@vitessce/vega 3.6.7 → 3.6.8

package/dist/index.js

@@ -48122,6 +48122,9 @@ const configSchema1_0_16 = configSchema1_0_13.extend({
 const configSchema1_0_17 = configSchema1_0_16.extend({
   version: z.literal("1.0.17")
 });
+const configSchema1_0_18 = configSchema1_0_17.extend({
+  version: z.literal("1.0.18")
+});
 configSchema1_0_0.shape.coordinationSpace.unwrap();
 configSchema1_0_0.shape.layout.element.shape.coordinationScopes.unwrap();
 function upgradeReplaceViewProp(prefix2, view, coordinationSpace) {
@@ -48629,7 +48632,54 @@ function upgradeFrom1_0_16(config) {
     version: "1.0.17"
   };
 }
-const latestConfigSchema = configSchema1_0_17;
+function upgradeFrom1_0_17(config) {
+  const newConfig = cloneDeep(config);
+  const { datasets } = newConfig;
+  const newDatasets = datasets.map((datasetDef) => {
+    const { files } = datasetDef;
+    const newFiles = files.map((fileDef) => {
+      const { fileType, options } = fileDef;
+      if (fileType === "spatialdata.zarr" || fileType === "spatialdata.zarr.zip") {
+        if (options.labels && options.shapes) {
+          throw new Error("Cannot upgrade both labels and shapes at the same time. For now, a workaround is to include two separate spatialdata.zarr file definitions, one for labels and one for shapes.");
+        }
+        if (options.labels) {
+          const newOptions = {
+            ...options,
+            obsSegmentations: options.labels
+          };
+          delete newOptions.labels;
+          return {
+            ...fileDef,
+            options: newOptions
+          };
+        }
+        if (options.shapes) {
+          const newOptions = {
+            ...options,
+            obsSegmentations: options.shapes
+          };
+          delete newOptions.shapes;
+          return {
+            ...fileDef,
+            options: newOptions
+          };
+        }
+      }
+      return fileDef;
+    });
+    return {
+      ...datasetDef,
+      files: newFiles
+    };
+  });
+  return {
+    ...newConfig,
+    datasets: newDatasets,
+    version: "1.0.18"
+  };
+}
+const latestConfigSchema = configSchema1_0_18;
 const SCHEMA_HANDLERS = [
   [configSchema0_1_0, upgradeFrom0_1_0],
   [configSchema1_0_0, upgradeFrom1_0_0],
@@ -48648,7 +48698,8 @@ const SCHEMA_HANDLERS = [
   [configSchema1_0_13, upgradeFrom1_0_13],
   [configSchema1_0_14, upgradeFrom1_0_14],
   [configSchema1_0_15, upgradeFrom1_0_15],
-  [configSchema1_0_16, upgradeFrom1_0_16]
+  [configSchema1_0_16, upgradeFrom1_0_16],
+  [configSchema1_0_17, upgradeFrom1_0_17]
 ];
 var re$2 = { exports: {} };
 var constants$1;
@@ -50680,9 +50731,7 @@ const FileType$1 = {
   OBS_SETS_SPATIALDATA_ZARR: "obsSets.spatialdata.zarr",
   OBS_SPOTS_SPATIALDATA_ZARR: "obsSpots.spatialdata.zarr",
   FEATURE_LABELS_SPATIALDATA_ZARR: "featureLabels.spatialdata.zarr",
-  // TODO:
-  // OBS_POINTS_SPATIALDATA_ZARR: 'obsPoints.spatialdata.zarr',
-  // OBS_LOCATIONS_SPATIALDATA_ZARR: 'obsLocations.spatialdata.zarr',
+  OBS_POINTS_SPATIALDATA_ZARR: "obsPoints.spatialdata.zarr",
   // SpatialData - zipped
   IMAGE_SPATIALDATA_ZARR_ZIP: "image.spatialdata.zarr.zip",
   LABELS_SPATIALDATA_ZARR_ZIP: "labels.spatialdata.zarr.zip",
@@ -50691,6 +50740,7 @@ const FileType$1 = {
   OBS_SETS_SPATIALDATA_ZARR_ZIP: "obsSets.spatialdata.zarr.zip",
   OBS_SPOTS_SPATIALDATA_ZARR_ZIP: "obsSpots.spatialdata.zarr.zip",
