@haniffalab/cherita-react 1.2.0 → 1.3.0-dev.2025-05-29.ee7e9b72

package/dist/cjs/components/var-list/VarItem.js

@@ -3,7 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.SingleSelectionItem = SingleSelectionItem;
+exports.SelectionItem = SelectionItem;
+exports.VarDiseaseInfo = VarDiseaseInfo;
 exports.VarItem = VarItem;
 var _react = _interopRequireWildcard(require("react"));
 var _freeSolidSvgIcons = require("@fortawesome/free-solid-svg-icons");
@@ -14,24 +15,30 @@ var _reactBootstrap = require("react-bootstrap");
 var _constants = require("../../constants/constants");
 var _DatasetContext = require("../../context/DatasetContext");
 var _FilterContext = require("../../context/FilterContext");
+var _SettingsContext = require("../../context/SettingsContext");
 var _Histogram = require("../../utils/Histogram");
 var _requests = require("../../utils/requests");
-var _VirtualizedList = require("../../utils/VirtualizedList");
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-function _getRequireWildcardCache(e) { if ("function" != typeof WeakMap) return null; var r = new WeakMap(), t = new WeakMap(); return (_getRequireWildcardCache = function (e) { return e ? t : r; })(e); }
-function _interopRequireWildcard(e, r) { if (!r && e && e.__esModule) return e; if (null === e || "object" != typeof e && "function" != typeof e) return { default: e }; var t = _getRequireWildcardCache(r); if (t && t.has(e)) return t.get(e); var n = { __proto__: null }, a = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var u in e) if ("default" !== u && {}.hasOwnProperty.call(e, u)) { var i = a ? Object.getOwnPropertyDescriptor(e, u) : null; i && (i.get || i.set) ? Object.defineProperty(n, u, i) : n[u] = e[u]; } return n.default = e, t && t.set(e, n), n; }
+function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
+function _extends() { return _extends = Object.assign ? Object.assign.bind() : function (n) { for (var e = 1; e < arguments.length; e++) { var t = arguments[e]; for (var r in t) ({}).hasOwnProperty.call(t, r) && (n[r] = t[r]); } return n; }, _extends.apply(null, arguments); }
+function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
+function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
+function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
+function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || "default"); if ("object" != typeof i) return i; throw new TypeError("@@toPrimitive must return a primitive value."); } return ("string" === r ? String : Number)(t); }
 function VarHistogram(_ref) {
   let {
     item
   } = _ref;
   const ENDPOINT = "var/histograms";
   const dataset = (0, _DatasetContext.useDataset)();
+  const settings = (0, _SettingsContext.useSettings)();
   const {
     obsIndices
   } = (0, _FilterContext.useFilteredData)();
   // @TODO: consider using Filter's isSliced; would trigger more re-renders/requests
   // const { obsIndices, isSliced } = useFilteredData();
-  const isSliced = dataset.sliceBy.obs || dataset.sliceBy.polygons;
+  const isSliced = settings.sliceBy.obs || settings.sliceBy.polygons;
   const [params, setParams] = (0, _react.useState)({
     url: dataset.url,
     varKey: item.matrix_index,
@@ -39,10 +46,9 @@ function VarHistogram(_ref) {
   });
   (0, _react.useEffect)(() => {
     setParams(p => {
-      return {
-        ...p,
+      return _objectSpread(_objectSpread({}, p), {}, {
         obsIndices: isSliced ? [...(obsIndices || [])] : null
-      };
+      });
     });
   }, [obsIndices, isSliced]);
   const {
@@ -59,20 +65,12 @@ function VarHistogram(_ref) {
   });
 }
 function VarDiseaseInfoItem(item) {
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
   return /*#__PURE__*/_react.default.createElement(_reactBootstrap.ListGroup.Item, {
     key: item.disease_id,
     className: "feature-disease-info"
   }, /*#__PURE__*/_react.default.createElement("button", {
     type: "button",
-    className: "btn btn-link disease-link",
-    onClick: () => {
-      dispatch({
-        type: "select.disease",
