@haniffalab/cherita-react 1.2.0-dev.2025-04-09.0f69cbd1 → 1.2.0-dev.2025-04-28.4a506cf2

package/dist/cjs/components/scatterplot/Scatterplot.js

@@ -13,6 +13,8 @@ var _editModes = require("@nebula.gl/edit-modes");
 var _layers2 = require("@nebula.gl/layers");
 var _lodash = _interopRequireDefault(require("lodash"));
 var _reactBootstrap = require("react-bootstrap");
+var _SpatialControls = require("./SpatialControls");
+var _Toolbox = require("./Toolbox");
 var _constants = require("../../constants/constants");
 var _DatasetContext = require("../../context/DatasetContext");
 var _FilterContext = require("../../context/FilterContext");
@@ -23,8 +25,6 @@ var _Legend = require("../../utils/Legend");
 var _LoadingIndicators = require("../../utils/LoadingIndicators");
 var _string = require("../../utils/string");
 var _zarrData = require("../../utils/zarrData");
-var _SpatialControls = require("./SpatialControls");
-var _Toolbox = require("./Toolbox");
 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; }

package/dist/cjs/helpers/zarr-helper.js

@@ -45,11 +45,11 @@ const fetchDataFromZarr = async (url, path, s, opts) => {
 const useZarr = function (_ref2) {
   let {
     url,
-    path
+    path,
+    s = null
   } = _ref2;
-  let s = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
-  let options = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : GET_OPTIONS;
-  let opts = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : {};
+  let options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : GET_OPTIONS;
+  let opts = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
   const {
     data = null,
     isLoading: isPending = false,

package/dist/cjs/utils/zarrData.js

@@ -6,25 +6,29 @@ Object.defineProperty(exports, "__esModule", {
 exports.useXData = exports.useObsmData = exports.useObsData = exports.useLabelObsData = void 0;
 var _react = require("react");
 var _lodash = _interopRequireDefault(require("lodash"));
+var _zarr = require("zarr");
 var _constants = require("../constants/constants");
 var _DatasetContext = require("../context/DatasetContext");
 var _zarrHelper = require("../helpers/zarr-helper");
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+// @TODO: support specifying slice to load from context
 const useObsmData = function () {
   let obsm = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
   const dataset = (0, _DatasetContext.useDataset)();
   obsm = obsm || dataset.selectedObsm;
   const [obsmParams, setObsmParams] = (0, _react.useState)({
     url: dataset.url,
-    path: "obsm/" + obsm
+    path: "obsm/" + obsm,
+    s: [null, (0, _zarr.slice)(null, 2)] // load only [:, :2]
   });
   (0, _react.useEffect)(() => {
     setObsmParams({
       url: dataset.url,
-      path: "obsm/" + obsm
+      path: "obsm/" + obsm,
+      s: [null, (0, _zarr.slice)(null, 2)]
     });
   }, [dataset.url, obsm]);
-  return (0, _zarrHelper.useZarr)(obsmParams, null, _zarrHelper.GET_OPTIONS, {
+  return (0, _zarrHelper.useZarr)(obsmParams, _zarrHelper.GET_OPTIONS, {
     enabled: !!obsm
   });
 };
@@ -83,7 +87,7 @@ const useObsData = function () {
       path: "obs/" + obs?.name + (obs?.type === _constants.OBS_TYPES.CATEGORICAL ? "/codes" : "")
     });
   }, [dataset.url, obs]);
-  return (0, _zarrHelper.useZarr)(obsParams, null, _zarrHelper.GET_OPTIONS, {
+  return (0, _zarrHelper.useZarr)(obsParams, _zarrHelper.GET_OPTIONS, {
     enabled: !!obs
   });
 };

package/dist/css/cherita.css

@@ -12056,7 +12056,7 @@ textarea.form-control-lg {
   height: 100%;
   width: 100%;
   display: flex;
-  z-index: 1;
+  z-index: 2;
   opacity: 0.75;
   position: absolute;
   justify-content: center;