   FEATURE_LABELS_SPATIALDATA_ZARR_ZIP: "featureLabels.spatialdata.zarr.zip",
+  OBS_POINTS_SPATIALDATA_ZARR_ZIP: "obsPoints.spatialdata.zarr.zip",
   // MuData
   OBS_FEATURE_MATRIX_MUDATA_ZARR: "obsFeatureMatrix.mudata.zarr",
   OBS_SETS_MUDATA_ZARR: "obsSets.mudata.zarr",
@@ -50937,6 +50987,7 @@ const CoordinationType$1 = {
   [FileType$1.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR]: DataType$1.OBS_FEATURE_MATRIX,
   [FileType$1.OBS_SETS_SPATIALDATA_ZARR]: DataType$1.OBS_SETS,
   [FileType$1.FEATURE_LABELS_SPATIALDATA_ZARR]: DataType$1.FEATURE_LABELS,
+  [FileType$1.OBS_POINTS_SPATIALDATA_ZARR]: DataType$1.OBS_POINTS,
   // For new file types to support old file types
   [FileType$1.OBS_EMBEDDING_CELLS_JSON]: DataType$1.OBS_EMBEDDING,
   [FileType$1.OBS_LOCATIONS_CELLS_JSON]: DataType$1.OBS_LOCATIONS,
@@ -51110,6 +51161,9 @@ const CoordinationType$1 = {
   },
   [FileType$1.FEATURE_LABELS_SPATIALDATA_ZARR]: {
     zip: FileType$1.FEATURE_LABELS_SPATIALDATA_ZARR_ZIP
+  },
+  [FileType$1.OBS_POINTS_SPATIALDATA_ZARR]: {
+    zip: FileType$1.OBS_POINTS_SPATIALDATA_ZARR_ZIP
   }
 });
 [
@@ -52129,10 +52183,14 @@ const imageSpatialdataSchema = z.object({
   coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSegmentationsSpatialdataSchema = z.object({
-  // TODO: should this be renamed labelsSpatialdataSchema?
-  // TODO: support obsTypesFromChannelNames?
-  path: z.string(),
-  tablePath: z.string().optional().describe("The path to a table which annotates the labels. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
+  // TODO: support obsTypesFromElementNames?
+  path: z.string().describe("The path to the segmentation data, stored in either shapes/ or labels/."),
+  tablePath: z.string().optional().describe("The path to a table which annotates the labels or shapes. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
+});
+const obsPointsSpatialdataSchema = z.object({
+  path: z.string().describe("The path to the point data."),
+  tablePath: z.string().optional().describe("The path to a table which annotates the points. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
   coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 z.object({
@@ -52252,13 +52310,10 @@ z.object({
   image: imageSpatialdataSchema,
   // TODO: should this be a special schema
   // to allow specifying fileUid (like for embeddingType)?
-  // TODO: allow multiple labels?
-  labels: obsSegmentationsSpatialdataSchema,
+  // TODO: allow multiple labels/shapes?
+  obsSegmentations: obsSegmentationsSpatialdataSchema,
+  obsPoints: obsPointsSpatialdataSchema,
   // TODO: allow multiple shapes?
-  // TODO: unify labels and shapes to obsSegmentations,
-  // then distinguish in expand function based on
-  // "labels/*" vs. "shapes/*" in path?
-  shapes: obsSegmentationsSpatialdataSchema,
   obsFeatureMatrix: obsFeatureMatrixSpatialdataSchema,
   obsSpots: obsSpotsSpatialdataSchema,
   // TODO: obsPoints

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vega",
-  "version": "3.6.7",
+  "version": "3.6.8",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -21,9 +21,9 @@
     "vega": "^5.21.0",
     "vega-lite": "^5.1.1",
     "vega-tooltip": "^0.27.0",
-    "@vitessce/styles": "3.6.7",
-    "@vitessce/tooltip": "3.6.7",
-    "@vitessce/legend": "3.6.7"
+    "@vitessce/styles": "3.6.8",
+    "@vitessce/tooltip": "3.6.8",
+    "@vitessce/legend": "3.6.8"
   },
   "devDependencies": {
     "react": "^18.0.0",