@aics/vole-app 2.13.6 → 2.14.0

package/es/aics-image-viewer/components/App/index.js

@@ -72,7 +72,8 @@ var defaultProps = {
   parentImageDownloadHref: "",
   pixelSize: undefined,
   canvasMargin: "0 0 0 0",
-  view3dRef: undefined
+  view3dRef: undefined,
+  showError: undefined
 };
 var CLIPPING_PANEL_ANIMATION_DURATION_MS = 300;
 var setIndicatorPositions = function setIndicatorPositions(view3d, panelOpen, hasTime, hasScenes, isMode3d) {
@@ -104,7 +105,7 @@ var setIndicatorPositions = function setIndicatorPositions(view3d, panelOpen, ha
   view3d.setScaleBarPosition(scaleBarX, scaleBarY);
 };
 var App = function App(props) {
-  var _getCurrentViewerChan, _scenes$length, _scenes2, _image$imageInfo$volu, _image$imageInfo$subr, _image$imageInfo$time, _props$transform2, _props$transform4;
+  var _props$showError, _getCurrentViewerChan, _scenes$length, _scenes2, _image$imageInfo$volu, _image$imageInfo$subr, _image$imageInfo$time, _props$transform2, _props$transform4;
   props = _objectSpread(_objectSpread({}, defaultProps), props);
 
   // State management /////////////////////////////////////////////////////////
@@ -121,6 +122,7 @@ var App = function App(props) {
     onResetChannel = _viewerState$current.onResetChannel;
   var _props = props,
     onControlPanelToggle = _props.onControlPanelToggle,
+    onImageTitleChange = _props.onImageTitleChange,
     metadata = _props.metadata,
     metadataFormatter = _props.metadataFormatter;
   useMemo(function () {
@@ -134,10 +136,14 @@ var App = function App(props) {
   if (props.view3dRef !== undefined) {
     props.view3dRef.current = view3d;
   }
+
+  // Allows AppWrapper to pass in its own `useErrorAlert` callbacks, but still keeps error
+  // messaging when App is used standalone.
   var _useErrorAlert = useErrorAlert(),
     _useErrorAlert2 = _slicedToArray(_useErrorAlert, 2),
     errorAlert = _useErrorAlert2[0],
-    showError = _useErrorAlert2[1];
+    _showError = _useErrorAlert2[1];
+  var showError = (_props$showError = props.showError) !== null && _props$showError !== void 0 ? _props$showError : _showError;
   useEffect(function () {
     // Get notifications of loading errors which occur after the initial load, e.g. on time change or new channel load
     view3d.setLoadErrorHandler(function (_vol, e) {
@@ -203,8 +209,9 @@ var App = function App(props) {
         };
       })
     });
+    onImageTitleChange === null || onImageTitleChange === void 0 || onImageTitleChange(newImage.imageInfo.imageInfo.name);
     view3d.updateActiveChannels(newImage);
-  }, [view3d, viewerState]);
+  }, [view3d, viewerState, onImageTitleChange]);
   var onChannelLoaded = useCallback(function (image, channelIndex, isInitialLoad) {
     // TODO this was once a search by name - is that still necessary or will the index always be correct?
     var thisChannelSettings = channelSettings[channelIndex];
@@ -263,10 +270,14 @@ var App = function App(props) {
       view3d.updateActiveChannels(image);
     }
   }, [view3d, channelSettings, maskChannelName, viewerState]);
+  var onError = useCallback(function (error) {
+    showError(error);
+    onImageTitleChange === null || onImageTitleChange === void 0 || onImageTitleChange(undefined);
+  }, [showError, onImageTitleChange]);
   var volume = useVolume(scenes, {
     onCreateImage: onCreateImage,
     onChannelLoaded: onChannelLoaded,
-    onError: showError,
+    onError: onError,
     maskChannelName: maskChannelName
   });
   var image = volume.image,

