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re-implement re-embeddings (#1679)

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* fix mispelling

* re-implement re-embedding

* always load base embedding to fetch counts

* format

* lint

* fix tests

* lint

* fix accept handling

* test log

* more debug

* more

* more

* more

* more

* remove logging

* logging

* jsonify

* remove debugging logs

* lint

* clean up errors a bit

* fix issue found in PR review

* PR review changes
This commit is contained in:
Bruce Martin
2020-07-30 12:31:36 -07:00
committed by GitHub
parent bd147abb3f
commit 75cb513dd9
18 changed files with 225 additions and 179 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/annoMatrix/loader.js
+45 -23
View File
@@ -6,6 +6,7 @@ import {
removeObsAnnoColumn,
addObsAnnoCategory,
removeObsAnnoCategory,
addObsLayout,
} from "../util/stateManager/schemaHelpers";
import { isArrayOrTypedArray } from "../util/typeHelpers";
import { _whereCacheCreate } from "./whereCache";
@@ -47,9 +48,9 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colSchema = _getColumnSchema(this.schema, "obs", col);
_writableCategoryTypeCheck(colSchema); // throws on error
const o = this._clone();
o.schema = addObsAnnoCategory(this.schema, col, category);
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, category);
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
@@ -59,13 +60,17 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colSchema = _getColumnSchema(this.schema, "obs", col);
_writableCategoryTypeCheck(colSchema); // throws on error
const o = await this.resetObsColumnValues(
const newAnnoMatrix = await this.resetObsColumnValues(
col,
category,
unassignedCategory
);
o.schema = removeObsAnnoCategory(o.schema, col, category);
return o;
newAnnoMatrix.schema = removeObsAnnoCategory(
newAnnoMatrix.schema,
col,
category
);
return newAnnoMatrix;
}
dropObsColumn(col) {
@@ -75,10 +80,10 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colSchema = _getColumnSchema(this.schema, "obs", col);
_writableCheck(colSchema); // throws on error
const o = this._clone();
o._cache.obs = this._cache.obs.dropCol(col);
o.schema = removeObsAnnoColumn(this.schema, col);
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col);
return newAnnoMatrix;
}
addObsColumn(colSchema, Ctor, value) {
@@ -98,7 +103,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
throw new Error("column already exists");
}
const o = this._clone();
const newAnnoMatrix = this._clone();
let data;
if (isArrayOrTypedArray(value)) {
if (value.constructor !== Ctor)
@@ -109,10 +114,13 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
} else {
data = new Ctor(this.nObs).fill(value);
}
o._cache.obs = this._cache.obs.withCol(colName, data);
_normalizeCategoricalSchema(colSchema, o._cache.obs.col(colName));
o.schema = addObsAnnoColumn(this.schema, colName, colSchema);
return o;
newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data);
_normalizeCategoricalSchema(
colSchema,
newAnnoMatrix._cache.obs.col(colName)
);
newAnnoMatrix.schema = addObsAnnoColumn(this.schema, colName, colSchema);
return newAnnoMatrix;
}
renameObsColumn(oldCol, newCol) {
@@ -155,13 +163,13 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
data[idx] = value;
}
const o = this._clone();
o._cache.obs = this._cache.obs.replaceColData(col, data);
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
const { categories } = colSchema;
if (!categories?.includes(value)) {
o.schema = addObsAnnoCategory(this.schema, col, value);
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, value);
}
return o;
return newAnnoMatrix;
}
async resetObsColumnValues(col, oldValue, newValue) {
@@ -185,13 +193,27 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
if (data[i] === oldValue) data[i] = newValue;
}
const o = this._clone();
o._cache.obs = this._cache.obs.replaceColData(col, data);
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
const { categories } = colSchema;
if (!categories?.includes(newValue)) {
o.schema = addObsAnnoCategory(this.schema, col, newValue);
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, newValue);
}
return o;
return newAnnoMatrix;
}
addEmbedding(colSchema) {
/*
add new layout to the obs embeddings
*/
const { name: colName } = colSchema;
if (_getColumnSchema(this.schema, "emb", colName)) {
throw new Error("column already exists");
}
const newAnnoMatrix = this._clone();
newAnnoMatrix.schema = addObsLayout(this.schema, colSchema);
return newAnnoMatrix;
}
/**