Added typings to annoMatrix dir. (#2365) (#2371)

* Added typings to annoMatrix directory. (#2365)

* Added review point updates. (#2365)

* Fixed viewOf defect. Added review point updates. (#2365)

* Updated test to use Field key interpolation. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* Updated test to use Field key interpolation. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* Updated test to use Field key interpolation. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* Updated test to use Field key interpolation. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* Linting. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* Simplified while condition in middleware GC. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* Reverted embedding.ts prettier to resolve conflict. (#2365)

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

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

@@ -10,6 +10,7 @@ import {
   isubsetMask,
 } from "../../../src/annoMatrix";
 import { Dataframe } from "../../../src/util/dataframe";
+import { Field } from "../../../src/common/types/schema";
 
 enableFetchMocks();
 
@@ -34,7 +35,7 @@ describe("AnnoMatrix", () => {
       expect(annoMatrix.nObs).toEqual(serverMocks.schema.schema.dataframe.nObs);
       expect(annoMatrix.nVar).toEqual(serverMocks.schema.schema.dataframe.nVar);
       expect(annoMatrix.isView).toBeFalsy();
-      expect(annoMatrix.viewOf).toBeUndefined();
+      expect(annoMatrix.viewOf).toBe(annoMatrix);
       expect(annoMatrix.rowIndex).toBeDefined();
     });
 
@@ -42,7 +43,7 @@ describe("AnnoMatrix", () => {
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).once(serverMocks.annotationsObs(["name_0"]));
 
-      const df = await annoMatrix.fetch("obs", "name_0");
+      const df = await annoMatrix.fetch(Field.obs, "name_0");
       expect(df).toBeInstanceOf(Dataframe);
       expect(df.colIndex.labels()).toEqual(["name_0"]);
       expect(df.dims).toEqual([annoMatrix.nObs, 1]);
@@ -55,7 +56,7 @@ describe("AnnoMatrix", () => {
         .once(serverMocks.annotationsObs(["n_genes"]));
 
       await expect(
-        annoMatrix.fetch("obs", ["name_0", "n_genes"])
+        annoMatrix.fetch(Field.obs, ["name_0", "n_genes"])
       ).resolves.toBeInstanceOf(Dataframe);
     });
 
@@ -72,7 +73,7 @@ describe("AnnoMatrix", () => {
         ).resolves.toBeInstanceOf(Dataframe);
       };
 
-      test("obs", async () => getLastTwo("obs"));
+      test(Field.obs, async () => getLastTwo(Field.obs));
       test("var", async () => getLastTwo("var"));
       test("emb", async () => getLastTwo("emb"));
     });
@@ -81,15 +82,15 @@ describe("AnnoMatrix", () => {
       // single string is a column name
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).once(serverMocks.annotationsObs(["n_genes"]));
-      await expect(annoMatrix.fetch("obs", "n_genes")).resolves.toBeInstanceOf(
+      await expect(
-        Dataframe
+        annoMatrix.fetch(Field.obs, "n_genes")
-      );
+      ).resolves.toBeInstanceOf(Dataframe);
 
       // array of column names, expecting n_genes to be cached.
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).once(serverMocks.annotationsObs(["percent_mito"]));
       await expect(
-        annoMatrix.fetch("obs", ["n_genes", "percent_mito"])
+        annoMatrix.fetch(Field.obs, ["n_genes", "percent_mito"])
       ).resolves.toBeInstanceOf(Dataframe);
 
       // more complex value filter query, enumerated
@@ -151,9 +152,9 @@ describe("AnnoMatrix", () => {
 
     test("schema accessors", () => {
       expect(annoMatrix.getMatrixFields()).toEqual(
-        expect.arrayContaining(["X", "obs", "emb", "var"])
+        expect.arrayContaining(["X", Field.obs, "emb", "var"])
       );
-      expect(annoMatrix.getMatrixColumns("obs")).toEqual(
+      expect(annoMatrix.getMatrixColumns(Field.obs)).toEqual(
         expect.arrayContaining(["name_0", "n_genes", "louvain"])
       );
       expect(annoMatrix.getColumnSchema("emb", "umap")).toEqual({
@@ -171,7 +172,7 @@ describe("AnnoMatrix", () => {
   	test the mask & label access to subset via isubset and isubsetMask
   	*/
     test("isubset", async () => {
-      const rowList = [0, 10];
+      const rowList = new Int32Array([0, 10]);
       const rowMask = new Uint8Array(annoMatrix.nObs);
       for (let i = 0; i < rowList.length; i += 1) {
         rowMask[rowList[i]] = 1;
@@ -188,8 +189,8 @@ describe("AnnoMatrix", () => {
       (fetch as any)
         .once(serverMocks.annotationsObs(["n_genes"]))
         .once(serverMocks.annotationsObs(["n_genes"]));
-      const ng1 = (await am1.fetch("obs", "n_genes")) as Dataframe;
+      const ng1 = (await am1.fetch(Field.obs, "n_genes")) as Dataframe;
-      const ng2 = (await am2.fetch("obs", "n_genes")) as Dataframe;
+      const ng2 = (await am2.fetch(Field.obs, "n_genes")) as Dataframe;
       expect(ng1).toBeDefined();
       expect(ng2).toBeDefined();
       expect(ng1).toHaveLength(ng2.length);
@@ -203,10 +204,10 @@ describe("AnnoMatrix", () => {
   describe("add/drop column", () => {
     // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type.
     async function addDrop(base) {
-      expect(base.getMatrixColumns("obs")).not.toContain("foo");
+      expect(base.getMatrixColumns(Field.obs)).not.toContain("foo");
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(base.fetch("obs", "foo")).rejects.toThrow(
+      await expect(base.fetch(Field.obs, "foo")).rejects.toThrow(
         "unknown column name"
       );
 
@@ -216,9 +217,9 @@ describe("AnnoMatrix", () => {
         Float32Array,
         0
       );
-      expect(base.getMatrixColumns("obs")).not.toContain("foo");
+      expect(base.getMatrixColumns(Field.obs)).not.toContain("foo");
-      expect(am1.getMatrixColumns("obs")).toContain("foo");
+      expect(am1.getMatrixColumns(Field.obs)).toContain("foo");
-      const foo: Dataframe = await am1.fetch("obs", "foo");
+      const foo: Dataframe = await am1.fetch(Field.obs, "foo");
       expect(foo).toBeDefined();
       expect(foo).toBeInstanceOf(Dataframe);
       expect(foo).toHaveLength(am1.nObs);
@@ -228,11 +229,11 @@ describe("AnnoMatrix", () => {
 
       /* drop */
       const am2 = am1.dropObsColumn("foo");
-      expect(base.getMatrixColumns("obs")).not.toContain("foo");
+      expect(base.getMatrixColumns(Field.obs)).not.toContain("foo");
-      expect(am2.getMatrixColumns("obs")).not.toContain("foo");
+      expect(am2.getMatrixColumns(Field.obs)).not.toContain("foo");
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(am2.fetch("obs", "foo")).rejects.toThrow(
+      await expect(am2.fetch(Field.obs, "foo")).rejects.toThrow(
         "unknown column name"
       );
     }
@@ -245,10 +246,10 @@ describe("AnnoMatrix", () => {
       const am1 = clip(annoMatrix, 0.1, 0.9);
       await addDrop(am1);
 
-      const am2 = isubset(am1, [0, 1, 2, 20, 30, 400]);
+      const am2 = isubset(am1, new Int32Array([0, 1, 2, 20, 30, 400]));
       await addDrop(am2);
 
-      const am3 = isubset(annoMatrix, [10, 0, 7, 3]);
+      const am3 = isubset(annoMatrix, new Int32Array([10, 0, 7, 3]));
       await addDrop(am3);
 
       const am4 = clip(am3, 0, 1);
@@ -257,10 +258,10 @@ describe("AnnoMatrix", () => {
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockResponse(serverMocks.responder);
 
-      await am1.fetch("obs", am1.getMatrixColumns("obs"));
+      await am1.fetch(Field.obs, am1.getMatrixColumns(Field.obs));
-      await am2.fetch("obs", am2.getMatrixColumns("obs"));
+      await am2.fetch(Field.obs, am2.getMatrixColumns(Field.obs));
-      await am3.fetch("obs", am3.getMatrixColumns("obs"));
+      await am3.fetch(Field.obs, am3.getMatrixColumns(Field.obs));
-      await am4.fetch("obs", am4.getMatrixColumns("obs"));
+      await am4.fetch(Field.obs, am4.getMatrixColumns(Field.obs));
 
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).resetMocks();
@@ -287,7 +288,7 @@ describe("AnnoMatrix", () => {
         "unassigned"
       );
 
-      const testVal = await am.fetch("obs", "test");
+      const testVal = await am.fetch(Field.obs, "test");
       expect(testVal.col("test").asArray()).toEqual(
         new Array(am.nObs).fill("unassigned")
       );
@@ -295,7 +296,7 @@ describe("AnnoMatrix", () => {
       /* set values in column */
       const whichRows = [1, 2, 10];
       const am1 = await am.setObsColumnValues("test", whichRows, "yo");
-      const testVal1 = await am1.fetch("obs", "test");
+      const testVal1 = await am1.fetch(Field.obs, "test");
       const expt = new Array(am1.nObs).fill("unassigned");
       for (let i = 0; i < whichRows.length; i += 1) {
         const offset = am1.rowIndex.getOffset(whichRows[i]);
@@ -303,8 +304,8 @@ describe("AnnoMatrix", () => {
       }
       expect(testVal1).not.toBe(testVal);
       expect(testVal1.col("test").asArray()).toEqual(expt);
-      expect(am1.getColumnSchema("obs", "test").type).toBe("categorical");
+      expect(am1.getColumnSchema(Field.obs, "test").type).toBe("categorical");
-      expect(am1.getColumnSchema("obs", "test").categories).toEqual(
+      expect(am1.getColumnSchema(Field.obs, "test").categories).toEqual(
         expect.arrayContaining(["unassigned", "red", "green", "yo"])
       );
 
@@ -312,7 +313,7 @@ describe("AnnoMatrix", () => {
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
       am = am1.dropObsColumn("test");
-      await expect(am.fetch("obs", "test")).rejects.toThrow(
+      await expect(am.fetch(Field.obs, "test")).rejects.toThrow(
         "unknown column name"
       );
     }
@@ -325,18 +326,18 @@ describe("AnnoMatrix", () => {
       const am1 = clip(annoMatrix, 0.1, 0.9);
       await addSetDrop(am1);
 
-      const am2 = isubset(am1, [0, 1, 2, 10, 20, 30, 400]);
+      const am2 = isubset(am1, new Int32Array([0, 1, 2, 10, 20, 30, 400]));
       await addSetDrop(am2);
 
-      const am3 = isubset(annoMatrix, [10, 1, 0, 30, 2]);
+      const am3 = isubset(annoMatrix, new Int32Array([10, 1, 0, 30, 2]));
       await addSetDrop(am3);
 
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockResponse(serverMocks.responder);
 
-      await am1.fetch("obs", am1.getMatrixColumns("obs"));
+      await am1.fetch(Field.obs, am1.getMatrixColumns(Field.obs));
-      await am2.fetch("obs", am2.getMatrixColumns("obs"));
+      await am2.fetch(Field.obs, am2.getMatrixColumns(Field.obs));
-      await am3.fetch("obs", am3.getMatrixColumns("obs"));
+      await am3.fetch(Field.obs, am3.getMatrixColumns(Field.obs));
 
       await addSetDrop(am1);
       await addSetDrop(am2);

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

@@ -14,6 +14,7 @@ import {
 } from "../../../src/annoMatrix";
 import { Dataframe } from "../../../src/util/dataframe";
 import { rangeFill } from "../../../src/util/range";
+import { Field, Schema } from "../../../src/common/types/schema";
 
 enableFetchMocks();
 
@@ -29,7 +30,7 @@ describe("AnnoMatrixCrossfilter", () => {
     // reset all fetch mocking state
     annoMatrix = new AnnoMatrixLoader(
       serverMocks.baseDataURL,
-      serverMocks.schema.schema
+      serverMocks.schema.schema as Schema
     );
     crossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
   });
@@ -76,7 +77,7 @@ describe("AnnoMatrixCrossfilter", () => {
       (fetch as any).once(
         serverMocks.dataframeResponse(["louvain"], [obsLouvain])
       );
-      let newCrossfilter = await crossfilter.select("obs", "louvain", {
+      let newCrossfilter = await crossfilter.select(Field.obs, "louvain", {
         mode: "none",
       });
 
@@ -87,7 +88,7 @@ describe("AnnoMatrixCrossfilter", () => {
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       expect((fetch as any).mock.calls).toHaveLength(1);
 
-      newCrossfilter = await crossfilter.select("obs", "louvain", {
+      newCrossfilter = await crossfilter.select(Field.obs, "louvain", {
         mode: "all",
       });
       expect(newCrossfilter.countSelected()).toEqual(annoMatrix.nObs);
@@ -100,7 +101,7 @@ describe("AnnoMatrixCrossfilter", () => {
       (fetch as any).once(
         serverMocks.dataframeResponse(["louvain"], [obsLouvain])
       );
-      xfltr = await crossfilter.select("obs", "louvain", {
+      xfltr = await crossfilter.select(Field.obs, "louvain", {
         mode: "exact",
         values: ["NK cells", "B cells"],
       });
@@ -133,7 +134,7 @@ describe("AnnoMatrixCrossfilter", () => {
         )
       );
 
-      const df: Dataframe = await annoMatrix.fetch("obs", "louvain");
+      const df: Dataframe = await annoMatrix.fetch(Field.obs, "louvain");
       const values = df.col("louvain").asArray();
       const selected = xfltr.allSelectedMask();
       values.every(
@@ -146,7 +147,7 @@ describe("AnnoMatrixCrossfilter", () => {
       (fetch as any).once(
         serverMocks.dataframeResponse(["n_genes"], [new Int32Array(obsNGenes)])
       );
-      xfltr = await xfltr.select("obs", "n_genes", {
+      xfltr = await xfltr.select(Field.obs, "n_genes", {
         mode: "range",
         lo: 0,
         hi: 500,
@@ -258,7 +259,7 @@ describe("AnnoMatrixCrossfilter", () => {
       (fetch as any).once(
         serverMocks.dataframeResponse(["louvain"], [obsLouvain])
       );
-      xfltr = await xfltr.select("obs", "louvain", {
+      xfltr = await xfltr.select(Field.obs, "louvain", {
         mode: "exact",
         values: ["NK cells", "B cells"],
       });
@@ -267,7 +268,7 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(xfltr.countSelected()).toEqual(240);
 
       const df: Dataframe = (await annoMatrixSubset.fetch(
-        "obs",
+        Field.obs,
         "louvain"
       )) as Dataframe;
       expect(df).toBeDefined();
@@ -291,7 +292,7 @@ describe("AnnoMatrixCrossfilter", () => {
 
