.verticalScrollPosition : 0,\n      zoomLevel: !isNaN(widgetData?.zoomLevel) ? widgetData.zoomLevel : 1,\n    };\n  }, [dashboardStore]);\n\n  const sortedLeafNames = useMemo(() => {\n    return sortedData.map(c => c.id);\n  }, [sortedData]);\n\n  const treeConfigurations = useMemo(() => TreeWidgetUtil.getTreeConfigurations(completeCaseType), [completeCaseType]);\n\n  const treeCanvasAriaLabel = useMemo(() => {\n    if (!treeConfiguration) {\n      return t('Phylogenetic tree visualization');\n    }\n\n    const label = treeConfiguration.col?.label || t('data');\n    const geneticDistanceProtocol = treeConfiguration.geneticDistanceProtocol?.name || t('unknown protocol');\n    const treeAlgorithm = treeConfiguration.treeAlgorithm?.name || t('unknown algorithm');\n\n    return t('Figure of a phylogenetic tree belonging to {{label}}. Generated using {{geneticDistanceProtocol}} and {{treeAlgorithm}}.', {\n      geneticDistanceProtocol,\n      label,\n      treeAlgorithm,\n    });\n  }, [treeConfiguration, t]);\n\n  useEffect(() => {\n    const unsubscribeHighlightingManager = dashboardContext.highlightSubject.subscribe((highlighting) => {\n      if (highlighting.origin === DASHBOARD_COMPONENT_NAME.TREE) {\n        return;\n      }\n      treeHighlightingSubject.next(highlighting);\n    });\n    const unsubscribeTreeHighlightingSubject = treeHighlightingSubject.subscribe((highlighting) => {\n      if (highlighting.origin !== DASHBOARD_COMPONENT_NAME.TREE) {\n        return;\n      }\n      dashboardContext.highlight(highlighting);\n    });\n\n    return () => {\n      unsubscribeHighlightingManager();\n      unsubscribeTreeHighlightingSubject();\n    };\n  }, [dashboardContext, treeHighlightingSubject]);\n\n  const caseIds = useMemo(() => filteredCases.map(c => c.id).sort(), [filteredCases]);\n\n  useEffect(() => {\n    resetTreeAddresses();\n  }, [caseIds, resetTreeAddresses]);\n\n  const hasEnoughSequencesToShowTree = useMemo(() => caseIds.length >= 2 && caseIds.every(x => !!x), [caseIds]);\n  const hasToManyResultsToShowTree = useMemo(() => caseIds.length > 0 && completeCaseType.props.read_max_tree_size > 0 && caseIds.length > completeCaseType.props.read_max_tree_size, [caseIds, completeCaseType.props.read_max_tree_size]);\n\n  const retrievePhylogeneticTreeRequestBody = useMemo<CaseDbRetrievePhylogeneticTreeRequestBody>(() => ({\n    case_ids: caseIds,\n    case_type_id: completeCaseType.id,\n    genetic_distance_col_id: treeConfiguration?.col.id,\n    tree_algorithm_code: treeConfiguration?.treeAlgorithm.code,\n  }), [caseIds, completeCaseType.id, treeConfiguration]);\n\n  const { data: treeData, error: treeError, isLoading: isTreeLoading } = useQueryMemo({\n    enabled: hasEnoughSequencesToShowTree && !!treeConfiguration && !hasToManyResultsToShowTree,\n    queryFn: async ({ signal }) => {\n      const response = await CaseDbCaseApi.getInstance().retrievePhylogeneticTree(retrievePhylogeneticTreeRequestBody, { signal });\n      return response.data;\n    },\n    queryKey: [CASEDB_QUERY_KEY.PHYLOGENETIC_TREE, JSON.stringify(retrievePhylogeneticTreeRequestBody)],\n    retry: false,\n    staleTime: Infinity,\n  });\n\n  const onOpenFiltersButtonClick = useCallback(() => {\n    EventBusService.getInstance().emit('openFiltersMenu');\n  }, []);\n\n  const isLoading = !!treeConfiguration && (isCaseDataLoading || (hasEnoughSequencesToShowTree && isTreeLoading));\n  const isTreeUnavailable = hasToManyResultsToShowTree || !isCaseDataLoading && ((!isLoading && !!treeError) || !hasEnoughSequencesToShowTree || tree?.maxBranchLength?.toNumber() === 0 || tree?.size === 0 || !treeConfiguration || (!isLoading && tree === null));\n  const shouldShowTree = !hasToManyResultsToShowTree && !!treeConfiguration && !isCaseDataLoading && !treeError && !isTreeLoading && tree?.size > 0 && hasEnoughSequencesToShowTree;\n\n  const widgetUnavailableReason = useMemo<ReactElement | string>(() => {\n    if (!isTreeUnavailable) {\n      return null;\n    }\n    if (!hasEnoughSequencesToShowTree) {\n      return t`The phylogenetic tree cannot be displayed because there are not enough sequences available for the shown cases. A minimum of 2 sequences is required to generate a phylogenetic tree.