-        id: item.disease_id,
-        name: item.disease_name
-      });
-    }
+    className: "btn btn-link disease-link"
   }, item.disease_name), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Table, {
     striped: true,
     size: "sm",
@@ -89,23 +87,23 @@ function VarDiseaseInfo(_ref2) {
   let {
     data
   } = _ref2;
-  return /*#__PURE__*/_react.default.createElement(_VirtualizedList.VirtualizedList, {
-    getDataAtIndex: index => data[index],
-    count: data.length,
-    estimateSize: 140,
-    maxHeight: "40vh",
-    ItemComponent: VarDiseaseInfoItem
-  });
+  return /*#__PURE__*/_react.default.createElement(_reactBootstrap.ListGroup, {
+    className: "feature-disease-info-list"
+  }, data.map(item => {
+    return /*#__PURE__*/_react.default.createElement(VarDiseaseInfoItem, _extends({
+      key: item.disease_id
+    }, item));
+  }));
 }
-function SingleSelectionItem(_ref3) {
+function SelectionItem(_ref3) {
   let {
     item,
     isActive,
     selectVar,
     removeVar,
-    isDiseaseGene = false,
     showSetColorEncoding = true,
-    showRemove = true
+    showRemove = true,
+    isMultiple = false
   } = _ref3;
   const ENDPOINT = "disease/gene";
   const [openInfo, setOpenInfo] = (0, _react.useState)(false);
@@ -123,9 +121,9 @@ function SingleSelectionItem(_ref3) {
     refetchOnMount: false,
     enabled: !!dataset.diseaseDatasets.length
   });
-  const hasDiseaseInfo = !isPending && !serverError && !!fetchedData?.length;
+  const hasDiseaseInfo = !isPending && !serverError && !!(fetchedData !== null && fetchedData !== void 0 && fetchedData.length);
   return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("div", {
-    className: `d-flex justify-content-between ${hasDiseaseInfo ? "cursor-pointer" : ""}`,
+    className: "d-flex justify-content-between ".concat(hasDiseaseInfo ? "cursor-pointer" : ""),
     onClick: () => {
       setOpenInfo(o => !o);
     }
@@ -133,7 +131,7 @@ function SingleSelectionItem(_ref3) {
     className: "d-flex justify-content-between align-items-center w-100"
   }, /*#__PURE__*/_react.default.createElement("div", null, item.name), /*#__PURE__*/_react.default.createElement("div", {
     className: "d-flex align-items-center gap-1"
-  }, hasDiseaseInfo && /*#__PURE__*/_react.default.createElement(_iconsMaterial.MoreVert, null), !isDiseaseGene && /*#__PURE__*/_react.default.createElement(VarHistogram, {
+  }, hasDiseaseInfo && /*#__PURE__*/_react.default.createElement(_iconsMaterial.MoreVert, null), /*#__PURE__*/_react.default.createElement(VarHistogram, {
     item: item
   }), showSetColorEncoding && /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
     type: "button",
@@ -148,7 +146,11 @@ function SingleSelectionItem(_ref3) {
     title: isNotInData ? "Not present in data" : "Set as color encoding"
   }, /*#__PURE__*/_react.default.createElement(_reactFontawesome.FontAwesomeIcon, {
     icon: _freeSolidSvgIcons.faDroplet
-  })), (!isDiseaseGene || !showRemove) && /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
+  }), isMultiple && /*#__PURE__*/_react.default.createElement(_reactFontawesome.FontAwesomeIcon, {
+    icon: _freeSolidSvgIcons.faPlus,
+    size: "xs",
+    className: "ps-xs-1"
+  })), showRemove && /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
     type: "button",
     className: "m-0 p-0 px-1",
     variant: "outline-secondary",
@@ -167,37 +169,14 @@ function SingleSelectionItem(_ref3) {
     data: fetchedData
   }))));
 }
-function MultipleSelectionItem(_ref4) {
-  let {
-    item,
-    isActive,
-    toggleVar
-  } = _ref4;
-  const isNotInData = item.matrix_index === -1;
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("div", {
-    className: "d-flex"
-  }, /*#__PURE__*/_react.default.createElement("div", {
-    className: "flex-grow-1"
-  }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
-    type: "button",
-    key: item.matrix_index,
-    variant: isActive ? "primary" : "outline-primary",
-    className: "m-0 p-0 px-1",
-    onClick: toggleVar,
