@haniffalab/cherita-react 0.2.0-dev.2024-09-26.d9293c4c → 0.2.0-dev.2024-09-26.1ea62883

package/dist/constants/constants.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.VIOLIN_MODES = exports.VIOLINPLOT_STANDARDSCALES = exports.UNSELECTED_POLYGON_FILLCOLOR = exports.SELECTION_MODES = exports.SELECTED_POLYGON_FILLCOLOR = exports.OBS_TYPES = exports.MATRIXPLOT_STANDARDSCALES = exports.LOCAL_STORAGE_KEY = exports.DOTPLOT_STANDARDSCALES = exports.COLOR_ENCODINGS = void 0;
+exports.VIOLIN_MODES = exports.VIOLINPLOT_SCALES = exports.UNSELECTED_POLYGON_FILLCOLOR = exports.SELECTION_MODES = exports.SELECTED_POLYGON_FILLCOLOR = exports.OBS_TYPES = exports.MATRIXPLOT_SCALES = exports.LOCAL_STORAGE_KEY = exports.DOTPLOT_SCALES = exports.COLOR_ENCODINGS = void 0;
 const LOCAL_STORAGE_KEY = exports.LOCAL_STORAGE_KEY = "CHERITA";
 const COLOR_ENCODINGS = exports.COLOR_ENCODINGS = {
   VAR: "var",
@@ -25,30 +25,41 @@ const VIOLIN_MODES = exports.VIOLIN_MODES = {
   MULTIKEY: "multikey",
   GROUPBY: "groupby"
 };
-const MATRIXPLOT_STANDARDSCALES = exports.MATRIXPLOT_STANDARDSCALES = [{
-  value: null,
-  name: "None"
-}, {
-  value: "group",
-  name: "Group"
-}, {
-  value: "var",
-  name: "Var"
-}];
-const DOTPLOT_STANDARDSCALES = exports.DOTPLOT_STANDARDSCALES = [{
-  value: null,
-  name: "None"
-}, {
-  value: "group",
-  name: "Group"
-}, {
-  value: "var",
-  name: "Var"
-}];
-const VIOLINPLOT_STANDARDSCALES = exports.VIOLINPLOT_STANDARDSCALES = [{
-  value: "width",
-  name: "Width"
-}, {
-  value: "count",
-  name: "Count"
-}];
+const MATRIXPLOT_SCALES = exports.MATRIXPLOT_SCALES = {
+  NONE: {
+    value: null,
+    name: "None"
+  },
+  GROUP: {
+    value: "group",
+    name: "Group"
+  },
+  VAR: {
+    value: "var",
+    name: "Var"
+  }
+};
+const DOTPLOT_SCALES = exports.DOTPLOT_SCALES = {
+  NONE: {
+    value: null,
+    name: "None"
+  },
+  GROUP: {
+    value: "group",
+    name: "Group"
+  },
+  VAR: {
+    value: "var",
+    name: "Var"
+  }
+};
+const VIOLINPLOT_SCALES = exports.VIOLINPLOT_SCALES = {
+  WIDTH: {
+    value: "width",
+    name: "Width"
+  },
+  COUNT: {
+    value: "count",
+    name: "Count"
+  }
+};

