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

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* 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>
This commit is contained in:
Mim Hastie
2021-08-18 13:18:54 -07:00
committed by GitHub
co-authored by Timmy Huang
parent 08b03ace60
commit b814489328
19 changed files with 1121 additions and 948 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/__tests__/util/annoMatrix/annoMatrix.test.ts
+38 -37
View File
@@ -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(
Dataframe
);
await expect(
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 ng2 = (await am2.fetch("obs", "n_genes")) as Dataframe;
const ng1 = (await am1.fetch(Field.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(am1.getMatrixColumns("obs")).toContain("foo");
const foo: Dataframe = await am1.fetch("obs", "foo");
expect(base.getMatrixColumns(Field.obs)).not.toContain("foo");
expect(am1.getMatrixColumns(Field.obs)).toContain("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(am2.getMatrixColumns("obs")).not.toContain("foo");
expect(base.getMatrixColumns(Field.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 am2.fetch("obs", am2.getMatrixColumns("obs"));
await am3.fetch("obs", am3.getMatrixColumns("obs"));
await am4.fetch("obs", am4.getMatrixColumns("obs"));
await am1.fetch(Field.obs, am1.getMatrixColumns(Field.obs));
await am2.fetch(Field.obs, am2.getMatrixColumns(Field.obs));
await am3.fetch(Field.obs, am3.getMatrixColumns(Field.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("obs", "test").categories).toEqual(
expect(am1.getColumnSchema(Field.obs, "test").type).toBe("categorical");
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 am2.fetch("obs", am2.getMatrixColumns("obs"));
await am3.fetch("obs", am3.getMatrixColumns("obs"));
await am1.fetch(Field.obs, am1.getMatrixColumns(Field.obs));
await am2.fetch(Field.obs, am2.getMatrixColumns(Field.obs));
await am3.fetch(Field.obs, am3.getMatrixColumns(Field.obs));
await addSetDrop(am1);
await addSetDrop(am2);