-    disabled: isNotInData,
-    title: isNotInData ? "Not present in data" : item.name
-  }, item.name))));
-}
-function VarItem(_ref5) {
+function VarItem(_ref4) {
   let {
     item,
     active,
-    setVarButtons,
-    mode = _constants.SELECTION_MODES.SINGLE,
-    isDiseaseGene = false
-  } = _ref5;
-  const dataset = (0, _DatasetContext.useDataset)();
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
+    mode = _constants.SELECTION_MODES.SINGLE
+  } = _ref4;
+  const settings = (0, _SettingsContext.useSettings)();
+  const dispatch = (0, _SettingsContext.useSettingsDispatch)();
   const selectVar = () => {
     if (mode === _constants.SELECTION_MODES.SINGLE) {
       dispatch({
@@ -220,8 +199,9 @@ function VarItem(_ref5) {
     }
   };
   const removeVar = () => {
-    setVarButtons(b => {
-      return b.filter(i => i.name !== item.name);
+    dispatch({
+      type: "remove.var",
+      var: item
     });
     if (mode === _constants.SELECTION_MODES.SINGLE) {
       if (active === item.matrix_index) {
@@ -239,28 +219,25 @@ function VarItem(_ref5) {
     }
   };
   const toggleVar = () => {
-    if (active.includes(item.matrix_index)) {
-      dispatch({
-        type: "deselect.multivar",
-        var: item
-      });
-    } else {
-      selectVar(item);
-    }
+    dispatch({
+      type: "toggle.multivar",
+      var: item
+    });
   };
   if (item && mode === _constants.SELECTION_MODES.SINGLE) {
-    return /*#__PURE__*/_react.default.createElement(SingleSelectionItem, {
+    return /*#__PURE__*/_react.default.createElement(SelectionItem, {
       item: item,
-      isActive: dataset.colorEncoding === _constants.COLOR_ENCODINGS.VAR && active === item.matrix_index,
+      isActive: settings.colorEncoding === _constants.COLOR_ENCODINGS.VAR && active === item.matrix_index,
       selectVar: selectVar,
-      removeVar: removeVar,
-      isDiseaseGene: isDiseaseGene
+      removeVar: removeVar
     });
   } else if (mode === _constants.SELECTION_MODES.MULTIPLE) {
-    return /*#__PURE__*/_react.default.createElement(MultipleSelectionItem, {
+    return /*#__PURE__*/_react.default.createElement(SelectionItem, {
       item: item,
       isActive: item.matrix_index !== -1 && _lodash.default.includes(active, item.matrix_index),
-      toggleVar: toggleVar
+      selectVar: toggleVar,
+      removeVar: removeVar,
+      isMultiple: true
     });
   } else {
     return null;

package/dist/cjs/components/var-list/VarList.js

@@ -10,16 +10,21 @@ var _reactFontawesome = require("@fortawesome/react-fontawesome");
 var _lodash = _interopRequireDefault(require("lodash"));
 var _reactBootstrap = require("react-bootstrap");
 var _ButtonGroup = _interopRequireDefault(require("react-bootstrap/ButtonGroup"));
+var _VarItem = require("./VarItem");
+var _VarListToolbar = require("./VarListToolbar");
+var _VarSet = require("./VarSet");
 var _constants = require("../../constants/constants");
 var _DatasetContext = require("../../context/DatasetContext");
+var _SettingsContext = require("../../context/SettingsContext");
 var _LoadingIndicators = require("../../utils/LoadingIndicators");
 var _requests = require("../../utils/requests");
-var _VarItem = require("./VarItem");
-var _VarListToolbar = require("./VarListToolbar");
-var _VarSet = require("./VarSet");
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-function _getRequireWildcardCache(e) { if ("function" != typeof WeakMap) return null; var r = new WeakMap(), t = new WeakMap(); return (_getRequireWildcardCache = function (e) { return e ? t : r; })(e); }
-function _interopRequireWildcard(e, r) { if (!r && e && e.__esModule) return e; if (null === e || "object" != typeof e && "function" != typeof e) return { default: e }; var t = _getRequireWildcardCache(r); if (t && t.has(e)) return t.get(e); var n = { __proto__: null }, a = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var u in e) if ("default" !== u && {}.hasOwnProperty.call(e, u)) { var i = a ? Object.getOwnPropertyDescriptor(e, u) : null; i && (i.get || i.set) ? Object.defineProperty(n, u, i) : n[u] = e[u]; } return n.default = e, t && t.set(e, n), n; }