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(crossfilter.select("obs", "foo")).rejects.toThrow(
+      await expect(crossfilter.select(Field.obs, "foo")).rejects.toThrow(
         "unknown column name"
       );
     });
@@ -304,7 +305,7 @@ describe("AnnoMatrixCrossfilter", () => {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
     async function helperAddTestCol(cf: any, colName: any, colSchema = null) {
       expect(
-        cf.annoMatrix.getMatrixColumns("obs").includes(colName)
+        cf.annoMatrix.getMatrixColumns(Field.obs).includes(colName)
       ).toBeFalsy();
 
       if (colSchema === null) {
@@ -326,7 +327,7 @@ describe("AnnoMatrixCrossfilter", () => {
           (v: any) => v.name === colName
         )
       ).toHaveLength(1);
-      const df = await xfltr.annoMatrix.fetch("obs", colName);
+      const df = await xfltr.annoMatrix.fetch(Field.obs, colName);
       expect(df.hasCol(colName)).toBeTruthy();
       return xfltr;
     }
@@ -334,7 +335,7 @@ describe("AnnoMatrixCrossfilter", () => {
     test("addObsColumn", async () => {
       expect(crossfilter.countSelected()).toBe(annoMatrix.nObs);
       expect(
-        crossfilter.annoMatrix.getMatrixColumns("obs").includes("foo")
+        crossfilter.annoMatrix.getMatrixColumns(Field.obs).includes("foo")
       ).toBeFalsy();
       const xfltr = crossfilter.addObsColumn(
         { name: "foo", type: "categorical", categories: ["A"] },
@@ -345,7 +346,7 @@ describe("AnnoMatrixCrossfilter", () => {
       // check schema updates correctly.
       expect(xfltr.countSelected()).toBe(annoMatrix.nObs);
       expect(
-        xfltr.annoMatrix.getMatrixColumns("obs").includes("foo")
+        xfltr.annoMatrix.getMatrixColumns(Field.obs).includes("foo")
       ).toBeTruthy();
       expect(xfltr.annoMatrix.schema.annotations.obsByName.foo).toMatchObject({
         name: "foo",
@@ -359,7 +360,7 @@ describe("AnnoMatrixCrossfilter", () => {
       ).toHaveLength(1);
 
       // check data update.
-      const df: Dataframe = await xfltr.annoMatrix.fetch("obs", "foo");
+      const df: Dataframe = await xfltr.annoMatrix.fetch(Field.obs, "foo");
       expect(
         df
           .col("foo")
@@ -408,13 +409,13 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(xfltr.annoMatrix.schema.annotations.obsByName.foo).toBeUndefined();
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow(
+      await expect(xfltr.annoMatrix.fetch(Field.obs, "foo")).rejects.toThrow(
         "unknown column name"
       );
 
       // now same, but ensure we have built an index before doing the drop
       xfltr = await helperAddTestCol(crossfilter, "bar");
-      xfltr = await xfltr.select("obs", "bar", {
+      xfltr = await xfltr.select(Field.obs, "bar", {
         mode: "exact",
         values: "whatever",
       });
@@ -422,9 +423,9 @@ describe("AnnoMatrixCrossfilter", () => {
 
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow(
+      await expect(
-        "unknown column name"
+        xfltr.select(Field.obs, "bar", { mode: "all" })
-      );
+      ).rejects.toThrow("unknown column name");
     });
 
     test("renameObsColumn", async () => {
@@ -441,23 +442,25 @@ describe("AnnoMatrixCrossfilter", () => {
       // add a column, then rename it.
       xfltr = await helperAddTestCol(crossfilter, "foo");
       xfltr = xfltr.renameObsColumn("foo", "bar");
-      expect(xfltr.annoMatrix.getColumnSchema("obs", "foo")).toBeUndefined();
+      expect(
-      expect(xfltr.annoMatrix.getColumnSchema("obs", "bar")).toMatchObject({
+        xfltr.annoMatrix.getColumnSchema(Field.obs, "foo")
+      ).toBeUndefined();
+      expect(xfltr.annoMatrix.getColumnSchema(Field.obs, "bar")).toMatchObject({
         name: "bar",
         type: "categorical",
       });
 
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow(
+      await expect(xfltr.annoMatrix.fetch(Field.obs, "foo")).rejects.toThrow(
         "unknown column name"
       );
-      const df = await xfltr.annoMatrix.fetch("obs", "bar");
+      const df = await xfltr.annoMatrix.fetch(Field.obs, "bar");
       expect(df.hasCol("bar")).toBeTruthy();
 
       // now same, but ensure we have built an index before doing the rename
       xfltr = await helperAddTestCol(crossfilter, "bar");
-      xfltr = await xfltr.select("obs", "bar", {
+      xfltr = await xfltr.select(Field.obs, "bar", {
         mode: "exact",
         values: "whatever",
       });
@@ -465,11 +468,11 @@ describe("AnnoMatrixCrossfilter", () => {
 
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
       (fetch as any).mockRejectOnce(new Error("unknown column name"));
-      await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow(
-        "unknown column name"
-      );
       await expect(
-        xfltr.select("obs", "xyz", { mode: "none" })
+        xfltr.select(Field.obs, "bar", { mode: "all" })
+      ).rejects.toThrow("unknown column name");
+      await expect(
+        xfltr.select(Field.obs, "xyz", { mode: "none" })
       ).resolves.toBeInstanceOf(AnnoMatrixObsCrossfilter);
     });
 
@@ -493,7 +496,7 @@ describe("AnnoMatrixCrossfilter", () => {
         categories: ["unassigned"],
       });
       xfltr = xfltr.addObsAnnoCategory("foo", "a-new-label");
-      expect(xfltr.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
+      expect(xfltr.annoMatrix.getColumnSchema(Field.obs, "foo")).toMatchObject({
         name: "foo",
         type: "categorical",
         categories: expect.arrayContaining(["a-new-label", "unassigned"]),
@@ -511,12 +514,12 @@ describe("AnnoMatrixCrossfilter", () => {
         type: "categorical",
         categories: ["unassigned"],
       });
-      xfltr = await xfltr.select("obs", "bar", {
+      xfltr = await xfltr.select(Field.obs, "bar", {
         mode: "exact",
         values: "something",
       });
       xfltr = xfltr.addObsAnnoCategory("bar", "a-new-label");
-      expect(xfltr.annoMatrix.getColumnSchema("obs", "bar")).toMatchObject({
+      expect(xfltr.annoMatrix.getColumnSchema(Field.obs, "bar")).toMatchObject({
         name: "bar",
         type: "categorical",
         categories: expect.arrayContaining(["a-new-label", "unassigned"]),
@@ -540,14 +543,14 @@ describe("AnnoMatrixCrossfilter", () => {
         type: "categorical",
         categories: ["unassigned", "red", "green", "blue"],
       });
-      xfltr = await xfltr.select("obs", "foo", { mode: "all" });
+      xfltr = await xfltr.select(Field.obs, "foo", { mode: "all" });
       expect(
-        (await xfltr.annoMatrix.fetch("obs", "foo"))
+        (await xfltr.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .every((v: any) => v === "unassigned")
       ).toBeTruthy();
-      expect(xfltr.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
+      expect(xfltr.annoMatrix.getColumnSchema(Field.obs, "foo")).toMatchObject({
         name: "foo",
         type: "categorical",
         categories: expect.arrayContaining([
@@ -561,21 +564,23 @@ describe("AnnoMatrixCrossfilter", () => {
       // remove an unused category
       const xfltr1 = await xfltr.removeObsAnnoCategory("foo", "red", "mumble");
       expect(
-        (await xfltr1.annoMatrix.fetch("obs", "foo"))
+        (await xfltr1.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .every((v: any) => v === "unassigned")
       ).toBeTruthy();
-      expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
+      expect(xfltr1.annoMatrix.getColumnSchema(Field.obs, "foo")).toMatchObject(
-        name: "foo",
+        {
-        type: "categorical",
+          name: "foo",
-        categories: expect.arrayContaining([
+          type: "categorical",
-          "unassigned",
+          categories: expect.arrayContaining([
-          "green",
+            "unassigned",
-          "blue",
+            "green",
-          "mumble",
+            "blue",
-        ]),
+            "mumble",
-      });
+          ]),
+        }
+      );
 
       // remove a used category
       const xfltr2 = await xfltr.removeObsAnnoCategory(
@@ -584,16 +589,18 @@ describe("AnnoMatrixCrossfilter", () => {
         "red"
       );
       expect(
-        (await xfltr2.annoMatrix.fetch("obs", "foo"))
+        (await xfltr2.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .every((v: any) => v === "red")
       ).toBeTruthy();
-      expect(xfltr2.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
+      expect(xfltr2.annoMatrix.getColumnSchema(Field.obs, "foo")).toMatchObject(
-        name: "foo",
+        {
-        type: "categorical",
+          name: "foo",
-        categories: expect.arrayContaining(["green", "blue", "red"]),
+          type: "categorical",
-      });
+          categories: expect.arrayContaining(["green", "blue", "red"]),
+        }
+      );
     });
 
     test("setObsColumnValues", async () => {
@@ -611,7 +618,7 @@ describe("AnnoMatrixCrossfilter", () => {
         type: "categorical",
         categories: ["unassigned", "red", "green", "blue"],
       });
-      xfltr = await xfltr.select("obs", "foo", { mode: "all" });
+      xfltr = await xfltr.select(Field.obs, "foo", { mode: "all" });
 
       // catch unknown row label
       await expect(() =>
@@ -620,14 +627,14 @@ describe("AnnoMatrixCrossfilter", () => {
 
       // set a few rows
       expect(
-        (await xfltr.annoMatrix.fetch("obs", "foo"))
+        (await xfltr.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .every((v: any) => v === "unassigned")
       ).toBeTruthy();
       const xfltr1 = await xfltr.setObsColumnValues("foo", [0, 10], "purple");
       expect(
-        (await xfltr1.annoMatrix.fetch("obs", "foo"))
+        (await xfltr1.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray()
           .every(
@@ -636,20 +643,22 @@ describe("AnnoMatrixCrossfilter", () => {
               v === "unassigned" || (v === "purple" && (i === 0 || i === 10))
           )
       ).toBeTruthy();
-      expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
+      expect(xfltr1.annoMatrix.getColumnSchema(Field.obs, "foo")).toMatchObject(
-        name: "foo",
+        {
-        type: "categorical",
+          name: "foo",
-        categories: expect.arrayContaining([
+          type: "categorical",
-          "unassigned",
+          categories: expect.arrayContaining([
-          "red",
+            "unassigned",
-          "green",
+            "red",
-          "blue",
+            "green",
-          "purple",
+            "blue",
-        ]),
+            "purple",
-      });
+          ]),
+        }
+      );
 
       expect(xfltr1.countSelected()).toEqual(xfltr1.annoMatrix.nObs);
-      const xfltr2 = await xfltr1.select("obs", "foo", {
+      const xfltr2 = await xfltr1.select(Field.obs, "foo", {
         mode: "exact",
         values: ["purple"],
       });
@@ -672,7 +681,7 @@ describe("AnnoMatrixCrossfilter", () => {
         type: "categorical",
         categories: ["unassigned", "red", "green", "blue"],
       });
-      xfltr = await xfltr.select("obs", "foo", {
+      xfltr = await xfltr.select(Field.obs, "foo", {
         mode: "exact",
         values: "red",
       });
@@ -683,12 +692,12 @@ describe("AnnoMatrixCrossfilter", () => {
       ).rejects.toThrow("unknown category");
 
       let xfltr1 = await xfltr.setObsColumnValues("foo", [0, 10], "purple");
-      xfltr1 = await xfltr1.select("obs", "foo", {
+      xfltr1 = await xfltr1.select(Field.obs, "foo", {
         mode: "exact",
         values: "purple",
       });
       expect(
-        (await xfltr1.annoMatrix.fetch("obs", "foo"))
+        (await xfltr1.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .filter((v: any) => v === "purple")
@@ -696,29 +705,31 @@ describe("AnnoMatrixCrossfilter", () => {
 
       xfltr1 = await xfltr1.resetObsColumnValues("foo", "purple", "magenta");
       expect(
-        (await xfltr1.annoMatrix.fetch("obs", "foo"))
+        (await xfltr1.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .filter((v: any) => v === "magenta")
       ).toHaveLength(2);
       expect(
-        (await xfltr1.annoMatrix.fetch("obs", "foo"))
+        (await xfltr1.annoMatrix.fetch(Field.obs, "foo"))
           .col("foo")
           .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
           .filter((v: any) => v === "purple")
       ).toHaveLength(0);
-      expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
+      expect(xfltr1.annoMatrix.getColumnSchema(Field.obs, "foo")).toMatchObject(
-        name: "foo",
+        {
-        type: "categorical",
+          name: "foo",
-        categories: expect.arrayContaining([
+          type: "categorical",
-          "unassigned",
+          categories: expect.arrayContaining([
-          "red",
+            "unassigned",
-          "green",
+            "red",
-          "blue",
+            "green",
-          "purple",
+            "blue",
-          "magenta",
+            "purple",
-        ]),
+            "magenta",
-      });
+          ]),
+        }
+      );
     });
   });
 
@@ -729,7 +740,7 @@ describe("AnnoMatrixCrossfilter", () => {
       (fetch as any).once(
         serverMocks.dataframeResponse(["louvain"], [obsLouvain])
       );
-      const xfltr = await crossfilter.select("obs", "louvain", {
+      const xfltr = await crossfilter.select(Field.obs, "louvain", {
         mode: "exact",
         values: "B cells",
       });

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

@@ -4,31 +4,34 @@ import {
   _whereCacheCreate,
   _whereCacheMerge,
 } from "../../../src/annoMatrix/whereCache";
+import { Field, Schema } from "../../../src/common/types/schema";
+import { Query } from "../../../src/annoMatrix/query";
 
-const schema = {};
+const schema = {} as Schema;
 
 describe("whereCache", () => {
   test("whereCacheGet - where query, missing cache values", () => {
     expect(
-      _whereCacheGet({}, schema, "X", {
+      _whereCacheGet({}, schema, Field.X, {
         where: {
-          field: "var",
+          field: Field.var,
           column: "foo",
           value: "bar",
         },
       })
     ).toEqual([undefined]);
     expect(
-      _whereCacheGet({}, schema, "X", {
+      _whereCacheGet({}, schema, Field.X, {
         summarize: {
-          field: "var",
+          method: "mean",
+          field: Field.var,
           column: "foo",
           values: ["bar"],
         },
       })
     ).toEqual([undefined]);
     expect(
-      _whereCacheGet({ where: { X: {} } }, schema, "X", {
+      _whereCacheGet({ where: { X: {} } }, schema, Field.X, {
         where: {
           field: "var",
           column: "foo",
@@ -37,7 +40,7 @@ describe("whereCache", () => {
       })
     ).toEqual([undefined]);
     expect(
-      _whereCacheGet({ where: { X: { var: new Map() } } }, schema, "X", {
+      _whereCacheGet({ where: { X: { var: new Map() } } }, schema, Field.X, {
         where: {
           field: "var",
           column: "foo",
@@ -49,7 +52,7 @@ describe("whereCache", () => {
       _whereCacheGet(
         { where: { X: { var: new Map([["foo", new Map()]]) } } },
         schema,
-        "X",
+        Field.X,
         {
           where: {
             field: "var",
@@ -63,7 +66,7 @@ describe("whereCache", () => {
 
   test("whereCacheGet - summarize query, missing cache values", () => {
     expect(
-      _whereCacheGet({}, schema, "X", {
+      _whereCacheGet({}, schema, Field.X, {
         summarize: {
           method: "mean",
           field: "var",
@@ -76,7 +79,7 @@ describe("whereCache", () => {
       _whereCacheGet(
         { summarize: { X: { mean: { var: new Map() } } } },
         schema,
-        "X",
+        Field.X,
         {
           summarize: {
             method: "mean",
@@ -122,7 +125,7 @@ describe("whereCache", () => {
     };
 