package/dist/esm/components/scatterplot/Scatterplot.js

@@ -7,6 +7,8 @@ import { ViewMode } from "@nebula.gl/edit-modes";
 import { EditableGeoJsonLayer } from "@nebula.gl/layers";
 import _ from "lodash";
 import { Alert } from "react-bootstrap";
+import { SpatialControls } from "./SpatialControls";
+import { Toolbox } from "./Toolbox";
 import { COLOR_ENCODINGS, OBS_TYPES, SELECTED_POLYGON_FILLCOLOR, UNSELECTED_POLYGON_FILLCOLOR } from "../../constants/constants";
 import { useDataset, useDatasetDispatch } from "../../context/DatasetContext";
 import { useFilteredData } from "../../context/FilterContext";
@@ -17,8 +19,6 @@ import { Legend } from "../../utils/Legend";
 import { LoadingLinear, LoadingSpinner } from "../../utils/LoadingIndicators";
 import { formatNumerical } from "../../utils/string";
 import { useLabelObsData } from "../../utils/zarrData";
-import { SpatialControls } from "./SpatialControls";
-import { Toolbox } from "./Toolbox";
 window.deck.log.level = 1;
 const INITIAL_VIEW_STATE = {
   longitude: 0,

package/dist/esm/helpers/zarr-helper.js

@@ -38,11 +38,11 @@ const fetchDataFromZarr = async (url, path, s, opts) => {
 export const useZarr = function (_ref2) {
   let {
     url,
-    path
+    path,
+    s = null
   } = _ref2;
-  let s = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
-  let options = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : GET_OPTIONS;
-  let opts = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : {};
+  let options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : GET_OPTIONS;
+  let opts = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
   const {
     data = null,
     isLoading: isPending = false,

package/dist/esm/utils/zarrData.js

@@ -1,23 +1,28 @@
 import { useEffect, useState } from "react";
 import _ from "lodash";
+import { slice } from "zarr";
 import { OBS_TYPES } from "../constants/constants";
 import { useDataset } from "../context/DatasetContext";
 import { GET_OPTIONS, useZarr, useMultipleZarr } from "../helpers/zarr-helper";
+
+// @TODO: support specifying slice to load from context
 export const useObsmData = function () {
   let obsm = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
   const dataset = useDataset();
   obsm = obsm || dataset.selectedObsm;
   const [obsmParams, setObsmParams] = useState({
     url: dataset.url,
-    path: "obsm/" + obsm
+    path: "obsm/" + obsm,
+    s: [null, slice(null, 2)] // load only [:, :2]
   });
   useEffect(() => {
     setObsmParams({
       url: dataset.url,
-      path: "obsm/" + obsm
+      path: "obsm/" + obsm,
+      s: [null, slice(null, 2)]
     });
   }, [dataset.url, obsm]);
-  return useZarr(obsmParams, null, GET_OPTIONS, {
+  return useZarr(obsmParams, GET_OPTIONS, {
     enabled: !!obsm
   });
 };
@@ -74,7 +79,7 @@ export const useObsData = function () {
       path: "obs/" + obs?.name + (obs?.type === OBS_TYPES.CATEGORICAL ? "/codes" : "")
     });
   }, [dataset.url, obs]);
-  return useZarr(obsParams, null, GET_OPTIONS, {
+  return useZarr(obsParams, GET_OPTIONS, {
     enabled: !!obs
   });
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@haniffalab/cherita-react",
-  "version": "1.2.0-dev.2025-04-09.0f69cbd1",
+  "version": "1.2.0-dev.2025-04-28.4a506cf2",
   "author": "Haniffa Lab",
   "license": "MIT",
   "keywords": [
@@ -124,5 +124,5 @@
     "url": "https://github.com/haniffalab/cherita-react/issues"
   },
   "homepage": "https://github.com/haniffalab/cherita-react#readme",
-  "prereleaseSha": "0f69cbd1439ad139d295962fe426d556504b7f75"
+  "prereleaseSha": "4a506cf297859fb7abb1e1320eb5d694a4979ee0"
 }

package/scss/cherita.scss

@@ -14,7 +14,7 @@ $prefix: "bs-" !default;
   height: 100%;
   width: 100%;
   display: flex;
-  z-index: 1;
+  z-index: 2;
   opacity: 0.75;
   position: absolute;
   justify-content: center;