+function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
+function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
+function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
+function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
+function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || "default"); if ("object" != typeof i) return i; throw new TypeError("@@toPrimitive must return a primitive value."); } return ("string" === r ? String : Number)(t); }
 const useVarMean = function (varKeys) {
   let enabled = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false;
   const ENDPOINT = "matrix/mean";
@@ -35,13 +40,12 @@ const useVarMean = function (varKeys) {
   });
   (0, _react.useEffect)(() => {
     setParams(p => {
-      return {
-        ...p,
+      return _objectSpread(_objectSpread({}, p), {}, {
         varKeys: _lodash.default.map(varKeys, v => v.isSet ? {
           name: v.name,
           indices: v.vars.map(v => v.index)
         } : v.index)
-      };
+      });
     });
   }, [varKeys]);
   return (0, _requests.useFetch)(ENDPOINT, params, {
@@ -54,173 +58,50 @@ const useVarMean = function (varKeys) {
 const sortMeans = (i, means) => {
   return means[i.name] || _lodash.default.min(_lodash.default.values(means)) - 1;
 };
-
-// @TODO: display where disease data comes from
-// add to disease dataset metadata
-function DiseaseVarList(_ref) {
-  let {
-    makeListItem
-  } = _ref;
-  const ENDPOINT = "disease/genes";
-  const dataset = (0, _DatasetContext.useDataset)();
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
-  const [diseaseVars, setDiseaseVars] = (0, _react.useState)([]);
-  const [sortedDiseaseVars, setSortedDiseaseVars] = (0, _react.useState)([]);
-  const [params, setParams] = (0, _react.useState)({
-    url: dataset.url,
-    col: dataset.varNamesCol,
-    diseaseId: dataset.selectedDisease?.id,
-    diseaseDatasets: dataset.diseaseDatasets
-  });
-  (0, _react.useEffect)(() => {
-    setParams(p => {
-      return {
-        ...p,
-        diseaseId: dataset.selectedDisease?.id
-      };
-    });
-  }, [dataset.selectedDisease]);
-  const diseaseData = (0, _requests.useFetch)(ENDPOINT, params, {
-    enabled: !!params.diseaseId,
-    refetchOnMount: false
-  });
-  (0, _react.useEffect)(() => {
-    if (!diseaseData.isPending && !diseaseData.serverError) {
-      setDiseaseVars(diseaseData.fetchedData);
-    }
-  }, [diseaseData.fetchedData, diseaseData.isPending, diseaseData.serverError]);
-  const varMeans = useVarMean(diseaseVars, !!diseaseVars?.length && dataset.varSort.disease.sort === _constants.VAR_SORT.MATRIX);
-  (0, _react.useEffect)(() => {
-    if (dataset.varSort.disease.sort === _constants.VAR_SORT.MATRIX) {
-      if (!varMeans.isPending && !varMeans.serverError) {
-        setSortedDiseaseVars(_lodash.default.orderBy(diseaseVars, o => {
-          return sortMeans(o, varMeans.fetchedData);
-        }, dataset.varSort.disease.sortOrder));
-      }
-    } else if (dataset.varSort.disease.sort === _constants.VAR_SORT.NAME) {
-      setSortedDiseaseVars(_lodash.default.orderBy(diseaseVars, "name", dataset.varSort.disease.sortOrder));
-    } else {
-      setSortedDiseaseVars(diseaseVars);
-    }
-  }, [dataset.varSort.disease.sort, dataset.varSort.disease.sortOrder, diseaseVars, varMeans.fetchedData, varMeans.isPending, varMeans.serverError]);
-  const diseaseVarList = _lodash.default.map(sortedDiseaseVars, item => {
-    return makeListItem(item, true);
-  });
-  const isPending = diseaseData.isPending || varMeans.isPending && dataset.varSort.disease.sort === _constants.VAR_SORT.MATRIX;
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, dataset.selectedDisease && (!isPending && !diseaseVars?.length ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("div", {
-    className: "d-flex justify-content-between mt-3"