package/dist/context/DatasetContext.js

@@ -28,7 +28,7 @@ const queryClient = new _reactQuery.QueryClient({
   },
   queryCache: new _reactQuery.QueryCache({
     onError: (error, query) => {
-      console.error(error);
+      console.error(error, query);
     }
   })
 });
@@ -61,6 +61,7 @@ const initialDataset = {
   selectedMultiVar: [],
   colorEncoding: null,
   labelObs: [],
+  varSets: [],
   sliceBy: {
     obs: false,
     polygons: false
@@ -75,16 +76,16 @@ const initialDataset = {
       cmin: 0,
       cmax: 1
     },
-    standardScale: null,
+    scale: {
+      dotplot: _constants.DOTPLOT_SCALES.NONE,
+      matrixplot: _constants.MATRIXPLOT_SCALES.NONE,
+      violinplot: _constants.VIOLINPLOT_SCALES.WIDTH
+    },
     meanOnlyExpressed: false,
     expressionCutoff: 0.0
   },
   diseaseDatasets: [],
-  selectedDisease: {
-    id: null,
-    name: null,
-    genes: []
-  }
+  selectedDisease: null
 };
 const initializer = initialState => {
   const localObj = (JSON.parse(localStorage.getItem(_constants.LOCAL_STORAGE_KEY)) || {})[initialState.url] || {};
@@ -172,7 +173,7 @@ function datasetReducer(dataset, action) {
       }
     case "select.multivar":
       {
-        if (dataset.selectedMultiVar.find(i => _lodash.default.isEqual(i, action.var))) {
+        if (dataset.selectedMultiVar.find(i => action.var.isSet ? i.name === action.var.name : i.matrix_index === action.var.matrix_index)) {
           return dataset;
         } else {
           return {
@@ -181,19 +182,23 @@ function datasetReducer(dataset, action) {
           };
         }
       }
-    case "deselect.var":
+    case "deselect.multivar":
       {
         return {
           ...dataset,
-          selectedVar: null,
-          colorEncoding: dataset.colorEncoding === _constants.COLOR_ENCODINGS.VAR ? null : dataset.colorEncoding
+          selectedMultiVar: dataset.selectedMultiVar.filter(a => action.var.isSet ? a.name !== action.var.name : a.matrix_index !== action.var.matrix_index)
         };
       }
-    case "deselect.multivar":
+    case "update.multivar":
       {
         return {
           ...dataset,
-          selectedMultiVar: dataset.selectedMultiVar.filter(a => a.matrix_index !== action.var.matrix_index)
+          selelectedMultiVar: dataset.selectedMultiVar.map(i => {
+            if (i.isSet) {
+              return action.vars.find(s => s.name === i.name);
+            }
+            return i;
+          })
         };
       }
     case "set.colorEncoding":
@@ -219,24 +224,72 @@ function datasetReducer(dataset, action) {
           colorEncoding: dataset.colorEncoding === _constants.COLOR_ENCODINGS.VAR ? null : dataset.colorEncoding
         };
       }
-    case "select.disease":
+    case "add.varSet":
       {
         return {
           ...dataset,
-          selectedDisease: {
-            id: action.id,
-            name: action.name,
-            genes: []
-          }
+          varSets: [...dataset.varSets, action.varSet]
+        };
+      }
+    case "remove.varSet":
+      {
+        return {
+          ...dataset,
+          varSets: dataset.varSets.filter(a => a.name !== action.varSet.name)
+        };
+      }
+    case "reset.varSets":
+      {
+        return {
+          ...dataset,
+          varSets: []
+        };
+      }
+    case "add.varSet.var":
+      {
+        const varSet = dataset.varSets.find(s => s.name === action.varSet.name);
+        if (varSet.vars.find(v => _lodash.default.isEqual(v, action.var))) {
+          return dataset;
+        } else {
+          return {
+            ...dataset,
+            varSets: dataset.varSets.map(s => {
+              if (s.name === varSet.name) {
+                return {
+                  ...s,
+                  vars: [...s.vars, action.var]
+                };
+              } else {
+                return s;
+              }
+            })
+          };
+        }
+      }
+    case "remove.varSet.var":
+      {
+        const varSet = dataset.varSets.find(s => s.name === action.varSet.name);
+        return {
+          ...dataset,
+          varSets: dataset.varSets.map(s => {
+            if (s.name === varSet.name) {
+              return {
+                ...s,
+                vars: s.vars.filter(v => v.name !== action.var.name)
+              };
+            } else {
+              return s;
+            }
+          })
         };
       }
-    case "set.disease.genes":
+    case "select.disease":
       {
         return {
           ...dataset,
           selectedDisease: {
-            ...dataset.selectedDisease,
-            genes: action.genes
+            id: action.id,
+            name: action.name
           }
         };
       }
@@ -244,11 +297,7 @@ function datasetReducer(dataset, action) {
       {
         return {
           ...dataset,
-          selectedDisease: {
-            id: null,
-            name: null,
-            genes: []
-          }
+          selectedDisease: null
         };
       }
     case "set.controls.colorScale":
@@ -331,13 +380,16 @@ function datasetReducer(dataset, action) {
           }
         };
       }
-    case "set.controls.standardScale":
+    case "set.controls.scale":
       {
         return {
           ...dataset,
           controls: {
             ...dataset.controls,
-            standardScale: action.standardScale
+            scale: {
+              ...dataset.controls.scale,
+              [action.plot]: action.scale
+            }
           }
         };
       }