`;\n    }\n    if (hasEnoughSequencesToShowTree && !tree) {\n      return t`The phylogenetic tree cannot be displayed because the tree could not be generated. Either there are no sequences available for the shown cases or the selected tree configuration does not yield a valid tree.`;\n    }\n    if (hasToManyResultsToShowTree) {\n      return (\n        (\n          <>\n            <Box\n              sx={{\n                marginBottom: 2,\n              }}\n            >\n              {t('The phylogenetic tree cannot be displayed because the number of cases ({{caseCount}}) exceeds the maximum allowed number of cases ({{maxSize}}) to display a phylogenetic tree. Refine your filters to reduce the number of results.', {\n                caseCount: caseIds.length,\n                maxSize: completeCaseType.props.read_max_tree_size,\n              })}\n            </Box>\n            <Button\n              color={'inherit'}\n              onClick={onOpenFiltersButtonClick}\n              variant={'outlined'}\n            >\n              {t`Refine filters`}\n            </Button>\n          </>\n        )\n      );\n    }\n  }, [caseIds.length, completeCaseType.props.read_max_tree_size, hasEnoughSequencesToShowTree, hasToManyResultsToShowTree, isTreeUnavailable, onOpenFiltersButtonClick, t, tree]);\n\n  useEffect(() => {\n    if (treeData) {\n      setPhylogeneticTreeResponse(treeData);\n    }\n  }, [treeData, setPhylogeneticTreeResponse]);\n\n  useEffect(() => {\n    if (!treeConfigurations?.length) {\n      setTreeConfiguration(null);\n      updateWidgetDataPersistable<TreeWidgetDataPersistable>(DASHBOARD_COMPONENT_NAME.TREE, {\n        treeConfiguration: null,\n      });\n      return;\n    }\n    const newConfig = dashboardStore.getState().getWidgetDataPersistable<TreeWidgetDataPersistable>(DASHBOARD_COMPONENT_NAME.TREE)?.treeConfiguration || treeConfigurations[0];\n\n    setTreeConfiguration(newConfig);\n    updateWidgetDataPersistable<TreeWidgetDataPersistable>(DASHBOARD_COMPONENT_NAME.TREE, {\n      treeConfiguration: newConfig,\n    });\n  }, [dashboardStore, treeConfigurations, updateWidgetDataPersistable]);\n\n  useEffect(() => {\n    if (sortByField && isTreeLinked && shouldShowTree) {\n      treeRef.current?.unlink({\n        positionX: 0,\n        positionY: 0,\n        zoomLevel: ConfigService.getInstance<CaseDbConfig>().config.tree.INITIAL_UNLINKED_ZOOM_LEVEL,\n      });\n    }\n  }, [isTreeLinked, shouldShowTree, sortByField]);\n\n  const updateEpiTreeWidgetDataDebounced = useDebouncedCallback((viewState: PhylogeneticTreeViewState) => {\n    updateWidgetData<TreeWidgetData>(DASHBOARD_COMPONENT_NAME.TREE, {\n      horizontalScrollPosition: viewState.horizontalScrollPosition,\n      verticalScrollPosition: viewState.verticalScrollPosition,\n      zoomLevel: viewState.zoomLevel,\n    });\n  }, 500);\n\n  const onTreeViewStateChange = useCallback((viewState: PhylogeneticTreeViewState) => {\n    updateEpiTreeWidgetDataDebounced(viewState);\n  }, [updateEpiTreeWidgetDataDebounced]);\n\n  const onTreeCanvasChange = useCallback((canvas?: HTMLCanvasElement) => {\n    setTreeCanvas(canvas);\n  }, []);\n\n  const onEpiContextMenuClose = useCallback(() => {\n    setContextMenuConfig(null);\n    setZoomInMenuItemConfig(null);\n  }, []);\n\n  const linkLineListToTree = useCallback(() => {\n    const perform = async () => {\n      await setSorting(null, null);\n      treeRef.current?.syncScrollToVisibleTree();\n    };\n\n    // eslint-disable-next-line @typescript-eslint/no-floating-promises\n    perform();\n\n  }, [setSorting]);\n\n  const onLinkButtonClick = useCallback(() => {\n    linkLineListToTree();\n\n  }, [linkLineListToTree]);\n\n  const resetZoomLevelAndScrollPosition = useCallback(() => {\n    treeRef.current?.link(0);\n  }, []);\n\n  const onAddTreeFilterMenuItemClick = useCallback(async (onMenuClose: () => void) => {\n    await addTreeFilter(zoomInMenuItemConfig.rootId);\n    resetZoomLevelAndScrollPosition();\n    onMenuClose();\n  }, [addTreeFilter, zoomInMenuItemConfig, resetZoomLevelAndScrollPosition]);\n\n  const onRemoveTreeFilterButtonClick = useCallback(async () => {\n    await removeTreeFilter();\n    resetZoomLevelAndScrollPosition();\n  }, [removeTreeFilter, resetZoomLevelAndScrollPosition]);\n\n  const onTreeFilterStepOutButtonClick = useCallback(async () => {\n    await treeFilterStepOut();\n    resetZoomLevelAndScrollPosition();\n  }, [resetZoomLevelAndScrollPosition, treeFilterStepOut]);\n\n  const onTreePathClick = useCallback(({ mouseEvent, pathProperties }: PhylogeneticTreePathClickEvent) => {\n    setZoomInMenuItemConfig(null);\n    setExtraLeafInfoId(null);\n\n    if (pathProperties?.treeNode) {\n      const { treeNode } = pathProperties;\n      setContextMenuConfig({\n        caseIds: treeNode.subTreeLeaveNames ? treeNode.subTreeLeaveNames : [treeNode.name],\n        mouseEvent,\n        position: {\n          left: mouseEvent.clientX,\n          top: mouseEvent.clientY,\n        },\n      });\n      if (treeNode.subTreeNames.length && treeNode.name && treeNode.maxBranchLength.toNumber()) {\n        setZoomInMenuItemConfig({\n          caseIds: treeNode.subTreeLeaveNames,\n          rootId: treeNode.name,\n        });\n      }\n      if (treeNode.name && !treeNode.subTreeNames.length) {\n        setExtraLeafInfoId(treeNode.name);\n      }\n      return;\n    }\n\n    if (pathProperties?.subTreeLeaveNames?.length) {\n      setContextMenuConfig({\n        caseIds: pathProperties.subTreeLeaveNames,\n        mouseEvent,\n        position: {\n          left: mouseEvent.clientX,\n          top: mouseEvent.clientY,\n        },\n      });\n    }\n  }, []);\n\n  const onShowDetailsSelectionMenuItemClick = useCallback((onMenuClose: () => void) => {\n    EventBusService.getInstance().emit('openCaseInfoDialog', {\n      caseId: baseData.find(c => c.id === extraLeafInfoId).id,\n      caseTypeId: completeCaseType.id,\n    });\n    onMenuClose();\n  }, [extraLeafInfoId, baseData, completeCaseType.id]);\n\n  const getEpiContextMenuExtraItems = useCallback((onMenuClose: () => void): ReactElement => {\n    if (zoomInMenuItemConfig) {\n      return (\n        <MenuItem\n          divider\n          // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n          onClick={async () => onAddTreeFilterMenuItemClick(onMenuClose)}\n        >\n          <ListItemIcon>\n            <FilterAltIcon fontSize={'small'} />\n          </ListItemIcon>\n          <ListItemText>\n            {t`Filter (show only this subtree)`}\n          </ListItemText>\n        </MenuItem>\n      );\n    }\n    if (extraLeafInfoId) {\n      return (\n        <MenuItem\n          divider\n          // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n          onClick={() => onShowDetailsSelectionMenuItemClick(onMenuClose)}\n        >\n          <ListItemIcon>\n            <InfoOutlinedIcon fontSize={'small'} />\n          </ListItemIcon>\n          <ListItemText>\n            {t`Show details`}\n          </ListItemText>\n        </MenuItem>\n      );\n    }\n  }, [extraLeafInfoId, onShowDetailsSelectionMenuItemClick, onAddTreeFilterMenuItemClick, t, zoomInMenuItemConfig]);\n\n  const titleMenu = useMemo<MenuItemData | string>(() => {\n    if (!treeConfigurations?.length) {\n      return t`Tree`;\n    }\n\n    const menu: MenuItemData = {\n      disabled: !treeConfiguration,\n      items: treeConfigurations?.map<MenuItemData>(config => ({\n        active: !!treeConfiguration && treeConfiguration.computedId === config.computedId,\n        callback: () => {\n          const perform = async () => {\n            await removeTreeFilter();\n            updateWidgetDataPersistable<TreeWidgetDataPersistable>(DASHBOARD_COMPONENT_NAME.TREE, {\n              treeConfiguration: config,\n            });\n            setTreeConfiguration(config);\n          };\n          // eslint-disable-next-line @typescript-eslint/no-floating-promises\n          perform();\n        },\n        label: TreeWidgetUtil.getTreeConfigurationLabel(config),\n        tooltip: (\n          <TreeDescription\n            treeConfiguration={config}\n          />\n        ),\n      })) ?? [],\n      label: treeConfiguration ? t('Tree: {{algorithm}}', { algorithm: TreeWidgetUtil.getTreeConfigurationLabel(treeConfiguration) }) : t`Tree`,\n      tooltip: treeConfiguration\n        ? (\n          <TreeDescription\n            treeConfiguration={treeConfiguration}\n          />\n        )\n        : undefined,\n    };\n\n    return menu;\n  }, [treeConfigurations, treeConfiguration, t, removeTreeFilter, updateWidgetDataPersistable]);\n\n  const primaryMenu = useMemo<MenuItemData[]>(() => {\n    return [\n      {\n        callback: onTreeFilterStepOutButtonClick,\n        disabled: !hasActiveTreeFilter,\n        label: t`Change tree filter to nearest ancestor`,\n        leftIcon: <ArrowUpwardIcon />,\n      },\n      {\n        callback: onRemoveTreeFilterButtonClick,\n        disabled: !hasActiveTreeFilter,\n        label: t`Remove tree filter`,\n        leftIcon: <ClearIcon />,\n      },\n      {\n        callback: onLinkButtonClick,\n        label: t`Link and snap the Line List to the Tree (resets tree zoom level and Line List sorting)`,\n        leftIcon: (\n          <LinkIcon\n            sx={{\n              color: isTreeLinked ? undefined : theme.palette.error.main,\n            }}\n          />\n        ),\n      },\n    ];\n  }, [hasActiveTreeFilter, isTreeLinked, onLinkButtonClick, onRemoveTreeFilterButtonClick, onTreeFilterStepOutButtonClick, t, theme.palette.error.main]);\n\n  useEffect(() => {\n    const emitDownloadOptions = () => {\n      const baseName = t('Phylogenetic Tree - {{geneticDistanceProtocol}} - {{treeAlgorithm}}',\n        {\n          geneticDistanceProtocol: treeConfiguration?.geneticDistanceProtocol.name ?? '',\n          treeAlgorithm: treeConfiguration?.treeAlgorithm.name ?? '',\n        });\n\n      EventBusService.getInstance().emit('onDownloadOptionsChanged', {\n        disabled: isTreeUnavailable,\n        items: [\n          {\n            callback: () => CaseDbDownloadUtil.downloadNewick(baseName, newick, completeCaseType, t),\n            label: t`Save as Newick`,\n          },\n          {\n            callback: () => CaseDbDownloadUtil.downloadCanvasImage(baseName, treeCanvas, 'jpeg', completeCaseType, t),\n            label: t`Save as JPEG`,\n          },\n          {\n            callback: () => CaseDbDownloadUtil.downloadCanvasImage(baseName, treeCanvas, 'png', completeCaseType, t),\n            label: t`Save as PNG`,\n          },\n        ],\n        zone: DASHBOARD_COMPONENT_NAME.TREE,\n        zoneLabel: t`Phylogenetic Tree`,\n      });\n    };\n\n\n    emitDownloadOptions();\n    const eventBusService = EventBusService.getInstance();\n    eventBusService.addEventListener('onDownloadOptionsRequested', emitDownloadOptions);\n\n    return () => {\n      eventBusService.emit('onDownloadOptionsChanged', {\n        items: null,\n        zone: DASHBOARD_COMPONENT_NAME.TREE,\n        zoneLabel: t`Tree`,\n      });\n      eventBusService.removeEventListener('onDownloadOptionsRequested', emitDownloadOptions);\n    };\n  }, [completeCaseType, isTreeLinked, isTreeUnavailable, newick, t, treeCanvas, treeConfiguration?.geneticDistanceProtocol.name, treeConfiguration?.treeAlgorithm.name]);\n\n\n  useEffect(() => {\n    // eslint-disable-next-line @eslint-react/web-api-no-leaked-event-listener\n    const removeEventListener = EventBusService.getInstance().addEventListener('onLinkLineListAndTree', () => treeRef.current?.link());\n    return () => {\n      removeEventListener();\n    };\n  }, []);\n\n\n  const onLinkStateChange = useCallback((linked: boolean) => {\n    setIsTreeLinked(linked);\n  }, [setIsTreeLinked]);\n\n  const phylogeneticTreeHighlightedNodeNamesSubject = useMemo(() => {\n    const subject = new