-  }, /*#__PURE__*/_react.default.createElement("h5", null, "Disease genes")), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Alert, {
-    variant: "light"
-  }, "No disease genes found.")) : /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("div", {
-    className: "d-flex justify-content-between my-2"
-  }, /*#__PURE__*/_react.default.createElement("h5", null, "Disease genes"), /*#__PURE__*/_react.default.createElement(_ButtonGroup.default, {
-    "aria-label": "Feature options",
-    size: "sm"
-  }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
-    variant: "info",
-    onClick: () => {
-      dispatch({
-        type: "reset.disease"
-      });
-    }
-  }, /*#__PURE__*/_react.default.createElement(_reactFontawesome.FontAwesomeIcon, {
-    icon: _freeSolidSvgIcons.faTimes,
-    className: "me-1"
-  }), "Clear"))), /*#__PURE__*/_react.default.createElement("p", null, dataset.selectedDisease?.name), /*#__PURE__*/_react.default.createElement(_VarListToolbar.VarListToolbar, {
-    varType: "disease"
-  }), /*#__PURE__*/_react.default.createElement("div", {
-    className: "position-relative"
-  }, isPending && /*#__PURE__*/_react.default.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/_react.default.createElement(_reactBootstrap.ListGroup, {
-    variant: "flush",
-    className: "cherita-list"
-  }, diseaseVarList)))));
-}
-function VarNamesList(_ref2) {
+function VarNamesList(_ref) {
+  var _settings$selectedVar, _settings$selectedVar2;
   let {
     mode = _constants.SELECTION_MODES.SINGLE,
-    displayName = "genes",
-    showDiseaseVarList = true
-  } = _ref2;
-  const dataset = (0, _DatasetContext.useDataset)();
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
-  const [varButtons, setVarButtons] = (0, _react.useState)(mode === _constants.SELECTION_MODES.SINGLE ? dataset.selectedVar ? _lodash.default.unionWith([dataset.selectedVar], dataset.varSets, _lodash.default.isEqual) : [...dataset.varSets] : [...dataset.selectedMultiVar, ...dataset.varSets]);
-  const [active, setActive] = (0, _react.useState)(mode === _constants.SELECTION_MODES.SINGLE ? dataset.selectedVar?.matrix_index || dataset.selectedVar?.name : dataset.selectedMultiVar.map(i => i.matrix_index || i.name));
-  const [sortedVarButtons, setSortedVarButtons] = (0, _react.useState)([]);
+    displayName = "genes"
+  } = _ref;
+  const settings = (0, _SettingsContext.useSettings)();
+  const dispatch = (0, _SettingsContext.useSettingsDispatch)();
+  const [active, setActive] = (0, _react.useState)(mode === _constants.SELECTION_MODES.SINGLE ? ((_settings$selectedVar = settings.selectedVar) === null || _settings$selectedVar === void 0 ? void 0 : _settings$selectedVar.matrix_index) || ((_settings$selectedVar2 = settings.selectedVar) === null || _settings$selectedVar2 === void 0 ? void 0 : _settings$selectedVar2.name) : settings.selectedMultiVar.map(i => i.matrix_index || i.name));
+  const [sortedVars, setSortedVars] = (0, _react.useState)([]);
   (0, _react.useEffect)(() => {
     if (mode === _constants.SELECTION_MODES.SINGLE) {
-      setVarButtons(v => {
-        if (dataset.selectedVar) {
-          return _lodash.default.unionWith(v, [dataset.selectedVar], _lodash.default.isEqual);
-        } else {
-          return v;
-        }
-      });
-      setActive(dataset.selectedVar?.matrix_index || dataset.selectedVar?.name);
+      var _settings$selectedVar3, _settings$selectedVar4;
+      setActive(((_settings$selectedVar3 = settings.selectedVar) === null || _settings$selectedVar3 === void 0 ? void 0 : _settings$selectedVar3.matrix_index) || ((_settings$selectedVar4 = settings.selectedVar) === null || _settings$selectedVar4 === void 0 ? void 0 : _settings$selectedVar4.name));
     }
-  }, [mode, dataset.selectedVar]);
+  }, [mode, settings.selectedVar]);
   (0, _react.useEffect)(() => {
     if (mode === _constants.SELECTION_MODES.MULTIPLE) {
-      setVarButtons(v => {
-        if (dataset.selectedMultiVar.length) {
-          return _lodash.default.unionWith(v, dataset.selectedMultiVar, _lodash.default.isEqual);
-        } else {