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      _whereCacheGet(whereCache, schema, Field.X, {
         where: {
           field: "var",
           column: "foo",
@@ -131,7 +134,7 @@ describe("whereCache", () => {
       })
     ).toEqual([0]);
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      _whereCacheGet(whereCache, schema, Field.X, {
         summarize: {
           method: "mean",
           field: "var",
@@ -141,7 +144,7 @@ describe("whereCache", () => {
       })
     ).toEqual([0]);
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      _whereCacheGet(whereCache, schema, Field.X, {
         where: {
           field: "var",
           column: "foo",
@@ -150,7 +153,7 @@ describe("whereCache", () => {
       })
     ).toEqual([1, 2]);
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      _whereCacheGet(whereCache, schema, Field.X, {
         summarize: {
           method: "mean",
           field: "var",
@@ -159,9 +162,12 @@ describe("whereCache", () => {
         },
       })
     ).toEqual([1, 2]);
-    expect(_whereCacheGet(whereCache, schema, "Y", {})).toEqual([undefined]);
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      // Force invalid field value Y
+      _whereCacheGet(whereCache, schema, "Y" as Field, {} as Query)
+    ).toEqual([undefined]);
+    expect(
+      _whereCacheGet(whereCache, schema, Field.X, {
         where: {
           field: "whoknows",
           column: "whatever",
@@ -170,7 +176,7 @@ describe("whereCache", () => {
       })
     ).toEqual([undefined]);
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      _whereCacheGet(whereCache, schema, Field.X, {
         where: {
           field: "var",
           column: "whatever",
@@ -179,7 +185,7 @@ describe("whereCache", () => {
       })
     ).toEqual([undefined]);
     expect(
-      _whereCacheGet(whereCache, schema, "X", {
+      _whereCacheGet(whereCache, schema, Field.X, {
         where: {
           field: "var",
           column: "foo",
@@ -198,7 +204,7 @@ describe("whereCache", () => {
       },
     };
     const wc = _whereCacheCreate(
-      "field",
+      Field.obs,
       {
         where: {
           field: "queryField",
@@ -212,7 +218,7 @@ describe("whereCache", () => {
     expect(wc).toEqual(
       expect.objectContaining({
         where: {
-          field: {
+          [Field.obs]: {
             queryField: expect.any(Map),
           },
         },
@@ -220,18 +226,19 @@ describe("whereCache", () => {
     );
     // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
     // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    expect((wc.where as any).field.queryField.has("queryColumn")).toEqual(true);
+    expect((wc.where as any)[Field.obs].queryField.has("queryColumn")).toEqual(true);
     expect(
       // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (wc.where as any).field.queryField.get("queryColumn")
+      (wc.where as any)[Field.obs].queryField.get("queryColumn")
     ).toBeInstanceOf(Map);
     expect(
       // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
       // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (wc.where as any).field.queryField.get("queryColumn").has("queryValue")
+      (wc.where as any)[Field.obs].queryField.get("queryColumn").has("queryValue")
     ).toEqual(true);
-    expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert wc to be non-null
+    expect(_whereCacheGet(wc!, schema, Field.obs, query)).toEqual([0, 1, 2]);
   });
 
   test("whereCacheCreate, summarize query", () => {
@@ -243,12 +250,14 @@ describe("whereCache", () => {
         values: ["queryValue"],
       },
     };
-    const wc = _whereCacheCreate("field", query, [0, 1, 2]);
+    const wc = _whereCacheCreate(Field.obs, query, [0, 1, 2]);
-    expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert wc to be non-null
+    expect(_whereCacheGet(wc!, schema, Field.obs, query)).toEqual([0, 1, 2]);
   });
 
   test("whereCacheCreate, unknown query type", () => {
-    expect(_whereCacheCreate("field", { foobar: true }, [1])).toEqual({});
+    // @ts-expect-error --- force invalid query {foobar: true}
+    expect(_whereCacheCreate(Field.obs, { foobar: true }, [1])).toEqual({});
   });
 
   test("whereCacheMerge, where queries", () => {
@@ -256,19 +265,20 @@ describe("whereCache", () => {
 
     // remember, will mutate dst
     const src = _whereCacheCreate(
-      "field",
+      Field.obs,
       { where: { field: "queryField", column: "queryColumn", value: "foo" } },
       ["foo"]
     );
 
     const dst1 = _whereCacheCreate(
-      "field",
+      Field.obs,
       { where: { field: "queryField", column: "queryColumn", value: "bar" } },
       ["dst1"]
     );
-    wc = _whereCacheMerge(dst1, src);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert dst1 and src to be non-null
+    wc = _whereCacheMerge(dst1!, src!);
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         where: {
           field: "queryField",
           column: "queryColumn",
@@ -277,7 +287,7 @@ describe("whereCache", () => {
       })
     ).toEqual(["foo"]);
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         where: {
           field: "queryField",
           column: "queryColumn",
@@ -287,13 +297,14 @@ describe("whereCache", () => {
     ).toEqual(["dst1"]);
 
     const dst2 = _whereCacheCreate(
-      "field",
+      Field.obs,
       { where: { field: "queryField", column: "queryColumn", value: "bar" } },
       ["dst2"]
     );
-    wc = _whereCacheMerge(dst2, dst1, src);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert dst2m, dst1 and src to be non-null
+    wc = _whereCacheMerge(dst2!, dst1!, src!);
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         where: {
           field: "queryField",
           column: "queryColumn",
@@ -302,7 +313,7 @@ describe("whereCache", () => {
       })
     ).toEqual(["foo"]);
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         where: {
           field: "queryField",
           column: "queryColumn",
@@ -311,17 +322,20 @@ describe("whereCache", () => {
       })
     ).toEqual(["dst1"]);
 
-    wc = _whereCacheMerge({}, src);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert src to be non-null
+    wc = _whereCacheMerge({}, src!);
     expect(wc).toEqual(src);
 
-    wc = _whereCacheMerge({ where: { field: { queryField: new Map() } } }, src);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert src to be non-null
+    wc = _whereCacheMerge({ where: { obs: { queryField: new Map() } } }, src!);
     expect(wc).toEqual(src);
   });
 
   test("whereCacheMerge, mixed queries", () => {
     const wc = _whereCacheMerge(
+      // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert wc to be non-null
       _whereCacheCreate(
-        "field",
+        Field.obs,
         {
           where: {
             field: "queryField",
@@ -330,9 +344,10 @@ describe("whereCache", () => {
           },
         },
         ["a"]
-      ),
+      )!,
+      // eslint-disable-next-line @typescript-eslint/no-non-null-assertion --- assert wc to be non-null
       _whereCacheCreate(
-        "field",
+        Field.obs,
         {
           summarize: {
             method: "mean",
@@ -342,11 +357,11 @@ describe("whereCache", () => {
           },
         },
         ["b"]
-      )
+      )!
     );
 
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         where: {
           field: "queryField",
           column: "queryColumn",
@@ -356,7 +371,7 @@ describe("whereCache", () => {
     ).toEqual(["a"]);
 
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         summarize: {
           method: "mean",
           field: "queryField",
@@ -367,7 +382,7 @@ describe("whereCache", () => {
     ).toEqual(["b"]);
 
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         where: {
           field: "queryField",
           column: "queryColumn",
@@ -377,7 +392,7 @@ describe("whereCache", () => {
     ).toEqual([undefined]);
 
     expect(
-      _whereCacheGet(wc, schema, "field", {
+      _whereCacheGet(wc, schema, Field.obs, {
         summarize: {
           method: "no-such-method",
           field: "queryField",

client/src/actions/embedding.ts

@@ -7,6 +7,7 @@ import { ThunkAction } from "redux-thunk";
 import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
 import type { AppDispatch, RootState } from "../reducers";
 import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
+import { Field } from "../common/types/schema";
 
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export async function _switchEmbedding(
@@ -26,7 +27,7 @@ export async function _switchEmbedding(
   const obsCrossfilter = await new AnnoMatrixObsCrossfilter(
     annoMatrix,
     prevCrossfilter.obsCrossfilter
-  ).select("emb", newEmbeddingName, {
+  ).select(Field.emb, newEmbeddingName, {
     mode: "all",
   });
   return [annoMatrix, obsCrossfilter];
@@ -41,17 +42,19 @@ export const layoutChoiceAction: ActionCreator<
   On layout choice, make sure we have selected all on the previous layout, AND the new
   layout.
   */
-    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevCrossfilter } =
+  const {
-      getState();
+    annoMatrix: prevAnnoMatrix,
-    const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
+    obsCrossfilter: prevCrossfilter,
-      prevAnnoMatrix,
+  } = getState();
-      prevCrossfilter,
+  const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
-      newLayoutChoice
+    prevAnnoMatrix,
-    );
+    prevCrossfilter,
-    dispatch({
+    newLayoutChoice
-      type: "set layout choice",
+  );
-      layoutChoice: newLayoutChoice,
+  dispatch({
-      obsCrossfilter,
+    type: "set layout choice",
-      annoMatrix,
+    layoutChoice: newLayoutChoice,
-    });
+    obsCrossfilter,
-  };
+    annoMatrix,
+  });
+};

client/src/annoMatrix/annoMatrix.ts

@@ -2,6 +2,9 @@ import {
   Dataframe,
   IdentityInt32Index,
   dataframeMemo,
+  LabelType,
+  DataframeValue,
+  DataframeValueArray,
 } from "../util/dataframe";
 import {
   _getColumnDimensionNames,
@@ -10,45 +13,70 @@ import {
   _getWritableColumns,
 } from "./schema";
 import { indexEntireSchema } from "../util/stateManager/schemaHelpers";
-import { _whereCacheGet, _whereCacheMerge } from "./whereCache";
+import {
+  _whereCacheGet,
+  _whereCacheMerge,
+  WhereCache,
+  WhereCacheColumnLabels,
+} from "./whereCache";
 import _shallowClone from "./clone";
-import { _queryValidate, _queryCacheKey } from "./query";
+import { _queryValidate, _queryCacheKey, Query } from "./query";
+import { GCHints } from "../common/types/entities";
+import {
+  AnnotationColumnSchema,
+  Category,
+  Field,
+  EmbeddingSchema,
+  Schema,
+  ArraySchema,
+  RawSchema,
+} from "../common/types/schema";
+import { LabelArray } from "../util/dataframe/types";
+import { LabelIndexBase } from "../util/dataframe/labelIndex";
 
 const _dataframeCache = dataframeMemo(128);
 
-export default class AnnoMatrix {
+interface Cache {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  [Field.obs]: Dataframe;
-  public isView: any;
+  [Field.var]: Dataframe;
+  [Field.emb]: Dataframe;
+  [Field.X]: Dataframe;
+}
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+interface PendingLoad {
-  public nObs: any;
+  [Field.obs]: { [key: string]: Promise<void> };
+  [Field.var]: { [key: string]: Promise<void> };
+  [Field.emb]: { [key: string]: Promise<void> };
+  [Field.X]: { [key: string]: Promise<void> };
+}
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+export interface UserFlags {
-  public nVar: any;
+  isUserSubsetView?: boolean;
+  isEmbSubsetView?: boolean;
+}
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+export default abstract class AnnoMatrix {
-  public rowIndex: any;
+  public isView: boolean;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public nObs: number;
-  public schema: any;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public nVar: number;
-  public userFlags: any;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public rowIndex: LabelIndexBase;
-  public viewOf: any;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public schema: Schema;
-  protected _cache: any;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public userFlags: UserFlags;
-  private _pendingLoad: any;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public viewOf: AnnoMatrix;
-  private _whereCache: any;
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  public _cache: Cache;
-  private _gcInfo: any;
+
+  private _pendingLoad: PendingLoad;
+
+  private _whereCache: WhereCache;
+
+  private _gcInfo: Map<string, number>;
 
   /*
   Abstract base class for all AnnoMatrix objects.  This class provides a proxy
@@ -80,16 +108,19 @@ export default class AnnoMatrix {
       subset(annoMatrix, rowLabels) -> annoMatrix
   etc.
   */
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  static fields(): Field[] {
-  static fields() {
     /*
     return the fields present in the AnnoMatrix instance.
     */
-    return ["obs", "var", "emb", "X"];
+    return [Field.obs, Field.var, Field.emb, Field.X];
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  constructor(
-  constructor(schema: any, nObs: any, nVar: any, rowIndex = null) {
+    schema: RawSchema,
+    nObs: number,
+    nVar: number,
+    rowIndex: LabelIndexBase | null = null
+  ) {
     /*
     Private constructor - this is an abstract base class.  Do not use.
     */
@@ -105,7 +136,7 @@ export default class AnnoMatrix {
       * rowIndex - a rowIndex shared by all data on this view (ie, the list of cells).
         The row index labels are as defined by the base dataset from the server.
       * isView - true if this is a view, false if not.
-      * viewOf - pointer to parent annomatrix if a view, undefined/null if not a view.
+      * viewOf - pointer to parent annomatrix if a view, self if not a view.
       * userFlags - container for any additional state a user of this API wants to hang
         off of an annoMatrix, and have propagated by the (shallow) cloning protocol.
     */
@@ -114,7 +145,7 @@ export default class AnnoMatrix {
     this.nVar = nVar;
     this.rowIndex = rowIndex || new IdentityInt32Index(nObs);
     this.isView = false;
-    this.viewOf = undefined;
+    this.viewOf = this;
     this.userFlags = {};
 
     /*
@@ -137,16 +168,14 @@ export default class AnnoMatrix {
       emb: {},
       X: {},
     };
-    this._whereCache = {};
+    this._whereCache = {} as WhereCache;
     this._gcInfo = new Map();
   }
 
   /**
    ** Schema helper/accessors
    **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  getMatrixColumns(field: Field): string[] {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  getMatrixColumns(field) {
     /*
     Return array of column names in the field.  ONLY supported on the
     obs, var and emb fields.  X currently unimplemented and will throw.
@@ -158,8 +187,8 @@ export default class AnnoMatrix {
     return _schemaColumns(this.schema, field);
   }
 
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- need to be able to call this on instances
+  // eslint-disable-next-line class-methods-use-this -- need to be able to call this on instances
-  getMatrixFields() {
+  getMatrixFields(): Field[] {
     /*
     Return array of fields in this annoMatrix.  Currently hard-wired to
     return:  ["X", "obs", "var", "emb"].
@@ -169,9 +198,7 @@ export default class AnnoMatrix {
     return AnnoMatrix.fields();
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  getColumnSchema(field: Field, col: LabelType): ArraySchema {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  getColumnSchema(field, col) {
     /*
     Return the schema for the field & column ,eg,
 
@@ -183,9 +210,7 @@ export default class AnnoMatrix {
     return _getColumnSchema(this.schema, field, col);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  getColumnDimensions(field: Field, col: LabelType): LabelArray | undefined {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  getColumnDimensions(field, col) {
     /*
     Return the dimensions on this field / column.  For most fields, which are 1D,
     this just return the column name.  Multi-dimensional columns, such as embeddings,
@@ -203,23 +228,19 @@ export default class AnnoMatrix {
   /**
    ** General utility methods
    **/
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  base(): AnnoMatrix {
-  base() {
     /*
     return the base of view, or `this` if not a view.
     */
-    // eslint-disable-next-line @typescript-eslint/no-this-alias --- FIXME: disabled temporarily on migrate to TS.
+    let annoMatrix = this._getViewOf();
-    let annoMatrix = this;
+    while (annoMatrix.isView) annoMatrix = annoMatrix._getViewOf();
-    while (annoMatrix.isView) annoMatrix = annoMatrix.viewOf;
     return annoMatrix;
   }
 
   /**
    ** Load / read interfaces
    **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  fetch(field: Field, q: Query | Query[]): Promise<Dataframe> {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  fetch(field, q): Dataframe {
     /*
 		Return the given query on a single matrix field as a single dataframe.
 		Currently supports ONLY full column query.
@@ -276,9 +297,7 @@ export default class AnnoMatrix {
     return this._fetch(field, q);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  prefetch(field: Field, q: Query): void {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  prefetch(field, q): void {
     /*
 		Start a data fetch & cache fill.  Identical to fetch() except it does
 		not return a value.
@@ -307,163 +326,147 @@ export default class AnnoMatrix {
    ** The actual implementation is in the sub-classes, which MUST override these.
    **/
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  /*
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
+  Add a new category value (aka "label") to a writable obs column, and return the new AnnoMatrix.
-  addObsAnnoCategory(col, category) {
+  Typical use is to add a new user-created label to a user-created obs categorical
-    /*
+  annotation.
-    Add a new category value (aka "label") to a writable obs column, and return the new AnnoMatrix.
-    Typical use is to add a new user-created label to a user-created obs categorical
-    annotation.
 