Subject<PhylogeneticTreeHighlightedNodeNamesSubjectValue>({\n      highlightedNodeNames: dashboardContext.highlightSubject.data.caseIds,\n    });\n    return subject;\n  }, [dashboardContext.highlightSubject.data.caseIds]);\n\n  useEffect(() => {\n    const unsubscribe = phylogeneticTreeHighlightedNodeNamesSubject.subscribe((data) => {\n      dashboardContext.highlight({\n        caseIds: data.highlightedNodeNames,\n        origin: DASHBOARD_COMPONENT_NAME.TREE,\n      });\n    });\n    return () => {\n      unsubscribe();\n    };\n  }, [phylogeneticTreeHighlightedNodeNamesSubject, dashboardContext]);\n\n  useEffect(() => {\n    const unsubscribe = dashboardContext.highlightSubject.subscribe(data => {\n      if (data.origin === DASHBOARD_COMPONENT_NAME.TREE) {\n        return;\n      }\n      phylogeneticTreeHighlightedNodeNamesSubject.next({\n        highlightedNodeNames: data.caseIds,\n      });\n    });\n    return () => {\n      unsubscribe();\n    };\n  }, [dashboardContext.highlightSubject, phylogeneticTreeHighlightedNodeNamesSubject]);\n\n  return (\n    <DashboardWidget\n      expandDisabled={isTreeUnavailable}\n      primaryMenu={primaryMenu}\n      title={titleMenu}\n      widgetName={DASHBOARD_COMPONENT_NAME.TREE}\n    >\n      <Box\n        sx={{\n          height: '100%',\n          overflow: 'clip',\n          position: 'relative',\n          width: '100%',\n        }}\n      >\n        {isTreeUnavailable && (\n          <>\n            <WidgetUnavailable\n              reason={widgetUnavailableReason}\n              widgetLabel={t`phylogenetic tree`}\n            />\n          </>\n        )}\n        {(isLoading && !isTreeUnavailable) && (\n          <Spinner\n            label={t`Loading`}\n            takingLongerTimeoutMs={ConfigService.getInstance<CaseDbConfig>().config.tree.TAKING_LONGER_TIMEOUT_MS}\n          />\n        )}\n        {!isTreeUnavailable && shouldShowTree && (\n          <PhylogeneticTree\n            ancestorDotRadius={treeConfig.ANCESTOR_DOT_RADIUS}\n            ariaLabel={treeCanvasAriaLabel}\n            backgroundColor={theme.palette.background.paper}\n            dimFn={theme['gen-epix-ui-casedb'].tree.dimFn}\n            fontFamily={theme.typography.fontFamily}\n            headerHeight={treeConfig.HEADER_HEIGHT}\n            highlightedNodeNamesSubject={phylogeneticTreeHighlightedNodeNamesSubject}\n            initialViewState={initialTreeViewState}\n            itemHeight={ConfigService.getInstance<CaseDbConfig>().config.lineList.TABLE_ROW_HEIGHT}\n            leafDotRadius={treeConfig.LEAF_DOT_RADIUS}\n            linkedScrollDebounceDelayMs={treeConfig.LINKED_SCROLL_DEBOUNCE_DELAY_MS}\n            maxScaleWidthPx={treeConfig.MAX_SCALE_WIDTH_PX}\n            maxZoomLevel={treeConfig.MAX_ZOOM_LEVEL}\n            maxZoomSpeed={treeConfig.MAX_ZOOM_SPEED}\n            minimumDistancePercentageToShowLabel={treeConfig.MINIMUM_DISTANCE_PERCENTAGE_TO_SHOW_LABEL}\n            minScaleWidthPx={treeConfig.MIN_SCALE_WIDTH_PX}\n            minZoomLevel={treeConfig.MIN_ZOOM_LEVEL}\n            minZoomSpeed={treeConfig.MIN_ZOOM_SPEED}\n            nodeNameColors={stratification?.caseIdColors}\n            onCanvasChange={onTreeCanvasChange}\n            onLinkStateChange={onLinkStateChange}\n            onPathClick={onTreePathClick}\n            onViewStateChange={onTreeViewStateChange}\n            panningThreshold={treeConfig.PANNING_THRESHOLD}\n            ref={treeRef}\n            regularFillColorSupportLine={treeConfig.REGULAR_FILL_COLOR_SUPPORT_LINE}\n            scaleColor={theme.palette.text.primary}\n            scaleIncrements={treeConfig.SCALE_INCREMENTS}\n            scrollSubject={dashboardContext.linkedScrollSubject}\n            shouldShowDistances={isShowDistancesEnabled}\n            shouldShowSupportLinesWhenUnlinked={isShowSupportLinesWhenUnlinkedEnabled}\n            sortedLeafNames={sortedLeafNames}\n            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package/dist/components/ui/Upload/Upload.d.ts

