feat: Spatial Mode User Story 1

client/__tests__/e2e/e2e.test.ts

@@ -1,4 +1,4 @@
 /**
  * Smoke test suite that will be run in GHA
  * Tests included in this file are expected to be relatively stable and test core features
  *
@@ -491,7 +491,7 @@
     page,
     true
   );
-  expect(page.getByTestId("lasso-element")).toBeVisible();
+  await expect(page.getByTestId("lasso-element")).toBeVisible();
 
   const initialCount = await getCellSetCount(1, page);
 
@@ -525,7 +525,7 @@
     true
   );
 
-  expect(page.getByTestId("lasso-element")).toBeVisible();
+  await expect(page.getByTestId("lasso-element")).toBeVisible();
 
   const initialCount = await getCellSetCount(1, page);
 

client/__tests__/e2e/playwright.global.setup.ts

@@ -42,15 +42,14 @@ const setup = async ({ page }: { page: Page }) => {
       },
     });
   });
-
-  // page.on("console", (message) => {
-  //   if (message.type() === "error") {
-  //     throw new Error(`CLIENT SIDE ERROR: ${  message.text()}`);
-  //   }
-  // });
-  // page.on("pageerror", (error) => {
-  //   throw new Error(`UNCAUGHT CLIENT ERROR: ${  error}`);
-  // });
+  page.on("console", (message) => {
+    if (message.type() === "error") {
+      throw new Error(`CLIENT SIDE ERROR: ${JSON.stringify(message)}`);
+    }
+  });
+  page.on("pageerror", (error) => {
+    throw new Error(`UNCAUGHT CLIENT ERROR: ${error}`);
+  });
 };
 
 export default setup;

client/src/actions/index.ts

@@ -16,7 +16,12 @@ import * as genesetActions from "./geneset";
 import { AppDispatch, GetState } from "../reducers";
 import { EmbeddingSchema, Field, Schema } from "../common/types/schema";
 import { ConvertedUserColors } from "../reducers/colors";
-import type { DatasetMetadata, Dataset, S3URI } from "../common/types/entities";
+import type {
+  DatasetMetadata,
+  Dataset,
+  S3URI,
+  DatasetSpatialMetadata,
+} from "../common/types/entities";
 import { postExplainNewTab } from "../components/framework/toasters";
 import { KEYS } from "../components/util/localStorage";
 import {
@@ -29,7 +34,11 @@ import { packDiffExPdu, DiffExMode, DiffExArguments } from "../util/diffexpdu";
 import { track } from "../analytics";
 import { EVENTS } from "../analytics/events";
 import AnnoMatrix from "../annoMatrix/annoMatrix";
-import { checkFeatureFlags } from "../util/featureFlags/featureFlags";
+import {
+  checkFeatureFlags,
+  getFeatureFlag,
+} from "../util/featureFlags/featureFlags";
+import { FEATURES } from "../util/featureFlags/features";
 import { DATASET_METADATA_RESPONSE } from "../../__tests__/__mocks__/apiMock";
 
 function setGlobalConfig(config: Config) {
@@ -126,6 +135,31 @@ async function datasetMetadataFetchAndLoad(
   });
 }
 
+/**
+ * Fetches and loads dataset spatial metadata.
+ * @param dispatch - Function facilitating update of store.
+ * @param oldPrefix - API prefix with dataset path that dataset metadata lives on. (Not S3 URI)
+ */
+async function datasetSpatialMetadataFetchAndLoad(
+  dispatch: AppDispatch,
+  oldPrefix: string
+): Promise<void> {
+  try {
+    const datasetSpatialMetadataResponse = await fetchJson<{
+      metadata: DatasetSpatialMetadata;
+    }>("spatial/meta", oldPrefix);
+    dispatch({
+      type: "request spatial metadata success",
+      data: datasetSpatialMetadataResponse,
+    });
+  } catch (error) {
+    dispatch({
+      type: "request spatial metadata error",
+      error,
+    });
+  }
+}
+
 interface GeneInfoAPI {
   ncbi_url: string;
   name: string;
@@ -178,6 +212,7 @@ const doInitialDataLoad = (): ((
 
     // check URL for feature flags
     checkFeatureFlags();
+    const isSpatial = getFeatureFlag(FEATURES.SPATIAL);
 
     try {
       const s3URI = await s3URIFetch();
@@ -190,7 +225,10 @@ const doInitialDataLoad = (): ((
       ]);
 
       datasetMetadataFetchAndLoad(dispatch, oldPrefix, config);
-
+      // TODO: add logic to ensure this is working for spatial datasets when flag removed
+      if (isSpatial) {
+        datasetSpatialMetadataFetchAndLoad(dispatch, oldPrefix);
+      }
       const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
       const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
       const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);

client/src/common/types/entities.ts

@@ -62,6 +62,9 @@ export interface DatasetMetadata {
   s3_URI: S3URI;
 }
 
+// TODO: proper typing after migration and final CXG schema
+export type DatasetSpatialMetadata = any;
+
 export type S3URI = string;
 