-    Will throw column does not exist or is not writable.
+  Will throw column does not exist or is not writable.
 
-    Example:
+  Example:
 
-      addObsAnnoCategory("my cell type", "left toenail") -> AnnoMatrix
+    addObsAnnoCategory("my cell type", "left toenail") -> AnnoMatrix
+
+  */
+  abstract addObsAnnoCategory(col: LabelType, category: string): AnnoMatrix;
+
+  /*
+  Remove a category value from an obs column, reassign any obs having that value
+  to the 'unassignedCategory' value, and return a promise for a new AnnoMatrix.
+  Typical use is to remove a user-created label from a user-created obs categorical
+  annotation.
+
+  Will throw column does not exist or is not writable.
+
+  An `unassignedCategory` value must be provided, for assignment to any obs/cells
+  that had the now-delete category label as their value.
+
+  Example:
+    await removeObsAnnoCategory("my-tissue-type", "right earlobe", "unassigned") -> AnnoMatrix
+
+  NOTE: method is async as it may need to fetch data to provide the reassignment.
+  */
+  abstract removeObsAnnoCategory(
+    col: LabelType,
+    category: Category,
+    unassignedCategory: string
+  ): Promise<AnnoMatrix>;
+
+  /*
+  Drop an entire writable column, eg a user-created obs annotation.  Typical use
+  is to provide the "Delete Category" implementation.  Returns the new AnnoMatrix.
+  Will throw if not a writable annotation.
+
+  Will throw column does not exist or is not writable.
+
+  Example:
+
+    dropObsColumn("old annotations") ->  AnnoMatrix
+  */
+  abstract dropObsColumn(col: LabelType): AnnoMatrix;
+
+  /*
+  Add a new writable OBS annotation column, with the caller-specified schema, initial value
+  type and value.
+
+  Value may be any one of:
+    * an array of values
+    * a primitive type, including null or undefined.
+  If an array, length must be the same as 'this.nObs', and constructor must equal 'Ctor'.
+  If a primitive, 'Ctor' will be used to create the initial value, which will be filled
+  with 'value'.
+
+  Throws if the name specified in 'colSchema' duplicates an existing obs column.
+
+  Returns a new AnnoMatrix.
+
+  Examples:
+
+    addObsColumn(
+      { name: "foo", type: "categorical", categories: "unassigned" },
+      Array,
+      "unassigned"
+    ) -> AnnoMatrix
+
+   */
+  abstract addObsColumn<T extends DataframeValueArray>(
+    colSchema: AnnotationColumnSchema,
+    Ctor: new (n: number) => T,
+    value: T
+  ): AnnoMatrix;
+
+  /*
+  Rename the obs column 'oldCol' to have name 'newCol' and returns new AnnoMatrix.
+
+  Will throw column does not exist or is not writable, or if 'newCol' is not unique.
+
+  Example:
+
+    renameObsColumn('cell type', 'old cell type') -> AnnoMatrix.
+
+  */
+  abstract renameObsColumn(oldCol: LabelType, newCol: LabelType): AnnoMatrix;
+
+  /*
+  Set all obs with label in array 'obsLabels' to have 'value'.  Typical use would be
+  to set a group of cells to have a label on a user-created categorical annotation
+  (eg set all selected cells to have a label).
+  
+  NOTE: async method, as it may need to fetch.
+  
+  Will throw column does not exist or is not writable.
+  
+  Example:
+    await setObsColmnValues("flavor", [383, 400], "tasty") -> AnnoMtarix
+  */
+  abstract setObsColumnValues(
+    col: LabelType,
+    obsLabels: Int32Array,
+    value: DataframeValue
+  ): Promise<AnnoMatrix>;
+
+  /*
+  Set by value - all elements in the column with value 'oldValue' are set to 'newValue'.
+  Async method - returns a promise for a new AnnoMatrix.
+
+  Typical use would be to set all labels of one value to another.
+
+  Will throw column does not exist or is not writable.
+
+  Example:
+    await resetObsColumnValues("my notes", "good", "not-good") -> AnnoMatrix
 
     */
-    _subclassResponsibility();
+  abstract resetObsColumnValues<T extends DataframeValue>(
-  }
+    col: LabelType,
+    oldValue: T,
+    newValue: T
+  ): Promise<AnnoMatrix>;
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  /*
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
+  Add a new obs embedding to the AnnoMatrix, with provided schema.
-  async removeObsAnnoCategory(col, category, unassignedCategory) {
+  Returns a new annomatrix.
-    /*
-    Remove a category value from an obs column, reassign any obs having that value
-    to the 'unassignedCategory' value, and return a promise for a new AnnoMatrix.
-    Typical use is to remove a user-created label from a user-created obs categorical
-    annotation.
 
-    Will throw column does not exist or is not writable.
+  Typical use will be to add a re-embedding that the server has calculated.
 
-    An `unassignedCategory` value must be provided, for assignment to any obs/cells
+  Will throw if the column schema is invalid (eg, duplicate name).
-    that had the now-delete category label as their value.
+  */
+  abstract addEmbedding(colSchema: EmbeddingSchema): AnnoMatrix;
 
-    Example:
+  getCacheKeys(
-      await removeObsAnnoCategory("my-tissue-type", "right earlobe", "unassigned") -> AnnoMatrix
+    field: Field,
-
+    query: Query
-    NOTE: method is async as it may need to fetch data to provide the reassignment.
+  ): WhereCacheColumnLabels | [undefined] {
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
-  dropObsColumn(col) {
-    /*
-    Drop an entire writable column, eg a user-created obs annotation.  Typical use
-    is to provide the "Delete Category" implementation.  Returns the new AnnoMatrix.
-    Will throw if not a writable annotation.
-
-    Will throw column does not exist or is not writable.
-
-    Example:
-
-      dropObsColumn("old annotations") ->  AnnoMatrix
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
-  addObsColumn(colSchema, Ctor, value) {
-    /*
-    Add a new writable OBS annotation column, with the caller-specified schema, initial value
-    type and value.
-
-    Value may be any one of:
-      * an array of values
-      * a primitive type, including null or undefined.
-    If an array, length must be the same as 'this.nObs', and constructor must equal 'Ctor'.
-    If a primitive, 'Ctor' will be used to create the initial value, which will be filled
-    with 'value'.
-
-    Throws if the name specified in 'colSchema' duplicates an existing obs column.
-
-    Returns a new AnnoMatrix.
-
-    Examples:
-
-      addObsColumn(
-        { name: "foo", type: "categorical", categories: "unassigned" },
-        Array,
-        "unassigned"
-      ) -> AnnoMatrix
-
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(6133) FIXME: 'oldCol' is declared but its value is never read.
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
-  renameObsColumn(oldCol, newCol) {
-    /*
-    Rename the obs column 'oldCol' to have name 'newCol' and returns new AnnoMatrix.
-
-    Will throw column does not exist or is not writable, or if 'newCol' is not unique.
-
-    Example:
-
-      renameObsColumn('cell type', 'old cell type') -> AnnoMatrix.
-
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
-  async setObsColumnValues(col, obsLabels, value) {
-    /*
-    Set all obs with label in array 'obsLabels' to have 'value'.  Typical use would be
-    to set a group of cells to have a label on a user-created categorical anntoation
-    (eg set all selected cells to have a label).
-
-    NOTE: async method, as it may need to fetch.
-
-    Will throw column does not exist or is not writable.
-
-    Example:
-      await setObsColmnValues("flavor", [383, 400], "tasty") -> AnnoMtarix
-
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
-  async resetObsColumnValues(col, oldValue, newValue) {
-    /*
-    Set by value - all elements in the column with value 'oldValue' are set to 'newValue'.
-    Async method - returns a promise for a new AnnoMatrix.
-
-    Typical use would be to set all labels of one value to another.
-
-    Will throw column does not exist or is not writable.
-
-    Example:
-      await resetObsColumnValues("my notes", "good", "not-good") -> AnnoMatrix
-
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
-  addEmbedding(colSchema) {
-    /*
-    Add a new obs embedding to the AnnoMatrix, with provided schema.
-    Returns a new annomatrix.
-
-    Typical use will be to add a re-embedding that the server has calculated.
-
-    Will throw if the column schema is invalid (eg, duplicate name).
-    */
-    _subclassResponsibility();
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  getCacheKeys(field, query) {
     /*
 Return cache keys for columns associated with this query.  May return
 [unknown] if no keys are known (ie, nothing is or was cached).
@@ -474,26 +477,20 @@ Return cache keys for columns associated with this query.  May return
   /**
    ** Private interfaces below.
    **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  _resolveCachedQueries(field: Field, queries: Query[]): LabelArray {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    return queries
-  _resolveCachedQueries(field, queries) {
+      .map((query: Query) =>
-    return (
+        // @ts-expect-error --- TODO revisit:
-      queries
+        // `filter`: This expression is not callable.
-        // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'query' implicitly has an 'any' type.
+        _whereCacheGet(this._whereCache, this.schema, field, query).filter(
-        .map((query) =>
+          (cacheKey?: LabelType) =>
-          _whereCacheGet(this._whereCache, this.schema, field, query).filter(
+            cacheKey !== undefined && this._cache[field].hasCol(cacheKey)
-            // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type.
-            (cacheKey) =>
-              cacheKey !== undefined && this._cache[field].hasCol(cacheKey)
-          )
         )
-        .flat()
+      )
-    );
+      .flat();
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  async _fetch(field: Field, q: Query | Query[]): Promise<Dataframe> {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  async _fetch(field, q): Dataframe {
     if (!AnnoMatrix.fields().includes(field)) return Dataframe.empty();
     const queries = Array.isArray(q) ? q : [q];
     queries.forEach(_queryValidate);
@@ -505,8 +502,7 @@ Return cache keys for columns associated with this query.  May return
     /* find any query not already cached */
     const uncachedQueries = queries.filter((query) =>
       _whereCacheGet(this._whereCache, this.schema, field, query).some(
-        // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type.
+        (cacheKey?: LabelType) =>
-        (cacheKey) =>
           cacheKey === undefined || !this._cache[field].hasCol(cacheKey)
       )
     );
@@ -515,17 +511,19 @@ Return cache keys for columns associated with this query.  May return
     if (uncachedQueries.length > 0) {
       await Promise.all(
         uncachedQueries.map((query) =>
-          // @ts-expect-error ts-migrate(7006) FIXME: Parameter '_field' implicitly has an 'any' type.
+          this._getPendingLoad(
-          this._getPendingLoad(field, query, async (_field, _query) => {
+            field,
-            /* fetch, then index.  _doLoad is subclass interface */
+            query,
-            // @ts-expect-error ts-migrate(2488) FIXME: Type 'void' must have a '[Symbol.iterator]()' meth... Remove this comment to see the full error message
+            async (_field: Field, _query: Query): Promise<void> => {
-            const [whereCacheUpdate, df] = await this._doLoad(_field, _query);
+              /* fetch, then index.  _doLoad is subclass interface */
-            this._cache[_field] = this._cache[_field].withColsFrom(df);
+              const [whereCacheUpdate, df] = await this._doLoad(_field, _query);
-            this._whereCache = _whereCacheMerge(
+              this._cache[_field] = this._cache[_field].withColsFrom(df);
-              this._whereCache,
+              this._whereCache = _whereCacheMerge(
-              whereCacheUpdate
+                this._whereCache,
-            );
+                whereCacheUpdate
-          })
+              );
+            }
+          )
         )
       );
     }
@@ -539,9 +537,11 @@ Return cache keys for columns associated with this query.  May return
     return response;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  async _getPendingLoad(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    field: Field,
-  async _getPendingLoad(field, query, fetchFn) {
+    query: Query,
+    fetchFn: (_field: Field, _query: Query) => Promise<void>
+  ): Promise<void> {
     /*
     Given a query on a field, ensure that we only have a single outstanding
     fetch at any given time.  If multiple requests occur while a fetch is
@@ -562,9 +562,22 @@ Return cache keys for columns associated with this query.  May return
     return this._pendingLoad[field][key];
   }
 
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
+  abstract _doLoad(
-  async _doLoad() {
+    field: Field,
-    _subclassResponsibility();
+    query: Query
+  ): Promise<[WhereCache | null, Dataframe]>;
+
+  /**
+   * Determines viewOf for this annoMatrix.
+   *
+   * @internal
+   * @returns - parent annoMatrix if this annoMatrix is a view, otherwise this annoMatrix if it's not a view.
+   */
+  _getViewOf(): AnnoMatrix {
+    if (this.isView) {
+      return this.viewOf;
+    }
+    return this;
   }
 
   /**
@@ -596,23 +609,21 @@ Return cache keys for columns associated with this query.  May return
   To be effective, the GC callback needs to be invoked from the undo/redo code,
   as much of the cache is pinned by that data structure.
   */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  _gcField(field: Field, isHot: boolean, pinnedColumns: LabelArray): void {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _gcField(field, isHot, pinnedColumns) {
     const maxColumns = isHot ? 256 : 10;
     const cache = this._cache[field];
     if (cache.colIndex.size() < maxColumns) return; // trivial rejection
 
     const candidates = cache.colIndex
       .labels()
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+      // @ts-expect-error --- TODO revisit:
-      .filter((col) => !pinnedColumns.includes(col));
+      // `col`: Argument of type 'LabelType' is not assignable to parameter of type 'number'. Type 'string' is not assignable to type 'number'.
+      .filter((col: LabelType) => !pinnedColumns.includes(col));
 
     const excessCount = candidates.length + pinnedColumns.length - maxColumns;
     if (excessCount > 0) {
       const { _gcInfo } = this;
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'a' implicitly has an 'any' type.
+      candidates.sort((a: LabelType, b: LabelType) => {
-      candidates.sort((a, b) => {
         let atime = _gcInfo.get(_columnCacheKey(field, a));
         if (atime === undefined) atime = 0;
 
@@ -629,49 +640,49 @@ Return cache keys for columns associated with this query.  May return
       //     ", "
       //   )}]`
       // );
+      // @ts-expect-error --- TODO revisit:
+      // `reduce`: This expression is not callable.
       this._cache[field] = toDrop.reduce(
-        // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type.
+        (df: Dataframe, col: LabelType) => df.dropCol(col),
-        (df, col) => df.dropCol(col),
         this._cache[field]
       );
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+      toDrop.forEach((col: LabelType) =>
-      toDrop.forEach((col) => _gcInfo.delete(_columnCacheKey(field, col)));
+        _gcInfo.delete(_columnCacheKey(field, col))
+      );
     }
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  _gcFetchCleanup(field: Field, pinnedColumns: LabelArray): void {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _gcFetchCleanup(field, pinnedColumns) {
     /*
     Called during data load/fetch.  By definition, this is 'hot', so we
     only want to gc X.
     */
-    if (field === "X") {
+    if (field === Field.X) {
       this._gcField(
         field,
         true,
+        // @ts-expect-error --- TODO revisit:
+        // Property 'concat' does not exist on type 'LabelArray'.
         pinnedColumns.concat(_getWritableColumns(this.schema, field))
       );
     }
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'hints' implicitly has an 'any' type.
+  _gc(hints: GCHints): void {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _gc(hints) {
     /*
     Called from middleware, or elsewhere.  isHot is true if we are in the active store, 
     or false if we are in some other context (eg, history state).
     */
     const { isHot } = hints;
-    const candidateFields = isHot ? ["X"] : ["X", "emb", "var", "obs"];
+    const candidateFields = isHot
+      ? [Field.X]
+      : [Field.X, Field.emb, Field.var, Field.obs];
     candidateFields.forEach((field) =>
       this._gcField(field, isHot, _getWritableColumns(this.schema, field))
     );
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  _gcUpdateStats(field: Field, dataframe: Dataframe): void {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _gcUpdateStats(field, dataframe) {
     /*
     called each time a query is performed, allowing the gc to update any bookkeeping
     information.  Currently, this is just a simple last-fetched timestamp, stored
@@ -680,8 +691,7 @@ Return cache keys for columns associated with this query.  May return
     const cols = dataframe.colIndex.labels();
     const { _gcInfo } = this;
     const now = Date.now();
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'c' implicitly has an 'any' type.
+    cols.forEach((c: LabelType) => {
-    cols.forEach((c) => {
       _gcInfo.set(_columnCacheKey(field, c), now);
     });
   }
@@ -698,9 +708,7 @@ Return cache keys for columns associated with this query.  May return
 