package/es/aics-image-viewer/components/ErrorAlert/index.js

@@ -37,7 +37,7 @@ var ERROR_TYPE_DESCRIPTIONS = _defineProperty(_defineProperty(_defineProperty(_d
 }, "start a bug report here"), ".")), VolumeLoadErrorType.INVALID_METADATA, /*#__PURE__*/React.createElement(React.Fragment, null, "The viewer was unable to read all necessary information from this volume's metadata. Check that your dataset's metadata is complete and properly formatted. If you believe your data is valid and should be supported by our viewer, let us know by ", /*#__PURE__*/React.createElement(IssueLink, null, "opening a GitHub issue"), ".")), VolumeLoadErrorType.INVALID_MULTI_SOURCE_ZARR, /*#__PURE__*/React.createElement(React.Fragment, null, "The viewer is currently configured to consolidate multiple OME-Zarr datasets into a single volume, but the provided datasets can't all be matched up. Ensure that all dataset URLs are correct and that at least one equivalently-sized scale level exists in all datasets."));
 var getErrorTitle = function getErrorTitle(error) {
   var _error$toString;
-  return error instanceof Error && ((_error$toString = error.toString) === null || _error$toString === void 0 ? void 0 : _error$toString.call(error)) || "Unknown error";
+  return error instanceof Error && ((_error$toString = error.toString) === null || _error$toString === void 0 ? void 0 : _error$toString.call(error)) || typeof error === "string" && error || "Unknown error";
 };
 var getErrorDescription = function getErrorDescription(error) {
   var _ERROR_TYPE_DESCRIPTI2;

package/es/aics-image-viewer/components/ViewerStateProvider/ResetStateProvider.js

@@ -132,7 +132,10 @@ var ResetStateProvider = /*#__PURE__*/function () {
       }, this.savedViewerState);
       var newChannelSettings = channelSettings.map(function (_, index) {
         var initialChannelSetting = initializeOneChannelSetting(channelSettings[index].name, index, getDefaultChannelColor(index), _this.savedViewerChannelSettings);
-        return initialChannelSetting;
+        return _objectSpread(_objectSpread({}, initialChannelSetting), {}, {
+          plotMin: channelSettings[index].plotMin,
+          plotMax: channelSettings[index].plotMax
+        });
       });
       this.resetToState(newViewerState, newChannelSettings);
       this.useDefaultViewerChannelSettings = false;

package/es/aics-image-viewer/shared/utils/datatypes.js

@@ -0,0 +1,29 @@
+import { isEqual } from "lodash";
+
+/**
+ * Returns a (shallow) copy of an object with all properties that are
+ * `undefined` removed.
+ */
+export function removeUndefinedProperties(obj) {
+  var result = {};
+  for (var key in obj) {
+    if (obj[key] !== undefined) {
+      result[key] = obj[key];
+    }
+  }
+  return result;
+}
+
+/**
+ * Returns a copy of `obj` where all properties with values that match the properties of `match`
+ * are removed. Matching is determined by deep equality (see `isDeepEqual()`).
+ */
+export function removeMatchingProperties(obj, match) {
+  var result = {};
+  for (var key in obj) {
+    if (!isEqual(obj[key], match[key])) {
+      result[key] = obj[key];
+    }
+  }
+  return result;
+}