 /**

client/src/components/embedding/index.tsx

@@ -21,13 +21,11 @@ import { EVENTS } from "../../analytics/events";
 type EmbeddingState = any;
 
 // @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
-@connect((state) => ({
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  layoutChoice: (state as any).layoutChoice,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  schema: (state as any).annoMatrix?.schema,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  crossfilter: (state as any).obsCrossfilter,
+@connect((state: RootState) => ({
+  layoutChoice: state.layoutChoice,
+  schema: state.annoMatrix?.schema,
+  crossfilter: state.obsCrossfilter,
+  imageUnderlay: state.imageUnderlay,
 }))
 // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS.
 class Embedding extends React.PureComponent<{}, EmbeddingState> {
@@ -41,14 +39,21 @@ class Embedding extends React.PureComponent<{}, EmbeddingState> {
     track(EVENTS.EXPLORER_LAYOUT_CHOICE_BUTTON_CLICKED);
   };
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  handleLayoutChoiceChange = (e: any) => {
+  handleLayoutChoiceChange = (e: React.ChangeEvent<HTMLInputElement>) => {
     // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
-    const { dispatch } = this.props;
+    const { dispatch, imageUnderlay } = this.props;
 
     track(EVENTS.EXPLORER_LAYOUT_CHOICE_CHANGE_ITEM_CLICKED);
 
     dispatch(actions.layoutChoiceAction(e.currentTarget.value));
+    if (
+      imageUnderlay.isActive &&
+      e.target.value !== globals.spatialEmbeddingKeyword
+    ) {
+      dispatch({
+        type: "toggle image underlay",
+      });
+    }
   };
 
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.

client/src/components/graph/drawSpatialImageRegl.ts

@@ -0,0 +1,66 @@
+import { Regl, Texture2D } from "regl";
+
+interface ReglProps {
+  rectCoords: Float32Array;
+  spatialImageAsTexture: Texture2D;
+  projView: number[];
+  imageWidth: number;
+  imageHeight: number;
+  count: number;
+}
+
+export default function drawSpatialImageRegl(regl: Regl) {
+  return regl({
+    frag: `
+            precision mediump float;
+            // our texture
+            uniform sampler2D u_image;
+            // the texCoords passed in from the vertex shader.
+            varying vec2 v_texCoord;
+            void main() {
+                gl_FragColor = texture2D(u_image, v_texCoord);
+            }`,
+
+    vert: `
+            attribute vec2 a_position;
+            attribute vec2 a_texCoord;
+            uniform vec2 u_resolution;
+            uniform mat3 projView;
+            varying vec2 v_texCoord;
+            void main() {
+                // convert the rectangle from pixels to 0.0 to 1.0
+                vec3 pos = vec3(a_position, 1.);
+                vec2 zeroToOne = pos.xy / u_resolution;
+                // convert from 0->1 to 0->2
+                vec2 zeroToTwo = zeroToOne * 2.0;
+                // convert from 0->2 to -1->+1 (clipspace)
+                vec2 clipSpace = zeroToTwo - 1.0;
+                vec3 pos2 = projView * vec3(clipSpace, 1.);
+                gl_Position = vec4(pos2.xy , 0, 1);
+                // pass the texCoord to the fragment shader
+                // The GPU will interpolate this value between points.
+                v_texCoord = a_texCoord;
+            }`,
+
+    attributes: {
+      a_texCoord: [0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0],
+      a_position: regl.prop<ReglProps, "rectCoords">("rectCoords"),
+    },
+
+    uniforms: {
+      projView: regl.prop<ReglProps, "projView">("projView"),
+      u_image: regl.prop<ReglProps, "spatialImageAsTexture">(
+        "spatialImageAsTexture"
+      ),
+      color: [1, 0, 0, 1],
+      u_resolution: [
+        regl.prop<ReglProps, "imageWidth">("imageWidth"),
+        regl.prop<ReglProps, "imageHeight">("imageHeight"),
+      ],
+      image_width: regl.prop<ReglProps, "imageWidth">("imageWidth"),
+    },
+    // This tells regl the number of vertices to draw in this command
+    // https://github.com/regl-project/regl
+    count: 6,
+  });
+}