package/dist/helpers/zarr-helper.js

@@ -66,21 +66,43 @@ const useZarr = function (_ref2) {
   };
 };
 exports.useZarr = useZarr;
+const fetchDataFromZarrs = async (inputs, opts) => {
+  try {
+    const results = await Promise.all(inputs.map(input => fetchDataFromZarr(input.url, input.path, input.s, opts)));
+    return results;
+  } catch (error) {
+    throw new Error(error.message);
+  }
+};
+const aggregateData = (inputs, data) => {
+  const dataObject = {};
+  data.forEach((result, index) => {
+    const key = inputs[index].key;
+    dataObject[key] = result;
+  });
+  return dataObject;
+};
 const useMultipleZarr = function (inputs) {
   let opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-  const [results, setResults] = (0, _react.useState)({});
+  let agg = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : aggregateData;
+  const [data, setData] = (0, _react.useState)(null);
+  const [isPending, setIsPending] = (0, _react.useState)(true);
+  const [serverError, setServerError] = (0, _react.useState)(null);
   (0, _react.useEffect)(() => {
-    const fetchData = async () => {
-      const results = await Promise.all(inputs.map(input => fetchDataFromZarr(input.url, input.path, input.s, opts)));
-      const dataObject = {};
-      results.forEach((result, index) => {
-        const key = inputs[index].key;
-        dataObject[key] = result;
-      });
-      setResults(dataObject);
-    };
-    fetchData();
-  }, [inputs, opts]);
-  return results;
+    setIsPending(true);
+    setServerError(null);
+    fetchDataFromZarrs(inputs, opts).then(data => {
+      setData(agg(inputs, data));
+    }).catch(error => {
+      setServerError(error.message);
+    }).finally(() => {
+      setIsPending(false);
+    });
+  }, [agg, inputs, opts]);
+  return {
+    data,
+    isPending,
+    serverError
+  };
 };
 exports.useMultipleZarr = useMultipleZarr;

package/dist/utils/search.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.useVarSearch = exports.useGetDisease = exports.useDiseaseSearch = void 0;
+exports.useVarSearch = exports.useDiseaseSearch = void 0;
 var _react = require("react");
 var _requests = require("./requests");
 var _DatasetContext = require("../context/DatasetContext");
@@ -28,7 +28,6 @@ exports.useDiseaseSearch = useDiseaseSearch;
 const useVarSearch = () => {
   const ENDPOINT = "var/names";
   const dataset = (0, _DatasetContext.useDataset)();
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
   const [params, setParams] = (0, _react.useState)({
     url: dataset.url,
     col: dataset.varNamesCol,
@@ -37,62 +36,10 @@ const useVarSearch = () => {
   const data = (0, _requests.useFetch)(ENDPOINT, params, {
     enabled: !!params.text.length
   });
-  const onSelect = item => {
-    dispatch({
-      type: "select.var",
-      var: item
-    });
-    dispatch({
-      type: "select.multivar",
-      var: item
-    });
-    dispatch({
-      type: "set.colorEncoding",
-      value: "var"
-    });
-  };
   return {
     params,
     setParams,
-    data,
-    onSelect
+    data
   };
 };
-exports.useVarSearch = useVarSearch;
-const useGetDisease = () => {
-  var _dataset$selectedDise, _dataset$selectedDise2, _params$diseaseName;
-  const ENDPOINT = "disease/genes";
-  const dataset = (0, _DatasetContext.useDataset)();
-  const dispatch = (0, _DatasetContext.useDatasetDispatch)();
-  const [params, setParams] = (0, _react.useState)({
-    url: dataset.url,
-    col: dataset.varNamesCol,
-    diseaseName: (_dataset$selectedDise = dataset.selectedDisease) === null || _dataset$selectedDise === void 0 ? void 0 : _dataset$selectedDise.name,
-    diseaseDatasets: dataset.diseaseDatasets
-  });
-  (0, _react.useEffect)(() => {
-    setParams(p => {
-      return {
-        ...p,
-        diseaseName: dataset.selectedDisease.name
-      };
-    });
-  }, [(_dataset$selectedDise2 = dataset.selectedDisease) === null || _dataset$selectedDise2 === void 0 ? void 0 : _dataset$selectedDise2.name]);
-  const {
-    fetchedData,
-    isPending,
-    serverError
-  } = (0, _requests.useFetch)(ENDPOINT, params, {
-    enabled: !!((_params$diseaseName = params.diseaseName) !== null && _params$diseaseName !== void 0 && _params$diseaseName.length)
-  });
-  (0, _react.useEffect)(() => {
-    if (!isPending && !serverError) {
-      dispatch({
-        type: "set.disease.genes",
-        genes: fetchedData
-      });
-    }
-  }, [dispatch, fetchedData, isPending, serverError]);
-  return;
-};
-exports.useGetDisease = useGetDisease;
+exports.useVarSearch = useVarSearch;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@haniffalab/cherita-react",
-  "version": "0.2.0-dev.2024-09-26.d9293c4c",
+  "version": "0.2.0-dev.2024-09-26.1ea62883",
   "author": "",
   "license": "",
   "main": "dist/index.js",
@@ -85,5 +85,5 @@
     "url": "https://github.com/haniffalab/cherita-react/issues"
   },
   "homepage": "https://github.com/haniffalab/cherita-react#readme",
-  "prereleaseSha": "d9293c4c3c66bc0c5d0c5012ccc39c0913e7bb93"
+  "prereleaseSha": "1ea628835d7acdea1f92e6058e59a72092d535c4"
 }