@genome-spy/app 0.77.0 → 0.78.0

package/package.json

@@ -8,7 +8,7 @@
   "contributors": [],
   "license": "MIT",
   "homepage": "https://genomespy.app/",
-  "version": "0.77.0",
+  "version": "0.78.0",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "type": "module",
@@ -70,7 +70,7 @@
     "@fortawesome/fontawesome-free": "^6.4.2",
     "@fortawesome/fontawesome-svg-core": "^6.4.2",
     "@fortawesome/free-solid-svg-icons": "^6.4.2",
-    "@genome-spy/core": "^0.77.0",
+    "@genome-spy/core": "^0.78.0",
     "@reduxjs/toolkit": "^2.11.0",
     "d3-color": "^3.1.0",
     "idb": "^7.1.1",
@@ -82,7 +82,7 @@
     "zarrita": "^0.6.1"
   },
   "devDependencies": {
-    "@genome-spy/app-agent": "^0.77.0"
+    "@genome-spy/app-agent": "^0.78.0"
   },
-  "gitHead": "2851e22e2069a70d7d02e3ab707b7556573aa17e"
+  "gitHead": "54041db3a590ae8df78fa43aa755b9e07fe3503c"
 }

package/src/bookmark/databaseSchema.d.ts

@@ -2,10 +2,15 @@ import { DBSchema } from "idb";
 import { ChromosomalLocus } from "@genome-spy/core/genome/genome.js";
 import { ViewSettingsPayload } from "../state.js";
 import { Action } from "../state/provenance.js";
+import { SampleAttributePlotDefinition } from "../charts/sampleAttributePlotTypes.js";
+
+export interface BookmarkPlotAttachment {
+    kind: "sample_attribute_plot";
+    definition: SampleAttributePlotDefinition;
+}
 
 export interface BookmarkEntry {
     name: string;
-    timestamp?: number;
 
     notes?: string;
 
@@ -23,6 +28,11 @@ export interface BookmarkEntry {
      * Settings such as view visibilities
      */
     viewSettings?: ViewSettingsPayload;
+
+    /**
+     * Plots attached to the bookmark.
+     */
+    plots?: BookmarkPlotAttachment[];
 }
 
 export interface BookmarkDB extends DBSchema {

package/src/charts/sampleAttributePlotTypes.d.ts

@@ -100,6 +100,7 @@ export type SampleAttributePlotCharacterization =
 export interface SampleAttributePlot {
     kind: "sample_attribute_plot";
     plotType: SampleAttributePlotType;
+    request: SampleAttributePlotDefinition;
     title: string;
     spec: RootSpec;
     namedData: RenderablePlotNamedData[];
@@ -129,9 +130,13 @@ export interface HierarchyScatterplotRequest {
     colorScaleRange?: string[];
 }
 
+/**
+ * User/API-facing plot request. This accepts convenience aliases and label
+ * hints that may be useful while resolving a plot, but are not persisted.
+ */
 export type SampleAttributePlotRequest =
     | {
-          plotType: "bar";
+          plotType: "bar" | "barplot";
           attribute: AttributeIdentifier;
           attributeLabel?: string;
       }
@@ -147,3 +152,23 @@ export type SampleAttributePlotRequest =
           xAttributeLabel?: string;
           yAttributeLabel?: string;
       };
+
+/**
+ * Normalized plot definition that is safe to persist in generated plots and
+ * bookmarks. It uses canonical plot type names and stores only stable attribute
+ * identifiers.
+ */
+export type SampleAttributePlotDefinition =
+    | {
+          plotType: "barplot";
+          attribute: AttributeIdentifier;
+      }
+    | {
+          plotType: "boxplot";
+          attribute: AttributeIdentifier;
+      }
+    | {
+          plotType: "scatterplot";
+          xAttribute: AttributeIdentifier;
+          yAttribute: AttributeIdentifier;
+      };