   Do not override _clone();
   **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'clone' implicitly has an 'any' type.
+  _cloneDeeper(clone: AnnoMatrix): AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _cloneDeeper(clone) {
     clone._cache = _shallowClone(this._cache);
     clone._gcInfo = new Map();
     clone._pendingLoad = {
@@ -712,8 +720,7 @@ Return cache keys for columns associated with this query.  May return
     return clone;
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  _clone(): AnnoMatrix {
-  _clone() {
     const clone = _shallowClone(this);
     this._cloneDeeper(clone);
     Object.seal(clone);
@@ -724,12 +731,6 @@ Return cache keys for columns associated with this query.  May return
 /*
 private utility functions below
 */
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+function _columnCacheKey(field: Field, column: LabelType): string {
-function _columnCacheKey(field, column) {
   return `${field}/${column}`;
 }
-
-function _subclassResponsibility() {
-  /* protect against bugs in subclass */
-  throw new Error("subclass failed to implement required method");
-}

client/src/annoMatrix/clone.ts

@@ -1,7 +1,7 @@
 /*
 Shallow clone an object, correctly handling prototype
 */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+
-export default function _shallowClone(orig: any) {
+export default function _shallowClone<T>(orig: T): T {
   return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig);
 }

client/src/annoMatrix/crossfilter.ts

@@ -9,38 +9,58 @@ AnnoMatrix stay in sync:
 */
 import Crossfilter from "../util/typedCrossfilter";
 import { _getColumnSchema } from "./schema";
+import {
+  AnnotationColumnSchema,
+  Field,
+  EmbeddingSchema,
+} from "../common/types/schema";
+import AnnoMatrix from "./annoMatrix";
+import {
+  Dataframe,
+  DataframeValue,
+  DataframeValueArray,
+  LabelType,
+} from "../util/dataframe";
+import { Query } from "./query";
+import { TypedArray } from "../common/types/arraytypes";
+import { LabelArray } from "../util/dataframe/types";
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+type ObsDimensionParams =
-function _dimensionNameFromDf(field, df) {
+  | [string, DataframeValueArray, DataframeValueArray]
+  | [string, DataframeValueArray]
+  | [string, DataframeValueArray, Int32ArrayConstructor]
+  | [string, DataframeValueArray, Float32ArrayConstructor];
+
+function _dimensionNameFromDf(field: Field, df: Dataframe): string {
   const colNames = df.colIndex.labels();
   return _dimensionName(field, colNames);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+function _dimensionName(
-function _dimensionName(field, colNames) {
+  field: Field,
+  colNames: LabelType | LabelArray
+): string {
   if (!Array.isArray(colNames)) return `${field}/${colNames}`;
   return `${field}/${colNames.join(":")}`;
 }
 
 export default class AnnoMatrixObsCrossfilter {
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
+  annoMatrix: AnnoMatrix;
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+
-  constructor(annoMatrix, _obsCrossfilter = null) {
+  obsCrossfilter: Crossfilter;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+
-    (this as any).annoMatrix = annoMatrix;
+  constructor(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    annoMatrix: AnnoMatrix,
-    (this as any).obsCrossfilter =
+    _obsCrossfilter: Crossfilter | null = null
+  ) {
+    this.annoMatrix = annoMatrix;
+    this.obsCrossfilter =
       _obsCrossfilter || new Crossfilter(annoMatrix._cache.obs);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    this.obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
-    (this as any).obsCrossfilter = (this as any).obsCrossfilter.setData(
-      annoMatrix._cache.obs
-    );
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  size(): number {
-  size() {
+    return this.obsCrossfilter.size();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (this as any).obsCrossfilter.size();
   }
 
   /**
@@ -50,44 +70,33 @@ export default class AnnoMatrixObsCrossfilter {
 
   See API documentation in annoMatrix.js.
   **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
+  addObsColumn<T extends DataframeValueArray>(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    colSchema: AnnotationColumnSchema,
-  addObsColumn(colSchema, Ctor, value) {
+    Ctor: new (n: number) => T,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    value: T
-    const annoMatrix = (this as any).annoMatrix.addObsColumn(
+  ): AnnoMatrixObsCrossfilter {
-      colSchema,
+    const annoMatrix = this.annoMatrix.addObsColumn(colSchema, Ctor, value);
-      Ctor,
+    const obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
-      value
-    );
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const obsCrossfilter = (this as any).obsCrossfilter.setData(
-      annoMatrix._cache.obs
-    );
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  dropObsColumn(col: LabelType): AnnoMatrixObsCrossfilter {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    const annoMatrix = this.annoMatrix.dropObsColumn(col);
-  dropObsColumn(col) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.dropObsColumn(col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
-    const dimName = _dimensionName("obs", col);
+    const dimName = _dimensionName(Field.obs, col);
     if (obsCrossfilter.hasDimension(dimName)) {
       obsCrossfilter = obsCrossfilter.delDimension(dimName);
     }
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
+  renameObsColumn(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    oldCol: LabelType,
-  renameObsColumn(oldCol, newCol) {
+    newCol: LabelType
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  ): AnnoMatrixObsCrossfilter {
-    const annoMatrix = (this as any).annoMatrix.renameObsColumn(oldCol, newCol);
+    const annoMatrix = this.annoMatrix.renameObsColumn(oldCol, newCol);
-    const oldDimName = _dimensionName("obs", oldCol);
+    const oldDimName = _dimensionName(Field.obs, oldCol);
-    const newDimName = _dimensionName("obs", newCol);
+    const newDimName = _dimensionName(Field.obs, newCol);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
     if (obsCrossfilter.hasDimension(oldDimName)) {
       obsCrossfilter = obsCrossfilter.renameDimension(oldDimName, newDimName);
@@ -95,16 +104,12 @@ export default class AnnoMatrixObsCrossfilter {
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  addObsAnnoCategory(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-  addObsAnnoCategory(col, category) {
+    category: string
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  ): AnnoMatrixObsCrossfilter {
-    const annoMatrix = (this as any).annoMatrix.addObsAnnoCategory(
+    const annoMatrix = this.annoMatrix.addObsAnnoCategory(col, category);
-      col,
+    const dimName = _dimensionName(Field.obs, col);
-      category
-    );
-    const dimName = _dimensionName("obs", col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
     if (obsCrossfilter.hasDimension(dimName)) {
       obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -112,17 +117,17 @@ export default class AnnoMatrixObsCrossfilter {
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  async removeObsAnnoCategory(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-  async removeObsAnnoCategory(col, category, unassignedCategory) {
+    category: string,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    unassignedCategory: string
-    const annoMatrix = await (this as any).annoMatrix.removeObsAnnoCategory(
+  ): Promise<AnnoMatrixObsCrossfilter> {
+    const annoMatrix = await this.annoMatrix.removeObsAnnoCategory(
       col,
       category,
       unassignedCategory
     );
-    const dimName = _dimensionName("obs", col);
+    const dimName = _dimensionName(Field.obs, col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
     if (obsCrossfilter.hasDimension(dimName)) {
       obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -130,17 +135,17 @@ export default class AnnoMatrixObsCrossfilter {
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  async setObsColumnValues(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-  async setObsColumnValues(col, rowLabels, value) {
+    rowLabels: Int32Array,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    value: DataframeValue
-    const annoMatrix = await (this as any).annoMatrix.setObsColumnValues(
+  ): Promise<AnnoMatrixObsCrossfilter> {
+    const annoMatrix = await this.annoMatrix.setObsColumnValues(
       col,
       rowLabels,
       value
     );
-    const dimName = _dimensionName("obs", col);
+    const dimName = _dimensionName(Field.obs, col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
     if (obsCrossfilter.hasDimension(dimName)) {
       obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -148,17 +153,17 @@ export default class AnnoMatrixObsCrossfilter {
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  async resetObsColumnValues<T extends DataframeValue>(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-  async resetObsColumnValues(col, oldValue, newValue) {
+    oldValue: T,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newValue: T
-    const annoMatrix = await (this as any).annoMatrix.resetObsColumnValues(
+  ): Promise<AnnoMatrixObsCrossfilter> {
+    const annoMatrix = await this.annoMatrix.resetObsColumnValues(
       col,
       oldValue,
       newValue
     );
-    const dimName = _dimensionName("obs", col);
+    const dimName = _dimensionName(Field.obs, col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
     if (obsCrossfilter.hasDimension(dimName)) {
       obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -166,35 +171,25 @@ export default class AnnoMatrixObsCrossfilter {
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
+  addEmbedding(colSchema: EmbeddingSchema): AnnoMatrixObsCrossfilter {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    const annoMatrix = this.annoMatrix.addEmbedding(colSchema);
-  addEmbedding(colSchema) {
+    return new AnnoMatrixObsCrossfilter(annoMatrix, this.obsCrossfilter);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.addEmbedding(colSchema);
-    return new AnnoMatrixObsCrossfilter(
-      annoMatrix,
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter
-    );
   }
 
   /**
    * Drop the crossfilter dimension. Do not change the annoMatrix. Useful when we
-   * want to stop trackin the selection state, but aren't sure we want to blow the
+   * want to stop tracking the selection state, but aren't sure we want to blow the
    * annomatrix cache.
    */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  dropDimension(field: Field, query: Query): AnnoMatrixObsCrossfilter {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  dropDimension(field, query) {
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
     const { annoMatrix } = this;
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
     const keys = annoMatrix
       .getCacheKeys(field, query)
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'k' implicitly has an 'any' type.
+      // @ts-expect-error ts-migrate --- suppressing TS defect (https://github.com/microsoft/TypeScript/issues/44373).
-      .filter((k) => k !== undefined);
+      // Compiler is complaining that expression is not callable on array union types. Remove suppression once fixed.
-    const dimName = _dimensionName(field, keys);
+      .filter((k?: string | number) => k !== undefined);
+    const dimName = _dimensionName(field, keys as string[]);
     if (obsCrossfilter.hasDimension(dimName)) {
       obsCrossfilter = obsCrossfilter.delDimension(dimName);
     }
@@ -206,12 +201,13 @@ export default class AnnoMatrixObsCrossfilter {
   are just wrappers to lazy create indices.
   **/
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  async select(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    field: Field,
-  async select(field, query, spec) {
+    query: Query,
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
+    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- TODO revisit: waiting for typings from util/typedCrossfilter
+    spec: any
+  ): Promise<AnnoMatrixObsCrossfilter> {
     const { annoMatrix } = this;
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
     let { obsCrossfilter } = this;
 
     if (!annoMatrix?._cache?.[field]) {
@@ -223,7 +219,9 @@ export default class AnnoMatrixObsCrossfilter {
 
     // grab the data, so we can grab the index.
     const df = await annoMatrix.fetch(field, query);
-
+    if (!df) {
+      throw new Error("Dataframe cannot be `undefined`");
+    }
     const dimName = _dimensionNameFromDf(field, df);
     if (!obsCrossfilter.hasDimension(dimName)) {
       // lazy index generation - add dimension when first used
@@ -240,86 +238,66 @@ export default class AnnoMatrixObsCrossfilter {
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  selectAll(): AnnoMatrixObsCrossfilter {
-  selectAll() {
     /*
 		Select all on any dimension in this field.
 		*/
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
     const { annoMatrix } = this;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const currentDims = this.obsCrossfilter.dimensionNames();
-    const currentDims = (this as any).obsCrossfilter.dimensionNames();
     const obsCrossfilter = currentDims.reduce(
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'xfltr' implicitly has an 'any' type.
       (xfltr, dim) => xfltr.select(dim, { mode: "all" }),
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      this.obsCrossfilter
-      (this as any).obsCrossfilter
+    );
-    ); // eslint-disable-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
     return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  countSelected(): number {
-  countSelected() {
     /* if no data yet indexed in the crossfilter, just say everything is selected */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    if (this.obsCrossfilter.size() === 0) return this.annoMatrix.nObs;
-    if ((this as any).obsCrossfilter.size() === 0)
+    return this.obsCrossfilter.countSelected();
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      return (this as any).annoMatrix.nObs;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (this as any).obsCrossfilter.countSelected();
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  allSelectedMask(): Uint8Array {
-  allSelectedMask() {
     /* if no data yet indexed in the crossfilter, just say everything is selected */
     if (
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      this.obsCrossfilter.size() === 0 ||
-      (this as any).obsCrossfilter.size() === 0 ||
+      this.obsCrossfilter.dimensionNames().length === 0
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.dimensionNames().length === 0
     ) {
       /* fake the mask */
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      return new Uint8Array(this.annoMatrix.nObs).fill(1);
-      return new Uint8Array((this as any).annoMatrix.nObs).fill(1);
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    return this.obsCrossfilter.allSelectedMask();
-    return (this as any).obsCrossfilter.allSelectedMask();
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  allSelectedLabels(): LabelArray {
-  allSelectedLabels() {
     /* if no data yet indexed in the crossfilter, just say everything is selected */
     if (
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      this.obsCrossfilter.size() === 0 ||
-      (this as any).obsCrossfilter.size() === 0 ||
+      this.obsCrossfilter.dimensionNames().length === 0
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.dimensionNames().length === 0
     ) {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      return this.annoMatrix.rowIndex.labels();
-      return (this as any).annoMatrix.rowIndex.labels();
     }
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const mask = this.obsCrossfilter.allSelectedMask();
-    const mask = (this as any).obsCrossfilter.allSelectedMask();
+    const index = this.annoMatrix.rowIndex.isubsetMask(mask);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const index = (this as any).annoMatrix.rowIndex.isubsetMask(mask);
     return index.labels();
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'array' implicitly has an 'any' type.
+  fillByIsSelected<A extends TypedArray>(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    array: A,
-  fillByIsSelected(array, selectedValue, deselectedValue) {
+    selectedValue: A[0],
+    deselectedValue: A[0]
+  ): A {
     /* if no data yet indexed in the crossfilter, just say everything is selected */
     if (
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      this.obsCrossfilter.size() === 0 ||
-      (this as any).obsCrossfilter.size() === 0 ||
+      this.obsCrossfilter.dimensionNames().length === 0
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.dimensionNames().length === 0
     ) {
+      // @ts-expect-error ts-migrate --- TODO revisit:
+      // Type 'Int8Array | Uint8Array | Int16Array | Uint16Array | Int32Array | Uint32Array | Float32Array | Float64Array' is not assignable to type 'A'...
       return array.fill(selectedValue);
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    return this.obsCrossfilter.fillByIsSelected(
-    return (this as any).obsCrossfilter.fillByIsSelected(
       array,
       selectedValue,
       deselectedValue
@@ -330,37 +308,35 @@ export default class AnnoMatrixObsCrossfilter {
    ** Private below
    **/
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
+  _addObsCrossfilterDimension(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    annoMatrix: AnnoMatrix,
-  _addObsCrossfilterDimension(annoMatrix, obsCrossfilter, field, df) {
+    obsCrossfilter: Crossfilter,
+    field: Field,
+    df: Dataframe
+  ): Crossfilter {
     if (field === "var") return obsCrossfilter;
     const dimName = _dimensionNameFromDf(field, df);
     const dimParams = this._getObsDimensionParams(field, df);
     obsCrossfilter = obsCrossfilter.setData(annoMatrix._cache.obs);
-    // @ts-expect-error ts-migrate(2488) FIXME: Type 'any[] | undefined' must have a '[Symbol.iter... Remove this comment to see the full error message
+    // @ts-expect-error ts-migrate --- TODO revisit:
+    // `...dimParams`: A spread argument must either have a tuple type or be passed to a rest parameter.
     obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams);
     return obsCrossfilter;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  _getColumnBaseType(field: Field, col: LabelType): string {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _getColumnBaseType(field, col) {
     /* Look up the primitive type for this field/col */
-    const colSchema = _getColumnSchema(
+    const colSchema = _getColumnSchema(this.annoMatrix.schema, field, col);
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).annoMatrix.schema,
-      field,
-      col
-    );
     return colSchema.type;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+  _getObsDimensionParams(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    field: Field,
-  _getObsDimensionParams(field, df) {
+    df: Dataframe
+  ): ObsDimensionParams | undefined {
     /* return the crossfilter dimensiontype type and params for this field/dataframe */
 