@@ -0,0 +1 @@
+export declare const Upload: () => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadCaseResultTable.d.ts

@@ -0,0 +1,18 @@
+import { StoreApi } from 'zustand';
+import { CaseDbCase, CaseDbCaseDataIssue, CaseDbCaseUploadResult, CaseDbCol, CaseDbCompleteCaseType } from '@gen-epix/api-casedb';
+import { TableRowAndColumnParams } from '@gen-epix/ui/models/table';
+import { TableStore } from '@gen-epix/ui/stores/tableStore';
+export type UploadCaseResultTableProps = {
+    readonly caseRightsColMap?: {
+        [colId: string]: string[];
+    };
+    readonly caseUploadResults?: CaseDbCaseUploadResult[];
+    readonly completeCaseType: CaseDbCompleteCaseType;
+    readonly getOriginalCellValue: (col: CaseDbCol, cellParams: TableRowAndColumnParams<CaseDbCaseUploadResult, null>, issue: CaseDbCaseDataIssue) => string;
+    readonly onCaseContentEditSubmit: (caseId: string, content: CaseDbCase['content']) => void;
+    readonly onColContentEditSubmit: (contentPerCaseId: {
+        [caseId: string]: CaseDbCase['content'];
+    }) => void;
+    readonly tableStore: StoreApi<TableStore<CaseDbCaseUploadResult>>;
+};
+export declare const UploadCaseResultTable: ({ caseRightsColMap, caseUploadResults, completeCaseType, getOriginalCellValue, onCaseContentEditSubmit, onColContentEditSubmit, tableStore }: UploadCaseResultTableProps) => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadCreateCases.d.ts