-          return v;
-        }
-      });
-      setActive(dataset.selectedMultiVar.map(i => i.matrix_index || i.name));
+      setActive(settings.selectedMultiVar.map(i => i.matrix_index || i.name));
     }
-  }, [mode, dataset.selectedMultiVar]);
-  (0, _react.useEffect)(() => {
-    setVarButtons(v => {
-      const updated = _lodash.default.compact(_lodash.default.map(v, i => {
-        if (i.isSet) {
-          return dataset.varSets.find(s => s.name === i.name);
-        } else return i;
-      }));
-      const newSets = _lodash.default.difference(dataset.varSets, updated);
-      return [...updated, ...newSets];
-    });
-    if (mode === _constants.SELECTION_MODES.SINGLE) {
-      if (dataset.selectedVar?.isSet) {
-        const selectedSet = dataset.varSets.find(s => s.name === dataset.selectedVar.name);
-        dispatch({
-          type: "select.var",
-          var: selectedSet
-        });
-      }
-    } else {
-      dispatch({
-        type: "update.multivar",
-        vars: dataset.varSets
-      });
-    }
-  }, [mode, dataset.varSets, dataset.selectedVar?.isSet, dataset.selectedVar?.name, dispatch]);
-  const varMeans = useVarMean(varButtons, dataset.varSort.var.sort === _constants.VAR_SORT.MATRIX);
+  }, [mode, settings.selectedMultiVar]);
+  const varMeans = useVarMean(settings.vars, settings.varSort.var.sort === _constants.VAR_SORT.MATRIX);
 
-  // @TODO: deferr sortedVarButtons ?
+  // @TODO: deferr sortedVars ?
   (0, _react.useEffect)(() => {
-    if (dataset.varSort.var.sort === _constants.VAR_SORT.MATRIX) {
+    if (settings.varSort.var.sort === _constants.VAR_SORT.MATRIX) {
       if (!varMeans.isPending && !varMeans.serverError && varMeans.fetchedData) {
-        setSortedVarButtons(_lodash.default.orderBy(varButtons, o => {
+        setSortedVars(_lodash.default.orderBy(settings.vars, o => {
           return sortMeans(o, varMeans.fetchedData);
-        }, dataset.varSort.var.sortOrder));
+        }, settings.varSort.var.sortOrder));
       }
-    } else if (dataset.varSort.var.sort === _constants.VAR_SORT.NAME) {
-      setSortedVarButtons(_lodash.default.orderBy(varButtons, "name", dataset.varSort.var.sortOrder));
+    } else if (settings.varSort.var.sort === _constants.VAR_SORT.NAME) {
+      setSortedVars(_lodash.default.orderBy(settings.vars, "name", settings.varSort.var.sortOrder));
     } else {
-      setSortedVarButtons(varButtons);
+      setSortedVars(settings.vars);
     }
-  }, [dataset.varSort.var.sort, dataset.varSort.var.sortOrder, varButtons, varMeans.isPending, varMeans.serverError, varMeans.fetchedData]);
-  const makeListItem = function (item) {
-    let isDiseaseGene = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false;
+  }, [settings.varSort.var.sort, settings.varSort.var.sortOrder, varMeans.isPending, varMeans.serverError, varMeans.fetchedData, settings.vars]);
+  const makeListItem = item => {
     return /*#__PURE__*/_react.default.createElement(_reactBootstrap.ListGroup.Item, {
       key: item.matrix_index
     }, /*#__PURE__*/_react.default.createElement(_VarItem.VarItem, {
       item: item,
       active: active,
-      setVarButtons: setVarButtons,
-      mode: mode,
-      isDiseaseGene: isDiseaseGene
+      mode: mode
     }));
   };
   const makeSetListItem = set => {
@@ -232,7 +113,7 @@ function VarNamesList(_ref2) {
       mode: mode
     }));
   };
-  const varList = _lodash.default.map(sortedVarButtons, item => {
+  const varList = _lodash.default.map(sortedVars, item => {
     if (item.isSet) {
       return makeSetListItem(item);
     } else {
@@ -241,17 +122,17 @@ function VarNamesList(_ref2) {
   });
   const newSetName = () => {
     let n = 1;
-    let setName = `Set ${n}`;
-    const setNameExists = name => {
-      return dataset.varSets.some(set => set.name === name);
+    let setName = "Set ".concat(n);
+    const nameExists = name => {
+      return settings.vars.some(v => v.name === name);
     };
-    while (setNameExists(setName)) {
+    while (nameExists(setName)) {
