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experimental re-embedding (#1186)

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* first cut at re-embedding route and back-end support

* update and expand config route tests

* add scanpy_umap

* add reembedding to config route parameters

* front-end support for reembedding fetch and UI

* remove unused imports

* add loading state

* save reembedding in reducer state

* improve withColsFrom

* transmit reembed schema to client; pick unique embedding names

* display embeddings

* format

* lint

* spaces, tab size 2

* lint

* test hack for smoke-test race

* back out hack sleep

* add check for backed mode

* add unit test for reembedding

* lint

* hide re-embedding CLI param from help
This commit is contained in:
Bruce Martin
2020-03-09 16:53:30 -07:00
committed by GitHub
parent b3e9719602
commit 144b19c449
25 changed files with 928 additions and 159 deletions
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client/__tests__/util/dataframe/dataframe.test.js
+123 -12
View File
@@ -321,7 +321,10 @@ describe("dataframe factories", () => {
test("KeyIndex", () => {
const df = new Dataframe.Dataframe(
[2, 2],
[["red", "blue"], [true, false]],
[
["red", "blue"],
[true, false]
],
null,
new Dataframe.KeyIndex(["colors", "bools"])
);
@@ -341,7 +344,10 @@ describe("dataframe factories", () => {
test("DenseInt32Index", () => {
const df = new Dataframe.Dataframe(
[2, 2],
[["red", "blue"], [true, false]],
[
["red", "blue"],
[true, false]
],
null,
new Dataframe.DenseInt32Index([74, 75])
);
@@ -363,7 +369,10 @@ describe("dataframe factories", () => {
test("DenseInt32Index promote", () => {
const df = new Dataframe.Dataframe(
[2, 2],
[["red", "blue"], [true, false]],
[
["red", "blue"],
[true, false]
],
null,
new Dataframe.DenseInt32Index([74, 75])
);
@@ -385,7 +394,10 @@ describe("dataframe factories", () => {
test("IdentityInt32Index with last", () => {
const df = new Dataframe.Dataframe(
[2, 2],
[["red", "blue"], [true, false]],
[
["red", "blue"],
[true, false]
],
null,
null
);
@@ -407,7 +419,10 @@ describe("dataframe factories", () => {
test("IdentityInt32Index promote", () => {
const df = new Dataframe.Dataframe(
[2, 2],
[["red", "blue"], [true, false]],
[
["red", "blue"],
[true, false]
],
null,
null
);
@@ -461,7 +476,11 @@ describe("dataframe factories", () => {
*/
const dfA = new Dataframe.Dataframe(
[2, 3],
[["red", "blue"], [true, false], [1, 0]],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
@@ -520,13 +539,87 @@ describe("dataframe factories", () => {
expect(dfC.col("colors").asArray()).toEqual(["red", "blue"]);
expect(dfC.col("bools").asArray()).toEqual([true, false]);
});
test("column picking", () => {
const dfEmpty = Dataframe.Dataframe.empty();
const dfA = new Dataframe.Dataframe(
[2, 1],
[["red", "blue"]],
null,
new Dataframe.KeyIndex(["colors"])
);
const dfB = new Dataframe.Dataframe(
[2, 3],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
const dfX = dfEmpty.withColsFrom(dfB, ["colors", "bools"]);
expect(dfX).toBeDefined();
expect(dfX.dims).toEqual([2, 2]);
expect(dfX.colIndex.keys()).toEqual(["colors", "bools"]);
expect(dfX.rowIndex).toEqual(dfB.rowIndex);
expect(dfX.icol(0).asArray()).toEqual(dfB.icol(0).asArray());
const dfY = dfA.withColsFrom(dfB, ["numbers"]);
expect(dfY).toBeDefined();
expect(dfY.dims).toEqual([2, 2]);
expect(dfY.colIndex.keys()).toEqual(["colors", "numbers"]);
expect(dfY.rowIndex).toEqual(dfA.rowIndex);
expect(dfY.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
const dfZ = dfA.withColsFrom(dfEmpty, []);
expect(dfZ).toBeDefined();
expect(dfZ.dims).toEqual(dfA.dims);
expect(dfZ.colIndex.keys()).toEqual(dfA.colIndex.keys());
expect(dfZ.rowIndex).toEqual(dfA.rowIndex);
expect(dfZ.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
expect(() => dfA.withColsFrom(dfB, ["bools", "colors"])).toThrow();
});
test("column aliasing", () => {
const dfA = new Dataframe.Dataframe(
[2, 1],
[["red", "blue"]],
null,
new Dataframe.KeyIndex(["colors"])
);
const dfB = new Dataframe.Dataframe(
[2, 3],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
const dfX = dfA.withColsFrom(dfB, { colors: "_colors", bools: "_bools" });
expect(dfX).toBeDefined();
expect(dfX.dims).toEqual([2, 3]);
expect(dfX.colIndex.keys()).toEqual(["colors", "_colors", "_bools"]);
expect(dfX.rowIndex).toEqual(dfA.rowIndex);
expect(dfX.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
expect(dfX.col("_colors").asArray()).toBe(dfB.col("colors").asArray());
});
});
describe("dropCol", () => {
test("KeyIndex", () => {
const df = new Dataframe.Dataframe(
[2, 3],
[["red", "blue"], [true, false], [1, 0]],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
@@ -545,7 +638,11 @@ describe("dataframe factories", () => {
test("IdentityInt32Index drop first", () => {
const df = new Dataframe.Dataframe(
[2, 3],
[["red", "blue"], [true, false], [1, 0]],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
null
);
@@ -565,7 +662,11 @@ describe("dataframe factories", () => {
test("IdentityInt32Index drop last", () => {
const df = new Dataframe.Dataframe(
[2, 3],
[["red", "blue"], [true, false], [1, 0]],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
null
);
@@ -585,7 +686,11 @@ describe("dataframe factories", () => {
test("DenseInt32Index", () => {
const df = new Dataframe.Dataframe(
[2, 3],
[["red", "blue"], [true, false], [1, 0]],
[
["red", "blue"],
[true, false],
[1, 0]
],
null,
new Dataframe.DenseInt32Index([102, 101, 100])
);
@@ -653,7 +758,10 @@ describe("dataframe factories", () => {
test("renameCol", () => {
const dfA = new Dataframe.Dataframe(
[2, 2],
[[true, false], [1, 0]],
[
[true, false],
[1, 0]
],
null,
new Dataframe.KeyIndex(["A", "B"])
);
@@ -671,7 +779,10 @@ describe("dataframe col", () => {
beforeEach(() => {
df = new Dataframe.Dataframe(
[2, 2],
[[true, false], [1, 0]],
[
[true, false],
[1, 0]
],
null,
new Dataframe.KeyIndex(["A", "B"])
);