-    if (field === "emb") {
+    if (field === Field.emb) {
       /* assumed to be 2D */
       return ["spatial", df.icol(0).asArray(), df.icol(1).asArray()];
     }
@@ -368,6 +344,8 @@ export default class AnnoMatrixObsCrossfilter {
     /* assumed to be 1D */
     const col = df.icol(0);
     const colName = df.colIndex.getLabel(0);
+    // @ts-expect-error --- TODO revisit:
+    // `colName` Argument of type 'LabelType | undefined' is not assignable to parameter of type 'LabelType'. Type 'undefined' is not assignable to type 'LabelType'.
     const type = this._getColumnBaseType(field, colName);
     if (type === "string" || type === "categorical" || type === "boolean") {
       return ["enum", col.asArray()];

client/src/annoMatrix/fetchHelpers.ts

@@ -1,8 +1,7 @@
 export { doBinaryRequest, doFetch } from "../util/actionHelpers";
 
 /* double URI encode - needed for query-param filters */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _dubEncURIComp(s: string | number | boolean): string {
-export function _dubEncURIComp(s: any) {
   return encodeURIComponent(encodeURIComponent(s));
 }
 

client/src/annoMatrix/loader.ts

@@ -2,33 +2,46 @@ import { doBinaryRequest, doFetch } from "./fetchHelpers";
 import { matrixFBSToDataframe } from "../util/stateManager/matrix";
 import { _getColumnSchema } from "./schema";
 import {
-  addObsAnnoColumn,
-  removeObsAnnoColumn,
   addObsAnnoCategory,
-  removeObsAnnoCategory,
+  addObsAnnoColumn,
   addObsLayout,
+  removeObsAnnoCategory,
+  removeObsAnnoColumn,
 } from "../util/stateManager/schemaHelpers";
 import { isAnyArray } from "../common/types/arraytypes";
-import { _whereCacheCreate } from "./whereCache";
+import { _whereCacheCreate, WhereCache } from "./whereCache";
 import AnnoMatrix from "./annoMatrix";
 import PromiseLimit from "../util/promiseLimit";
 import {
-  _expectSimpleQuery,
   _expectComplexQuery,
-  _urlEncodeLabelQuery,
+  _expectSimpleQuery,
-  _urlEncodeComplexQuery,
   _hashStringValues,
+  _urlEncodeComplexQuery,
+  _urlEncodeLabelQuery,
+  ComplexQuery,
+  Query,
 } from "./query";
 import {
   normalizeResponse,
   normalizeWritableCategoricalSchema,
 } from "./normalize";
+import {
+  AnnotationColumnSchema,
+  Field,
+  EmbeddingSchema,
+  RawSchema,
+} from "../common/types/schema";
+import {
+  Dataframe,
+  DataframeValue,
+  DataframeValueArray,
+  LabelType,
+} from "../util/dataframe";
 
 const promiseThrottle = new PromiseLimit(5);
 
 export default class AnnoMatrixLoader extends AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  baseURL: string;
-  baseURL: any;
 
   /*
   AnnoMatrix implementation which proxies to HTTP server using the CXG REST API.
@@ -40,8 +53,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     new AnnoMatrixLoader(serverBaseURL, schema) -> instance
 
   */
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  constructor(baseURL: string, schema: RawSchema) {
-  constructor(baseURL: any, schema: any) {
     const { nObs, nVar } = schema.dataframe;
     super(schema, nObs, nVar);
 
@@ -56,33 +68,36 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
   /**
    ** Public.  API described in base class.
    **/
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  addObsAnnoCategory(col: LabelType, category: string): AnnoMatrix {
-  addObsAnnoCategory(col: any, category: any) {
     /*
     Add a new category (aka label) to the schema for an obs column.
     */
-    const colSchema = _getColumnSchema(this.schema, "obs", col);
+    const colSchema = _getColumnSchema(
-    _writableCategoryTypeCheck(colSchema); // throws on error
+      this.schema,
+      Field.obs,
+      col
+    ) as AnnotationColumnSchema;
+    _writableObsCategoryTypeCheck(colSchema); // throws on error
 
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, category);
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async removeObsAnnoCategory(
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-    col: any,
+    category: string,
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+    unassignedCategory: string
-    category: any,
+  ): Promise<AnnoMatrix> {
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    unassignedCategory: any
-  ) {
     /*
     Remove a single "category" (aka "label") from the data & schema of an obs column.
     */
-    const colSchema = _getColumnSchema(this.schema, "obs", col);
+    const colSchema = _getColumnSchema(
-    _writableCategoryTypeCheck(colSchema); // throws on error
+      this.schema,
+      Field.obs,
+      col
+    ) as AnnotationColumnSchema;
+    _writableObsCategoryTypeCheck(colSchema); // throws on error
 
     const newAnnoMatrix = await this.resetObsColumnValues(
       col,
@@ -97,24 +112,28 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  dropObsColumn(col: LabelType): AnnoMatrix {
-  dropObsColumn(col: any) {
     /*
 		drop column from field
 		*/
-    const colSchema = _getColumnSchema(this.schema, "obs", col);
+    const colSchema = _getColumnSchema(
-    _writableCheck(colSchema); // throws on error
+      this.schema,
+      Field.obs,
+      col
+    ) as AnnotationColumnSchema;
+    _writableObsCheck(colSchema); // throws on error
 
     const newAnnoMatrix = this._clone();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.dropCol(col);
     newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col);
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
+  addObsColumn<T extends DataframeValueArray>(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    colSchema: AnnotationColumnSchema,
-  addObsColumn(colSchema, Ctor, value) {
+    Ctor: new (n: number) => T,
+    value: T
+  ): AnnoMatrix {
     /*
 		add a column to field, initializing with value.  Value may 
     be one of:
@@ -125,9 +144,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     colSchema.writable = true;
     const colName = colSchema.name;
     if (
-      _getColumnSchema(this.schema, "obs", colName) ||
+      _getColumnSchema(this.schema, Field.obs, colName) ||
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      this._cache.obs.hasCol(colName)
-      (this as any)._cache.obs.hasCol(colName)
     ) {
       throw new Error("column already exists");
     }
@@ -143,8 +161,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     } else {
       data = new Ctor(this.nObs).fill(value);
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.withCol(colName, data);
     normalizeWritableCategoricalSchema(
       colSchema,
       newAnnoMatrix._cache.obs.col(colName)
@@ -153,47 +170,55 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
+  renameObsColumn(oldCol: LabelType, newCol: LabelType): AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  renameObsColumn(oldCol, newCol) {
     /*
     Rename the obs oldColName to newColName.  oldCol must be writable.
     */
-    const oldColSchema = _getColumnSchema(this.schema, "obs", oldCol);
+    const oldColSchema = _getColumnSchema(
-    _writableCheck(oldColSchema);
+      this.schema,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      Field.obs,
-    const value = (this as any)._cache.obs.hasCol(oldCol)
+      oldCol
-      ? // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    ) as AnnotationColumnSchema;
-        (this as any)._cache.obs.col(oldCol).asArray()
+    _writableObsCheck(oldColSchema);
+    const value = this._cache.obs.hasCol(oldCol)
+      ? this._cache.obs.col(oldCol).asArray()
       : undefined;
     return this.dropObsColumn(oldCol).addObsColumn(
       {
         ...oldColSchema,
+        // @ts-expect-error ts-migrate --- TODO revisit:
+        // `name`: Type 'LabelType' is not assignable to type 'string'. Type 'number' is not assignable to type 'string'.
         name: newCol,
       },
+      // @ts-expect-error ts-migrate --- TODO revisit:
+      // `value`: Object is possibly 'undefined'.
       value.constructor,
       value
     );
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  async setObsColumnValues(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-  async setObsColumnValues(col, rowLabels, value) {
+    rowLabels: Int32Array,
+    value: DataframeValue
+  ): Promise<AnnoMatrix> {
     /*
 		Set all rows identified by rowLabels to value.
 		*/
-    const colSchema = _getColumnSchema(this.schema, "obs", col);
+    const colSchema = _getColumnSchema(
-    _writableCategoryTypeCheck(colSchema); // throws on error
+      this.schema,
+      Field.obs,
+      col
+    ) as AnnotationColumnSchema;
+    _writableObsCategoryTypeCheck(colSchema); // throws on error
 
     // ensure that we have the data in cache before we manipulate it
-    await this.fetch("obs", col);
+    await this.fetch(Field.obs, col);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    if (!this._cache.obs.hasCol(col))
-    if (!(this as any)._cache.obs.hasCol(col))
       throw new Error("Internal error - user annotation data missing");
 
     const rowIndices = this.rowIndex.getOffsets(rowLabels);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const data = this._cache.obs.col(col).asArray().slice();
-    const data = (this as any)._cache.obs.col(col).asArray().slice();
     for (let i = 0, len = rowIndices.length; i < len; i += 1) {
       const idx = rowIndices[i];
       if (idx === -1) throw new Error("Unknown row label");
@@ -201,11 +226,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     }
 
     const newAnnoMatrix = this._clone();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
-      col,
-      data
-    );
     const { categories } = colSchema;
     if (!categories?.includes(value)) {
       newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, value);
@@ -213,37 +234,39 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
+  async resetObsColumnValues<T extends DataframeValue>(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-  async resetObsColumnValues(col, oldValue, newValue) {
+    oldValue: T,
+    newValue: T
+  ): Promise<AnnoMatrix> {
     /*
     Set all rows with value 'oldValue' to 'newValue'.
     */
-    const colSchema = _getColumnSchema(this.schema, "obs", col);
+    const colSchema = _getColumnSchema(
-    _writableCategoryTypeCheck(colSchema); // throws on error
+      this.schema,
+      Field.obs,
+      col
+    ) as AnnotationColumnSchema;
+    _writableObsCategoryTypeCheck(colSchema); // throws on error
 
+    // @ts-expect-error ts-migrate --- TODO revisit:
+    // `colSchema.categories`: Object is possibly 'undefined'.
     if (!colSchema.categories.includes(oldValue)) {
       throw new Error("unknown category");
     }
 
     // ensure that we have the data in cache before we manipulate it
-    await this.fetch("obs", col);
+    await this.fetch(Field.obs, col);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    if (!this._cache.obs.hasCol(col))
-    if (!(this as any)._cache.obs.hasCol(col))
       throw new Error("Internal error - user annotation data missing");
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const data = this._cache.obs.col(col).asArray().slice();
-    const data = (this as any)._cache.obs.col(col).asArray().slice();
     for (let i = 0, l = data.length; i < l; i += 1) {
       if (data[i] === oldValue) data[i] = newValue;
     }
 
     const newAnnoMatrix = this._clone();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
-      col,
-      data
-    );
     const { categories } = colSchema;
     if (!categories?.includes(newValue)) {
       newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, newValue);
@@ -251,14 +274,12 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
+  addEmbedding(colSchema: EmbeddingSchema): AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  addEmbedding(colSchema) {
     /*
     add new layout to the obs embeddings
     */
     const { name: colName } = colSchema;
-    if (_getColumnSchema(this.schema, "emb", colName)) {
+    if (_getColumnSchema(this.schema, Field.emb, colName)) {
       throw new Error("column already exists");
     }
 
@@ -270,9 +291,10 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
   /**
    ** Private below
    **/
-  // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixLoader' is n... Remove this comment to see the full error message
+  async _doLoad(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    field: Field,
-  async _doLoad(field, query) {
+    query: Query
+  ): Promise<[WhereCache | null, Dataframe]> {
     /*
     _doLoad - evaluates the query against the field. Returns:
       * whereCache update: column query map mapping the query to the column labels
@@ -300,7 +322,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
         throw new Error("Unknown field name");
     }
     const buffer = await promiseThrottle.priorityAdd(priority, doRequest);
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'unknown' is not assignable to parameter of type 'ArrayBuffer | ArrayBuffer[]'.... Remove this comment to see the full error message
+    // @ts-expect-error --- TODO revisit:
+    // `buffer`:  Argument of type 'unknown' is not assignable to parameter of type 'ArrayBuffer | ArrayBuffer[]'. Type 'unknown' is not assignable to type 'ArrayBuffer[]'.
     let result = matrixFBSToDataframe(buffer);
     if (!result || result.isEmpty()) throw Error("Unknown field/col");
 
@@ -320,23 +343,26 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
 Utility functions below
 */
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
+function _writableObsCheck(obsColSchema: AnnotationColumnSchema): void {
-function _writableCheck(colSchema) {
+  if (!obsColSchema?.writable) {
-  if (!colSchema?.writable) {
     throw new Error("Unknown or readonly obs column");
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
+function _writableObsCategoryTypeCheck(
-function _writableCategoryTypeCheck(colSchema) {
+  obsColSchema: AnnotationColumnSchema
-  _writableCheck(colSchema);
+): void {
-  if (colSchema.type !== "categorical") {
+  _writableObsCheck(obsColSchema);
+  if (obsColSchema.type !== "categorical") {
     throw new Error("column must be categorical");
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
+function _embLoader(
-function _embLoader(baseURL, _field, query) {
+  baseURL: string,
+  _field: Field,
+  query: Query
+): () => Promise<ArrayBuffer> {
   _expectSimpleQuery(query);
 
   const urlBase = `${baseURL}layout/obs`;
@@ -345,8 +371,11 @@ function _embLoader(baseURL, _field, query) {
   return () => doBinaryRequest(url);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
+function _obsOrVarLoader(
-function _obsOrVarLoader(baseURL, field, query) {
+  baseURL: string,
+  field: Field,
+  query: Query
+): () => Promise<ArrayBuffer> {
   _expectSimpleQuery(query);
 
   const urlBase = `${baseURL}annotations/${field}`;
@@ -355,20 +384,26 @@ function _obsOrVarLoader(baseURL, field, query) {
   return () => doBinaryRequest(url);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
+function _XLoader(
-function _XLoader(baseURL, field, query) {
+  baseURL: string,
+  _field: Field,
+  query: Query
+): () => Promise<ArrayBuffer> {
   _expectComplexQuery(query);
 
-  if (query.where) {
+  // Casting here as query is validated to be complex in _expectComplexQuery above.
+  const complexQuery = query as ComplexQuery;
+
+  if ("where" in complexQuery) {
     const urlBase = `${baseURL}data/var`;
-    const urlQuery = _urlEncodeComplexQuery(query);
+    const urlQuery = _urlEncodeComplexQuery(complexQuery);
     const url = `${urlBase}?${urlQuery}`;
     return () => doBinaryRequest(url);
   }
 
-  if (query.summarize) {
+  if ("summarize" in complexQuery) {
     const urlBase = `${baseURL}summarize/var`;
-    const urlQuery = _urlEncodeComplexQuery(query);
+    const urlQuery = _urlEncodeComplexQuery(complexQuery);
 
     if (urlBase.length + urlQuery.length < 2000) {
       const url = `${urlBase}?${urlQuery}`;

client/src/annoMatrix/middleware.ts

@@ -11,17 +11,24 @@ Undoable metareducer and the AnnoMatrix private API.  It would be helpful
 to make the Undoable interface better factored.
 */
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+import { Action, Dispatch, MiddlewareAPI } from "redux";
-const annoMatrixGC = (store: any) => (next: any) => (action: any) => {
+import AnnoMatrix from "./annoMatrix";
-  if (_itIsTimeForGC()) {
+import { GCHints } from "../common/types/entities";
-    _doGC(store);
+
-  }
+const annoMatrixGC =
-  return next(action);
+  (store: MiddlewareAPI) =>
-};
+  // GC middleware doesn't add any extra types to dispatch; it just executes GC and continues.
+  (next: Dispatch) =>
+  (action: Action): Action => {
+    if (_itIsTimeForGC()) {
+      _doGC(store);
+    }
+    return next(action);
+  };
 
 let lastGCTime = 0;
 const InterGCDelayMS = 30 * 1000; // 30 seconds
-function _itIsTimeForGC() {
+function _itIsTimeForGC(): boolean {
   /*
   we don't want to run GC on every dispatch, so throttle it a bit.
 