package/es/aics-image-viewer/shared/utils/firebase/index.js

@@ -0,0 +1,109 @@
+function _typeof(o) { "@babel/helpers - typeof"; return _typeof = "function" == typeof Symbol && "symbol" == typeof Symbol.iterator ? function (o) { return typeof o; } : function (o) { return o && "function" == typeof Symbol && o.constructor === Symbol && o !== Symbol.prototype ? "symbol" : typeof o; }, _typeof(o); }
+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 _defineProperties(e, r) { for (var t = 0; t < r.length; t++) { var o = r[t]; o.enumerable = o.enumerable || !1, o.configurable = !0, "value" in o && (o.writable = !0), Object.defineProperty(e, _toPropertyKey(o.key), o); } }
+function _createClass(e, r, t) { return r && _defineProperties(e.prototype, r), t && _defineProperties(e, t), Object.defineProperty(e, "prototype", { writable: !1 }), e; }
+function _classCallCheck(a, n) { if (!(a instanceof n)) throw new TypeError("Cannot call a class as a function"); }
+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); }
+// TODO: These types are shared with Cell Feature Explorer. Can they be moved to
+// a shared package?
+
+function isDevOrStagingSite(host) {
+  // first condition is for testing with no client
+  return !host || host.includes("localhost") || host.includes("staging") || host.includes("stg");
+}
+var FirebaseRequest = /*#__PURE__*/_createClass(
+// TODO: These properties are private and unused. Remove?
+
+function FirebaseRequest(firestore) {
+  var _this = this;
+  _classCallCheck(this, FirebaseRequest);
+  _defineProperty(this, "getDoc", function (docPath) {
+    return _this.firestore.doc(docPath).get();
+  });
+  _defineProperty(this, "getAvailableDatasets", function () {
+    return _this.firestore.collection("dataset-descriptions").get().then(function (snapShot) {
+      var datasets = [];
+      snapShot.forEach(function (doc) {
+        var metadata = doc.data();
+        /** if running the site in a local development env or on staging.cfe.allencell.org
+         * include all cards, otherwise, only include cards with a production flag.
+         * this is based on hostname instead of a build time variable so we don't
+         * need a separate build for staging and production
+         */
+
+        if (isDevOrStagingSite(location.hostname)) {
+          datasets.push(metadata);
+        } else if (metadata.production) {
+          datasets.push(metadata);
+        }
+      });
+      return datasets;
+    });
+  });
+  _defineProperty(this, "setCollectionRef", function (id) {
+    _this.collectionRef = _this.firestore.collection("cfe-datasets").doc(id);
+  });
+  _defineProperty(this, "getManifest", function (ref) {
+    return _this.firestore.doc(ref).get().then(function (manifestDoc) {
+      return manifestDoc.data();
+    });
+  });
+  _defineProperty(this, "selectDataset", function (ref) {
+    return _this.getManifest(ref).then(function (data) {
+      _this.featuresDataPath = data.featuresDataPath;
+      _this.thumbnailRoot = data.thumbnailRoot;
+      _this.downloadRoot = data.downloadRoot;
+      _this.volumeViewerDataRoot = data.volumeViewerDataRoot;
+      _this.featuresDisplayOrder = data.featuresDisplayOrder;
+      _this.cellLineDataPath = data.cellLineDataPath;
+      _this.fileInfoPath = data.fileInfoPath;
+      _this.featuresDataOrder = data.featuresDataOrder;
+      _this.featureDefsPath = data.featureDefsPath;
+      _this.albumPath = data.albumPath;
+      return _objectSpread({}, data);
+    });
+  });
+  _defineProperty(this, "getFileInfoByCellId", function (cellId) {
+    return _this.getDoc("".concat(_this.fileInfoPath, "/").concat(cellId)).then(function (doc) {
+      var data = doc.data();
+      if (!data) {
+        return;
+      }
+      return _objectSpread(_objectSpread({}, data), {}, {
+        CellId: data.CellId.toString(),
+        FOVId: data.FOVId.toString()
+      });
+    });
+  });
+  _defineProperty(this, "getFileInfoByArrayOfCellIds", function (cellIds) {
+    return Promise.all(cellIds.map(function (id) {
+      return _this.getDoc("".concat(_this.fileInfoPath, "/").concat(id)).then(function (doc) {
+        var data = doc.data();
+        if (!data) {
+          return;
+        }
+        return _objectSpread(_objectSpread({}, data), {}, {
+          CellId: data.CellId.toString(),
+          FOVId: data.FOVId.toString()
+        });
+      });
+    }));
+  });
+  this.firestore = firestore;
+  this.featuresDataPath = "";
+  this.cellLineDataPath = "";
+  this.thumbnailRoot = "";
+  this.downloadRoot = "";
+  this.volumeViewerDataRoot = "";
+  this.featuresDisplayOrder = [];
+  this.fileInfoPath = "";
+  this.datasetId = "";
+  this.featuresDataOrder = [];
+  this.albumPath = "";
+  this.featureDefsPath = "";
+  this.collectionRef = firestore.collection("cfe-datasets").doc("v1");
+});
+export default FirebaseRequest;

package/es/aics-image-viewer/shared/utils/math.js

@@ -0,0 +1,3 @@
+export function clamp(value, min, max) {
+  return Math.min(Math.max(value, min), max);
+}