TS typing for Dataframe (#2382)

* initial TS typing

* first cut at Dataframe TS typing

* more Dataframe typing

* comments

* more Dataframe cleanup

* PR review fixes and improvements

client/__tests__/util/annoMatrix/annoMatrix.test.ts

@@ -188,8 +188,10 @@ describe("AnnoMatrix", () => {
       (fetch as any)
         .once(serverMocks.annotationsObs(["n_genes"]))
         .once(serverMocks.annotationsObs(["n_genes"]));
-      const ng1 = await am1.fetch("obs", "n_genes");
-      const ng2 = await am2.fetch("obs", "n_genes");
+      const ng1 = (await am1.fetch("obs", "n_genes")) as Dataframe;
+      const ng2 = (await am2.fetch("obs", "n_genes")) as Dataframe;
+      expect(ng1).toBeDefined();
+      expect(ng2).toBeDefined();
       expect(ng1).toHaveLength(ng2.length);
       expect(ng1.colIndex.labels()).toEqual(ng2.colIndex.labels());
       expect(ng1.col("n_genes").asArray()).toEqual(
@@ -216,7 +218,7 @@ describe("AnnoMatrix", () => {
       );
       expect(base.getMatrixColumns("obs")).not.toContain("foo");
       expect(am1.getMatrixColumns("obs")).toContain("foo");
-      const foo = await am1.fetch("obs", "foo");
+      const foo: Dataframe = await am1.fetch("obs", "foo");
       expect(foo).toBeDefined();
       expect(foo).toBeInstanceOf(Dataframe);
       expect(foo).toHaveLength(am1.nObs);

client/__tests__/util/annoMatrix/crossfilter.test.ts

@@ -12,6 +12,7 @@ import {
   AnnoMatrixObsCrossfilter,
   isubsetMask,
 } from "../../../src/annoMatrix";
+import { Dataframe } from "../../../src/util/dataframe";
 import { rangeFill } from "../../../src/util/range";
 
 enableFetchMocks();
@@ -132,7 +133,7 @@ describe("AnnoMatrixCrossfilter", () => {
         )
       );
 
-      const df = await annoMatrix.fetch("obs", "louvain");
+      const df: Dataframe = await annoMatrix.fetch("obs", "louvain");
       const values = df.col("louvain").asArray();
       const selected = xfltr.allSelectedMask();
       values.every(
@@ -265,7 +266,11 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(xfltr).toBeDefined();
       expect(xfltr.countSelected()).toEqual(240);
 
-      const df = await annoMatrixSubset.fetch("obs", "louvain");
+      const df: Dataframe = (await annoMatrixSubset.fetch(
+        "obs",
+        "louvain"
+      )) as Dataframe;
+      expect(df).toBeDefined();
       const values = df.col("louvain").asArray();
       const selected = xfltr.allSelectedMask();
       values.every(
@@ -354,7 +359,7 @@ describe("AnnoMatrixCrossfilter", () => {
       ).toHaveLength(1);
 
       // check data update.
-      const df = await xfltr.annoMatrix.fetch("obs", "foo");
+      const df: Dataframe = await xfltr.annoMatrix.fetch("obs", "foo");
       expect(
         df
           .col("foo")
@@ -649,7 +654,7 @@ describe("AnnoMatrixCrossfilter", () => {
         values: ["purple"],
       });
       expect(xfltr2.countSelected()).toEqual(2);
-      expect(xfltr2.allSelectedLabels()).toEqual(Int32Array.from([0, 10]));
+      expect(xfltr2.allSelectedLabels()).toEqual(Array.from([0, 10]));
     });
 
     test("resetObsColumnValues", async () => {

client/__tests__/util/annoMatrix/serverMocks/routes.ts

@@ -43,7 +43,6 @@ function getEncodedDataframe(colNames: any, length: any, colSchemas: any) {
   const colIndex = new KeyIndex(colNames);
   // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
   const columns = colSchemas.map((s: any) => makeMockColumn(s, length));
-  // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
   const df = new Dataframe([length, colNames.length], columns, null, colIndex);
   const body = encodeMatrixFBS(df);
   return body;
@@ -56,7 +55,6 @@ export function dataframeResponse(colNames: any, columns: any) {
     [columns[0].length, colNames.length],
     columns,
     null,
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
     colIndex
   );
   const body = encodeMatrixFBS(df);

client/__tests__/util/centroid.test.ts

@@ -1,19 +1,19 @@
 import cloneDeep from "lodash.clonedeep";
 
+import { NumberArray } from "../../src/common/types/arraytypes";
 import calcCentroid from "../../src/util/centroid";
 import quantile from "../../src/util/quantile";
 import { matrixFBSToDataframe } from "../../src/util/stateManager/matrix";
 import * as REST from "./stateManager/sampleResponses";
 import { indexEntireSchema } from "../../src/util/stateManager/schemaHelpers";
 import { normalizeWritableCategoricalSchema } from "../../src/annoMatrix/normalize";
+import { Dataframe } from "../../src/util/dataframe";
 
 describe("centroid", () => {
   // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
   let schema: any;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  let obsAnnotations: any;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  let obsLayout: any;
+  let obsAnnotations: Dataframe;
+  let obsLayout: Dataframe;
 
   beforeAll(() => {
     schema = indexEntireSchema(cloneDeep(REST.schema.schema));
@@ -43,8 +43,8 @@ describe("centroid", () => {
 
     // This expected result assumes that all cells belong in all categorical values inside of sample response
     const expectedResult = [
-      quantile([0.5], obsLayout.col("umap_0").asArray())[0],
-      quantile([0.5], obsLayout.col("umap_1").asArray())[0],
+      quantile([0.5], obsLayout.col("umap_0").asArray() as NumberArray)[0],
+      quantile([0.5], obsLayout.col("umap_1").asArray() as NumberArray)[0],
     ];
 
     // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
@@ -68,8 +68,8 @@ describe("centroid", () => {
 
     // This expected result assumes that all cells belong in all categorical values inside of sample response
     const expectedResult = [
-      quantile([0.5], obsLayout.col("umap_0").asArray())[0],
-      quantile([0.5], obsLayout.col("umap_1").asArray())[0],
+      quantile([0.5], obsLayout.col("umap_0").asArray() as NumberArray)[0],
+      quantile([0.5], obsLayout.col("umap_1").asArray() as NumberArray)[0],
     ];
 
     // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.