@@ -35,20 +42,22 @@ function _itIsTimeForGC() {
   return false;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _doGC(store: MiddlewareAPI): void {
-function _doGC(store: any) {
   const state = store.getState();
 
   // these should probably be a function imported from undoable.js, etc, as
-  // they have overly intimiate knowledge of our reducers.
+  // they have overly intimate knowledge of our reducers.
   const undoablePast = state["@@undoable/past"];
   const undoableFuture = state["@@undoable/future"];
   const undoableStack = undoablePast
     .concat(undoableFuture)
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- TODO revisit: waiting for typings from /reducers
     .flatMap((snapshot: any) =>
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      snapshot
-      snapshot.filter((v: any) => v[0] === "annoMatrix").map((v: any) => v[1])
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- TODO revisit: waiting for typings from /reducers
+        .filter((v: any) => v[0] === "annoMatrix")
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- TODO revisit: waiting for typings from /reducers
+        .map((v: any) => v[1])
     );
   const currentAnnoMatrix = state.annoMatrix;
 
@@ -56,18 +65,16 @@ function _doGC(store: any) {
   We want to identify those matrixes currently "hot", ie, linked from the current annoMatrix,
   as our current gc algo is more aggressive with those not hot.
   */
-  const allAnnoMatrices = new Map(
+  const allAnnoMatrices = new Map<AnnoMatrix, GCHints>(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    undoableStack.map((m: AnnoMatrix) => [m, { isHot: false }])
-    undoableStack.map((m: any) => [m, { isHot: false }])
   );
   let am = currentAnnoMatrix;
-  while (am) {
+  while (am?.isView) {
     allAnnoMatrices.set(am, { isHot: true });
     am = am.viewOf;
   }
-  allAnnoMatrices.forEach((hints, annoMatrix) =>
+  allAnnoMatrices.forEach((hints, annoMatrix: AnnoMatrix) =>
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    annoMatrix._gc(hints)
-    (annoMatrix as any)._gc(hints)
   );
 }
 

client/src/annoMatrix/normalize.ts

@@ -1,4 +1,3 @@
-import { Schema } from "../common/types/schema";
 import { _getColumnSchema, _isIndex } from "./schema";
 import catLabelSort from "../util/catLabelSort";
 import {
@@ -7,9 +6,15 @@ import {
   globalConfig,
 } from "../globals";
 import { Dataframe, LabelType, DataframeColumn } from "../util/dataframe";
+import {
+  AnnotationColumnSchema,
+  ArraySchema,
+  Field,
+  Schema,
+} from "../common/types/schema";
 
 export function normalizeResponse(
-  field: string,
+  field: Field,
   schema: Schema,
   response: Dataframe
 ): Dataframe {
@@ -37,11 +42,15 @@ export function normalizeResponse(
    */
 
   // currently no data or schema normalization necessary for X or emb
-  if (field !== "obs" && field !== "var") return response;
+  if (field !== Field.obs && field !== Field.var) return response;
 
   const colLabels = response.colIndex.labels();
   for (const colLabel of colLabels) {
-    const colSchema = _getColumnSchema(schema, field, colLabel);
+    const colSchema = _getColumnSchema(
+      schema,
+      field,
+      colLabel
+    ) as AnnotationColumnSchema;
     const isIndex = _isIndex(schema, field, colLabel);
     const { type, writable } = colSchema;
 
@@ -73,11 +82,10 @@ function castColumnToBoolean(df: Dataframe, label: LabelType): Dataframe {
   return df;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
 export function normalizeWritableCategoricalSchema(
-  colSchema: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  colSchema: AnnotationColumnSchema, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
   col: DataframeColumn
-) {
+): ArraySchema {
   /*
   Ensure all enum writable / categorical schema have a categories array, that
   the categories array contains all unique values in the data array, AND that
@@ -96,7 +104,7 @@ export function normalizeWritableCategoricalSchema(
 export function normalizeCategorical(
   df: Dataframe,
   colLabel: LabelType,
-  colSchema: any // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  colSchema: AnnotationColumnSchema
 ): Dataframe {
   /*
   If writable, ensure schema matches data and we have an unassigned label
@@ -106,7 +114,6 @@ export function normalizeCategorical(
   */
   const { writable } = colSchema;
   const col = df.col(colLabel);
-
   if (writable) {
     // writable (aka user) annotations
     normalizeWritableCategoricalSchema(colSchema, col);

client/src/annoMatrix/query.ts

@@ -1,22 +1,52 @@
 import sha1 from "sha1";
 import { _dubEncURIComp } from "./fetchHelpers";
+import { Field } from "../common/types/schema";
+import { LabelType } from "../util/dataframe";
 
 /**
  * Query utilities, mostly for debugging support and validation.
  */
 
+export type ComplexQuery = SummarizeQuery | WhereQuery;
+
+export type Query = LabelType | ComplexQuery;
+
+interface SummarizeQuery {
+  summarize: SummarizeQueryTerm;
+}
+
+interface SummarizeQueryTerm {
+  column: string;
+  field: string;
+  method: string;
+  values: string[];
+}
+
+interface WhereQuery {
+  where: WhereQueryTerm;
+}
+
+interface WhereQueryTerm {
+  column: string;
+  field: string;
+  value: string;
+}
+
+export function _expectSimpleQuery(query: Query): void {
+  if (typeof query === "object") throw new Error("expected simple query");
+}
+
 /**
  * Normalize & error check the query.
- * @param {object | string} query - the query
+ * @param {Query} query - the query
- * @returns {object | string} - the normalized query
+ * @returns {Query} - the normalized query
  */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _queryValidate(query: Query): Query {
-export function _queryValidate(query: any) {
   if (typeof query !== "object") return query;
 
-  if (query.where && query.summarize)
+  if ("where" in query && "summarize" in query)
     throw new Error("query may not specify both where and summarize");
-  if (query.where) {
+  if ("where" in query) {
     const {
       field: queryField,
       column: queryColumn,
@@ -26,7 +56,7 @@ export function _queryValidate(query: any) {
       throw new Error("Incomplete where query");
     return query;
   }
-  if (query.summarize) {
+  if ("summarize" in query) {
     const {
       field: queryField,
       column: queryColumn,
@@ -41,13 +71,7 @@ export function _queryValidate(query: any) {
   throw new Error("query must specify one of where or summarize");
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _expectComplexQuery(query: Query): void {
-export function _expectSimpleQuery(query: any) {
-  if (typeof query === "object") throw new Error("expected simple query");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function _expectComplexQuery(query: any) {
   if (typeof query !== "object") throw new Error("expected complex query");
 }
 
@@ -56,13 +80,12 @@ export function _expectComplexQuery(query: any) {
  *
  * @param {string} field
  * @param {string|object} query
- * @returns the key
+ * @returns {string} the key
  */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _queryCacheKey(field: Field, query: Query): string {
-export function _queryCacheKey(field: any, query: any) {
   if (typeof query === "object") {
     // complex query
-    if (query.where) {
+    if ("where" in query) {
       const {
         field: queryField,
         column: queryColumn,
@@ -70,7 +93,7 @@ export function _queryCacheKey(field: any, query: any) {
       } = query.where;
       return `${field}/${queryField}/${queryColumn}/${queryValue}`;
     }
-    if (query.summarize) {
+    if ("summarize" in query) {
       const {
         method,
         field: queryField,
@@ -88,38 +111,34 @@ export function _queryCacheKey(field: any, query: any) {
   return `${field}/${query}`;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _urlEncodeWhereQuery(q: WhereQueryTerm): string {
-function _urlEncodeWhereQuery(q: any) {
   const { field: queryField, column: queryColumn, value: queryValue } = q;
   return `${_dubEncURIComp(queryField)}:${_dubEncURIComp(
     queryColumn
   )}=${_dubEncURIComp(queryValue)}`;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _urlEncodeSummarizeQuery(q: SummarizeQueryTerm): string {
-function _urlEncodeSummarizeQuery(q: any) {
   const { method, field, column, values } = q;
-  const filter = values // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  const filter = values
-    .map((value: any) => _urlEncodeWhereQuery({ field, column, value }))
+    .map((value: string) => _urlEncodeWhereQuery({ field, column, value }))
     .join("&");
   return `method=${method}&${filter}`;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _urlEncodeComplexQuery(q: ComplexQuery): string {
-export function _urlEncodeComplexQuery(q: any) {
   if (typeof q === "object") {
-    if (q.where) {
+    if ("where" in q) {
       return _urlEncodeWhereQuery(q.where);
     }
-    if (q.summarize) {
+    if ("summarize" in q) {
       return _urlEncodeSummarizeQuery(q.summarize);
     }
   }
   throw new Error("Unrecognized complex query type");
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _urlEncodeLabelQuery(colKey: string, q: Query): string {
-export function _urlEncodeLabelQuery(colKey: any, q: any) {
   if (!colKey) throw new Error("Unsupported query by name");
   if (typeof q !== "string") throw new Error("Query must be a simple label.");
   return `${colKey}=${encodeURIComponent(q)}`;
@@ -128,8 +147,6 @@ export function _urlEncodeLabelQuery(colKey: any, q: any) {
 /**
  * Generate the column key the server will send us for this query.
  */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _hashStringValues(arrayOfString: string[]): string {
-export function _hashStringValues(arrayOfString: any) {
+  return sha1(arrayOfString.join(""));
-  const hash = sha1(arrayOfString.join(""));
-  return hash;
 }

client/src/annoMatrix/schema.ts

@@ -1,37 +1,54 @@
 /*
 Private helper functions related to schema
 */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+import {
-export function _getColumnSchema(schema: any, field: any, col: any) {
+  AnnotationColumnSchema,
+  ArraySchema,
+  Field,
+  Schema,
+} from "../common/types/schema";
+import { LabelArray, LabelType } from "../util/dataframe/types";
+
+export function _getColumnSchema(
+  schema: Schema,
+  field: Field,
+  col: LabelType
+): ArraySchema {
   /* look up the column definition */
   switch (field) {
-    case "obs":
+    case Field.obs:
       if (typeof col === "object")
         throw new Error("unable to get column schema by query");
       return schema.annotations.obsByName[col];
-    case "var":
+    case Field.var:
       if (typeof col === "object")
         throw new Error("unable to get column schema by query");
       return schema.annotations.varByName[col];
-    case "emb":
+    case Field.emb:
       if (typeof col === "object")
         throw new Error("unable to get column schema by query");
       return schema.layout.obsByName[col];
-    case "X":
+    case Field.X:
       return schema.dataframe;
     default:
       throw new Error(`unknown field name: ${field}`);
   }
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _isIndex(
-export function _isIndex(schema: any, field: any, col: any): boolean {
+  schema: Schema,
+  field: Field.obs | Field.var,
+  col: LabelType
+): boolean {
   const index = schema.annotations?.[field].index;
-  return index && index === col;
+  return !!(index && index === col);
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+export function _getColumnDimensionNames(
-export function _getColumnDimensionNames(schema: any, field: any, col: any) {
+  schema: Schema,
+  field: Field,
+  col: LabelType
+): LabelArray | undefined {
   /*
 		field/col may be an alias for multiple columns. Currently used to map ND 
 		values to 1D dataframe columns for embeddings/layout. Signified by the presence
@@ -41,40 +58,33 @@ export function _getColumnDimensionNames(schema: any, field: any, col: any) {
   if (!colSchema) {
     return undefined;
   }
-  return colSchema.dims || [col];
+  if ("dims" in colSchema) {
+    return colSchema.dims;
+  }
+  return [col];
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
+export function _schemaColumns(schema: Schema, field: Field): string[] {
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export function _schemaColumns(schema, field) {
   switch (field) {
-    case "obs":
+    case Field.obs:
       return Object.keys(schema.annotations.obsByName);
-    case "var":
+    case Field.var:
       return Object.keys(schema.annotations.varByName);
-    case "emb":
+    case Field.emb:
       return Object.keys(schema.layout.obsByName);
     default:
       throw new Error(`unknown field name: ${field}`);
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
+export function _getWritableColumns(schema: Schema, field: Field): string[] {
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  if (field !== Field.obs) return [];
-export function _getWritableColumns(schema, field) {
+  return schema.annotations.obs.columns
-  if (field !== "obs") return [];
+    .filter((v: AnnotationColumnSchema) => v.writable)
-  return (
+    .map((v: AnnotationColumnSchema) => v.name);
-    schema.annotations.obs.columns
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type.
-      .filter((v) => v.writable)
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type.
-      .map((v) => v.name)
-  );
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
+export function _isContinuousType(schema: ArraySchema): boolean {
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export function _isContinuousType(schema) {
   const { type } = schema;
   return !(type === "string" || type === "boolean" || type === "categorical");
 }

client/src/annoMatrix/viewCreators.ts

@@ -4,9 +4,18 @@ instances of AnnoMatrix, implementing common UI functions.
 */
 
 import { AnnoMatrixRowSubsetView, AnnoMatrixClipView } from "./views";
+import AnnoMatrix from "./annoMatrix";
+import {
+  DenseInt32Index,
+  IdentityInt32Index,
+  KeyIndex,
+} from "../util/dataframe";
+import { OffsetArray } from "../util/dataframe/types";
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function isubsetMask(
-export function isubsetMask(annoMatrix: any, obsMask: any) {
+  annoMatrix: AnnoMatrix,
+  obsMask: Uint8Array
+): AnnoMatrixRowSubsetView {
   /*
 		Subset annomatrix to contain the rows which have truish value in the mask.
     Maks length must equal annoMatrix.nObs (row count).
@@ -14,9 +23,10 @@ export function isubsetMask(annoMatrix: any, obsMask: any) {
   return isubset(annoMatrix, _maskToList(obsMask));
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
+export function isubset(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  annoMatrix: AnnoMatrix,
-export function isubset(annoMatrix, obsOffsets) {
+  obsOffsets: OffsetArray
+): AnnoMatrixRowSubsetView {
   /*
 		Subset annomatrix to contain the positions contained in the obsOffsets array
 