       n++;
-      setName = `Set ${n}`;
+      setName = "Set ".concat(n);
     }
     return setName;
   };
-  const isPending = varMeans.isPending && dataset.varSort.var.sort === _constants.VAR_SORT.MATRIX;
+  const isPending = varMeans.isPending && settings.varSort.var.sort === _constants.VAR_SORT.MATRIX;
   return /*#__PURE__*/_react.default.createElement("div", {
     className: "position-relative"
   }, /*#__PURE__*/_react.default.createElement("div", {
@@ -265,8 +146,8 @@ function VarNamesList(_ref2) {
     variant: "info",
     onClick: () => {
       dispatch({
-        type: "add.varSet",
-        varSet: {
+        type: "add.var",
+        var: {
           name: newSetName(),
           vars: [],
           isSet: true
@@ -276,12 +157,8 @@ function VarNamesList(_ref2) {
   }, "New set"), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
     variant: "info",
     onClick: () => {
-      setVarButtons([]);
-      dispatch({
-        type: mode === _constants.SELECTION_MODES.SINGLE ? "reset.var" : "reset.multiVar"
-      });
       dispatch({
-        type: "reset.varSets"
+        type: "reset.vars"
       });
     }
   }, /*#__PURE__*/_react.default.createElement(_reactFontawesome.FontAwesomeIcon, {
@@ -294,7 +171,5 @@ function VarNamesList(_ref2) {
   }, isPending && /*#__PURE__*/_react.default.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/_react.default.createElement(_reactBootstrap.ListGroup, {
     variant: "flush",
     className: "cherita-list"
-  }, varList)))), /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, showDiseaseVarList && /*#__PURE__*/_react.default.createElement(DiseaseVarList, {
-    makeListItem: makeListItem
-  }))));
+  }, varList))))));
 }

package/dist/cjs/components/var-list/VarListToolbar.js

@@ -9,19 +9,18 @@ var _freeSolidSvgIcons = require("@fortawesome/free-solid-svg-icons");
 var _reactFontawesome = require("@fortawesome/react-fontawesome");
 var _reactBootstrap = require("react-bootstrap");
 var _constants = require("../../constants/constants");
-var _DatasetContext = require("../../context/DatasetContext");
-function _getRequireWildcardCache(e) { if ("function" != typeof WeakMap) return null; var r = new WeakMap(), t = new WeakMap(); return (_getRequireWildcardCache = function (e) { return e ? t : r; })(e); }
-function _interopRequireWildcard(e, r) { if (!r && e && e.__esModule) return e; if (null === e || "object" != typeof e && "function" != typeof e) return { default: e }; var t = _getRequireWildcardCache(r); if (t && t.has(e)) return t.get(e); var n = { __proto__: null }, a = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var u in e) if ("default" !== u && {}.hasOwnProperty.call(e, u)) { var i = a ? Object.getOwnPropertyDescriptor(e, u) : null; i && (i.get || i.set) ? Object.defineProperty(n, u, i) : n[u] = e[u]; } return n.default = e, t && t.set(e, n), n; }
+var _SettingsContext = require("../../context/SettingsContext");
+function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
 // @TODO: set option for "var" and "disease"
 function VarListToolbar(_ref) {
   let {
     varType = "var"
   } = _ref;
-  const dataset = (0, _DatasetContext.useDataset)();
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
-  const [sort, setSort] = (0, _react.useState)(dataset.varSort.var.sort);
-  const [nameSortOrder, setNameSortOrder] = (0, _react.useState)(dataset.varSort.var.sortOrder);
-  const [matrixSortOrder, setMatrixSortOrder] = (0, _react.useState)(dataset.varSort.var.sortOrder);
+  const settings = (0, _SettingsContext.useSettings)();
+  const dispatch = (0, _SettingsContext.useSettingsDispatch)();
+  const [sort, setSort] = (0, _react.useState)(settings.varSort.var.sort);
+  const [nameSortOrder, setNameSortOrder] = (0, _react.useState)(settings.varSort.var.sortOrder);
+  const [matrixSortOrder, setMatrixSortOrder] = (0, _react.useState)(settings.varSort.var.sortOrder);
   const handleSort = (sortValue, sortOrder, setSortOrder) => {
     if (sort !== sortValue) {
       setSort(sortValue);