@@ -0,0 +1 @@
+export declare const UploadCreateCases: () => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadEditColumnValuesDialog.d.ts

@@ -0,0 +1,12 @@
+import { CaseDbCase, CaseDbCompleteCaseType } from '@gen-epix/api-casedb';
+import { WithDialogRefMethods, WithDialogRenderProps } from '@gen-epix/ui/hoc/withDialog';
+export interface UploadEditColumnValuesDialogOpenProps {
+    colId: string;
+    completeCaseType: CaseDbCompleteCaseType;
+    shouldShowRightsWarning?: boolean;
+}
+export interface UploadEditColumnValuesDialogProps extends WithDialogRenderProps<UploadEditColumnValuesDialogOpenProps> {
+    onSubmit: (content: CaseDbCase['content']) => void;
+}
+export type UploadEditColumnValuesDialogRefMethods = WithDialogRefMethods<UploadEditColumnValuesDialogProps, UploadEditColumnValuesDialogOpenProps>;
+export declare const UploadEditColumnValuesDialog: import('react').ComponentClass<UploadEditColumnValuesDialogProps, import('@gen-epix/ui/hoc/withDialog').WithDialogState<UploadEditColumnValuesDialogOpenProps>>;

package/dist/components/ui/Upload/UploadMapColumns.d.ts

@@ -0,0 +1 @@
+export declare const UploadMapColumns: () => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadMapSequences.d.ts

@@ -0,0 +1 @@
+export declare const UploadMapSequences: () => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadNavigation.d.ts

@@ -0,0 +1,10 @@
+import { ContainerOwnProps } from '@mui/material';
+export type UploadNavigationProps = {
+    readonly backLabel?: string;
+    readonly containerProps?: ContainerOwnProps;
+    readonly onGoBackButtonClick?: () => void;
+    readonly onProceedButtonClick?: () => void;
+    readonly proceedDisabled?: boolean;
+    readonly proceedLabel?: string;
+};
+export declare const UploadNavigation: ({ backLabel, onGoBackButtonClick: onGoBack, onProceedButtonClick: onProceedButtonClick, proceedDisabled, proceedLabel, }: UploadNavigationProps) => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadPreview.d.ts

@@ -0,0 +1,4 @@
+export type UploadPreviewProps = {
+    readonly caseTypeId: string;
+};
+export declare const UploadPreview: import('react').ComponentType<UploadPreviewProps>;

package/dist/components/ui/Upload/UploadPreviewNavigation.d.ts

@@ -0,0 +1,5 @@
+export type UploadPreviewNavigationProps = {
+    readonly onGoBackButtonClick: () => void;
+    readonly onProceedButtonClick: () => void;
+};
+export declare const UploadPreviewNavigation: ({ onGoBackButtonClick, onProceedButtonClick }: UploadPreviewNavigationProps) => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadSelectFile.d.ts

@@ -0,0 +1 @@
+export declare const UploadSelectFile: () => import("react").JSX.Element;

package/dist/components/ui/Upload/UploadSelectSequenceFiles.d.ts

@@ -0,0 +1 @@
+export declare const UploadSelectSequenceFiles: () => import("react").JSX.Element;

package/dist/components/ui/Upload/index.d.ts

@@ -0,0 +1 @@
+export * from './Upload';

package/dist/components/ui/Upload/index.js

@@ -0,0 +1,2 @@
+import { t as e } from "../../../_chunks/Upload.js";
+export { e as Upload };