@@ -28,9 +38,10 @@ export function isubset(annoMatrix, obsOffsets) {
   return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
+export function subset(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  annoMatrix: AnnoMatrix,
-export function subset(annoMatrix, obsLabels) {
+  obsLabels: Int32Array
+): AnnoMatrixRowSubsetView {
   /*
 		subset based on labels
   */
@@ -38,18 +49,21 @@ export function subset(annoMatrix, obsLabels) {
   return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
+export function subsetByIndex(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  annoMatrix: AnnoMatrix,
-export function subsetByIndex(annoMatrix, obsIndex) {
+  obsIndex: DenseInt32Index | IdentityInt32Index | KeyIndex
+): AnnoMatrixRowSubsetView {
   /*
   subset based upon the new obs index.
   */
   return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
+export function clip(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  annoMatrix: AnnoMatrix,
-export function clip(annoMatrix, qmin, qmax) {
+  qmin: number,
+  qmax: number
+): AnnoMatrix {
   /*
 		Create a view that clips all continuous data to the [min, max] range.
 		The matrix shape does not change, but the continuous values outside the
@@ -62,12 +76,8 @@ export function clip(annoMatrix, qmin, qmax) {
 Private utility functions below
 */
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'mask' implicitly has an 'any' type.
+function _maskToList(mask: Uint8Array): OffsetArray {
-function _maskToList(mask) {
   /* convert masks to lists - method wastes space, but is fast */
-  if (!mask) {
-    return null;
-  }
   const list = new Int32Array(mask.length);
   let elems = 0;
   for (let i = 0, l = mask.length; i < l; i += 1) {

client/src/annoMatrix/views.ts

@@ -5,21 +5,40 @@ Views on the annomatrix.  all API here is defined in viewCreators.js and annoMat
 */
 import clip from "../util/clip";
 import AnnoMatrix from "./annoMatrix";
-import { _whereCacheCreate } from "./whereCache";
+import { _whereCacheCreate, WhereCache } from "./whereCache";
 import { _isContinuousType, _getColumnSchema } from "./schema";
+import {
+  Dataframe,
+  DataframeValue,
+  DataframeValueArray,
+  LabelType,
+} from "../util/dataframe";
+import { Query } from "./query";
+import {
+  AnnotationColumnSchema,
+  ArraySchema,
+  Field,
+  EmbeddingSchema,
+} from "../common/types/schema";
+import { LabelIndexBase } from "../util/dataframe/labelIndex";
 
-class AnnoMatrixView extends AnnoMatrix {
+type MapFn = (
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  field: Field,
-  constructor(viewOf: any, rowIndex = null) {
+  colLabel: LabelType,
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
+  colSchema: ArraySchema,
+  colData: DataframeValueArray,
+  df: Dataframe
+) => DataframeValueArray;
+
+abstract class AnnoMatrixView extends AnnoMatrix {
+  constructor(viewOf: AnnoMatrix, rowIndex: LabelIndexBase | null = null) {
     const nObs = rowIndex ? rowIndex.size() : viewOf.nObs;
     super(viewOf.schema, nObs, viewOf.nVar, rowIndex || viewOf.rowIndex);
     this.viewOf = viewOf;
     this.isView = true;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  addObsAnnoCategory(col: LabelType, category: string): AnnoMatrix {
-  addObsAnnoCategory(col: any, category: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
@@ -27,13 +46,10 @@ class AnnoMatrixView extends AnnoMatrix {
   }
 
   async removeObsAnnoCategory(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    col: LabelType,
-    col: any,
+    category: string,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    unassignedCategory: string
-    category: any,
+  ): Promise<AnnoMatrix> {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    unassignedCategory: any
-  ) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory(
       col,
@@ -44,8 +60,7 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  dropObsColumn(col: LabelType): AnnoMatrix {
-  dropObsColumn(col: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col);
     newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
@@ -53,24 +68,29 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  addObsColumn<T extends DataframeValueArray>(
-  addObsColumn(colSchema: any, Ctor: any, value: any) {
+    colSchema: AnnotationColumnSchema,
+    Ctor: new (n: number) => T,
+    value: T
+  ): AnnoMatrix {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  renameObsColumn(oldCol: LabelType, newCol: LabelType): AnnoMatrix {
-  renameObsColumn(oldCol: any, newCol: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async setObsColumnValues(
-  async setObsColumnValues(col: any, rowLabels: any, value: any) {
+    col: LabelType,
+    rowLabels: Int32Array,
+    value: DataframeValue
+  ): Promise<AnnoMatrix> {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues(
       col,
@@ -82,8 +102,11 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async resetObsColumnValues<T extends DataframeValue>(
-  async resetObsColumnValues(col: any, oldValue: any, newValue: any) {
+    col: LabelType,
+    oldValue: T,
+    newValue: T
+  ): Promise<AnnoMatrix> {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues(
       col,
@@ -95,8 +118,7 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  addEmbedding(colSchema: EmbeddingSchema): AnnoMatrix {
-  addEmbedding(colSchema: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
@@ -105,26 +127,32 @@ class AnnoMatrixView extends AnnoMatrix {
 }
 
 class AnnoMatrixMapView extends AnnoMatrixView {
+  mapFn: MapFn;
+
   /*
-	A view which knows how to transform its data.
+    A view which knows how to transform its data.
-	*/
+    */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
+  constructor(viewOf: AnnoMatrix, mapFn: MapFn) {
-  constructor(viewOf, mapFn) {
     super(viewOf);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    this.mapFn = mapFn;
-    (this as any).mapFn = mapFn;
   }
 
-  // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixMapView' is ... Remove this comment to see the full error message
+  async _doLoad(
-  async _doLoad(field, query) {
+    field: Field,
+    query: Query
+  ): Promise<[WhereCache | null, Dataframe]> {
     const df = await this.viewOf._fetch(field, query);
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colData' implicitly has an 'any' type.
+    const dfMapped = df.mapColumns(
-    const dfMapped = df.mapColumns((colData, colIdx) => {
+      (colData: DataframeValueArray, colIdx: number) => {
-      const colLabel = df.colIndex.getLabel(colIdx);
+        const colLabel = df.colIndex.getLabel(colIdx);
-      const colSchema = _getColumnSchema(this.schema, field, colLabel);
+        // @ts-expect-error ts-migrate --- TODO revisit:
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        // `colLabel`: Argument of type 'LabelType | undefined' is not assignable to parameter of type 'LabelType'.
-      return (this as any).mapFn(field, colLabel, colSchema, colData, df);
+        const colSchema = _getColumnSchema(this.schema, field, colLabel);
-    });
+        // @ts-expect-error ts-migrate --- TODO revisit:
+        // `colLabel`: Argument of type 'LabelType | undefined' is not assignable to parameter of type 'LabelType'.
+        return this.mapFn(field, colLabel, colSchema, colData, df);
+      }
+    );
     const whereCacheUpdate = _whereCacheCreate(
       field,
       query,
@@ -135,42 +163,47 @@ class AnnoMatrixMapView extends AnnoMatrixView {
 }
 
 export class AnnoMatrixClipView extends AnnoMatrixMapView {
+  clipRange: [number, number];
+
+  isClipped: boolean;
+
   /*
-	A view which is a clipped transformation of its parent
+    A view which is a clipped transformation of its parent
-	*/
+    */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
+  constructor(viewOf: AnnoMatrix, qmin: number, qmax: number) {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    super(
-  constructor(viewOf, qmin, qmax) {
+      viewOf,
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+      (
-    super(viewOf, (field, colLabel, colSchema, colData, df) =>
+        field: Field,
-      _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax)
+        colLabel: LabelType,
+        colSchema: ArraySchema,
+        colData: DataframeValueArray,
+        df: Dataframe
+      ) => _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax)
     );
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    this.isClipped = true;
-    (this as any).isClipped = true;
+    this.clipRange = [qmin, qmax];
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (this as any).clipRange = [qmin, qmax];
     Object.seal(this);
   }
 }
 
 export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
   /*
-	A view which is a subset of total rows.
+    A view which is a subset of total rows.
-	*/
+    */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
+  constructor(viewOf: AnnoMatrix, rowIndex: LabelIndexBase) {
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  constructor(viewOf, rowIndex) {
     super(viewOf, rowIndex);
     Object.seal(this);
   }
 
-  // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixRowSubsetVie... Remove this comment to see the full error message
+  async _doLoad(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+    field: Field,
-  async _doLoad(field, query) {
+    query: Query
+  ): Promise<[WhereCache | null, Dataframe]> {
     const df = await this.viewOf._fetch(field, query);
 
     // don't try to row-subset the var dimension.
-    if (field === "var") {
+    if (field === Field.var) {
       return [null, df];
     }
 
@@ -188,10 +221,17 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
 Utility functions below
 */
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+function _clipAnnoMatrix(
-function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) {
+  field: Field,
+  colLabel: LabelType,
+  colSchema: ArraySchema,
+  colData: DataframeValueArray,
+  df: Dataframe,
+  qmin: number,
+  qmax: number
+): DataframeValueArray {
   /* only clip obs and var scalar columns */
-  if (field !== "obs" && field !== "X") return colData;
+  if (field !== Field.obs && field !== Field.X) return colData;
   if (!_isContinuousType(colSchema)) return colData;
   if (qmin < 0) qmin = 0;
   if (qmax > 1) qmax = 1;

client/src/annoMatrix/whereCache.ts

@@ -2,7 +2,7 @@
 Private support functions.
 
 This implements a query resolver cache, mapping a query onto the column labels
-resolved by that query. These labels are then used to manage the acutal data cache,
+resolved by that query. These labels are then used to manage the actual data cache,
 which stores data by the resolved label.
 
 There are three query forms:
@@ -49,19 +49,33 @@ creates a cache entry of:
 }
 */
 import { _getColumnDimensionNames } from "./schema";
-import { _hashStringValues } from "./query";
+import { _hashStringValues, Query } from "./query";
+import { Field, Schema } from "../common/types/schema";
+import { LabelArray } from "../util/dataframe/types";
+
+export interface WhereCache {
+  summarize?: {
+    [key: string]: {
+      [key: string]: WhereCacheTerms;
+    };
+  };
+  where?: {
+    [key: string]: WhereCacheTerms;
+  };
+}
+
+export type WhereCacheColumnLabels = LabelArray;
+
+interface WhereCacheTerms {
+  [key: string]: Map<string, Map<string, WhereCacheColumnLabels>>;
+}
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function _whereCacheGet(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  whereCache: WhereCache,
-  whereCache: any,
+  schema: Schema,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  field: Field,
-  schema: any,
+  query: Query
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+): WhereCacheColumnLabels | [undefined] {
-  field: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  query: any
-) {
   /* 
 	query will either be an where query (object) or a column name (string).
 
@@ -69,7 +83,7 @@ export function _whereCacheGet(
 	*/
 
   if (typeof query === "object") {
-    if (query.where) {
+    if ("where" in query) {
       const {
         field: queryField,
         column: queryColumn,
@@ -78,7 +92,7 @@ export function _whereCacheGet(
       const columnMap = whereCache?.where?.[field]?.[queryField];
       return columnMap?.get(queryColumn)?.get(queryValue) ?? [undefined];
     }
-    if (query.summarize) {
+    if ("summarize" in query) {
       const {
         method,
         field: queryField,
@@ -95,15 +109,17 @@ export function _whereCacheGet(
   return _getColumnDimensionNames(schema, field, query) ?? [undefined];
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
+export function _whereCacheCreate(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  field: Field,
-export function _whereCacheCreate(field, query, columnLabels) {
+  query: Query,
+  columnLabels: LabelArray
+): WhereCache | null {
   /*
 	Create a new whereCache
 	*/
   if (typeof query !== "object") return null;
 
-  if (query.where) {
+  if ("where" in query) {
     const {
       field: queryField,
       column: queryColumn,
@@ -119,7 +135,7 @@ export function _whereCacheCreate(field, query, columnLabels) {
       },
     };
   }
-  if (query.summarize) {
+  if ("summarize" in query) {
     const {
       method,
       field: queryField,
@@ -143,23 +159,25 @@ export function _whereCacheCreate(field, query, columnLabels) {
   return {};
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type.
+function __mergeQueries(dst: WhereCacheTerms, src: WhereCacheTerms) {
-function __mergeQueries(dst, src) {
   for (const [queryField, columnMap] of Object.entries(src)) {
     dst[queryField] = dst[queryField] || new Map();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    for (const [queryColumn, valueMap] of columnMap) {
-    for (const [queryColumn, valueMap] of columnMap as any) {
       if (!dst[queryField].has(queryColumn))
         dst[queryField].set(queryColumn, new Map());
       for (const [queryValue, columnLabels] of valueMap) {
+        // @ts-expect-error ts-migrate --- TODO revisit:
+        // `dst[queryField].get(queryColumn)` Object is possibly 'undefined'.
         dst[queryField].get(queryColumn).set(queryValue, columnLabels);
       }
     }
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type.
+function __whereCacheMerge(
-function __whereCacheMerge(dst, src) {
+  dst: WhereCache,
+  src: WhereCache | null
+): WhereCache {
   /*
 	merge src into dst (modifies dst)
 	*/
@@ -176,7 +194,6 @@ function __whereCacheMerge(dst, src) {
     dst.summarize = dst.summarize || {};
     for (const [field, method] of Object.entries(src.summarize)) {
       dst.summarize[field] = dst.summarize[field] || {};
-      // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
       for (const [methodName, query] of Object.entries(method)) {
         dst.summarize[field][methodName] =
           dst.summarize[field][methodName] || {};
@@ -187,8 +204,6 @@ function __whereCacheMerge(dst, src) {
   return dst;
 }
 
-// @ts-expect-error ts-migrate(7019) FIXME: Rest parameter 'caches' implicitly has an 'any[]' ... Remove this comment to see the full error message
+export function _whereCacheMerge(...caches: (WhereCache | null)[]): WhereCache {
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  return caches.reduce(__whereCacheMerge, {} as WhereCache);
-export function _whereCacheMerge(...caches) {
-  return caches.reduce(__whereCacheMerge, {});
 }

client/src/common/types/entities.ts

@@ -1,3 +1,8 @@
 // If a globally shared type or interface doesn't have a clear owner, put it here
 
-export {};
+/**
+ * Flags informing garbage collection-related logic.
+ */
+export interface GCHints {
+  isHot: boolean;
+}

client/src/common/types/schema.ts

@@ -1,4 +1,4 @@
-type Category = number | string | boolean;
+export type Category = number | string | boolean;
 
 export interface AnnotationColumnSchema {
   categories?: Category[];
@@ -7,7 +7,7 @@ export interface AnnotationColumnSchema {
   writable: boolean;
 }
 
-interface XMatrixSchema {
+export interface XMatrixSchema {
   nObs: number;
   nVar: number;
   // TODO(thuang): Not sure what other types are available
@@ -56,3 +56,21 @@ export interface Schema extends RawSchema {
   annotations: AnnotationsSchema;
   layout: LayoutSchema;
 }
+
+/**
+ * Sub-schema objects describing the schema for a primitive Array or Matrix in one of the fields.
+ */
+export type ArraySchema =
+  | AnnotationColumnSchema
+  | EmbeddingSchema
+  | XMatrixSchema;
+
+/**
+ * Set of data / metadata objects that must be specified in a CXG.
+ */
+export enum Field {
+  "obs" = "obs",
+  "var" = "var",
+  "emb" = "emb",
+  "X" = "X",
+}

client/src/util/stateManager/schemaHelpers.ts

@@ -14,6 +14,7 @@ import {
   EmbeddingSchema,
   AnnotationColumnSchema,
 } from "../../common/types/schema";
+import { LabelType } from "../dataframe/types";
 
 /*
 System wide schema assumptions:
@@ -75,7 +76,7 @@ function _reindexObsLayout(schema: Schema) {
   return schema;
 }
 
-export function removeObsAnnoColumn(schema: Schema, name: string): Schema {
+export function removeObsAnnoColumn(schema: Schema, name: LabelType): Schema {
   const newSchema = _copyObsAnno(schema);
   newSchema.annotations.obs.columns = schema.annotations.obs.columns.filter(
     (v) => v.name !== name
@@ -97,7 +98,7 @@ export function addObsAnnoColumn(
 
 export function removeObsAnnoCategory(
   schema: Schema,
-  name: string,
+  name: LabelType,
   category: string
 ): Schema {
   /* remove a category from a categorical annotation */