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TS migration. #2288. (#2328)

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* Added TS. Updated build and linting config. Added types.

* [ts-migrate][.] Rename files from JS/JSX to TS/TSX

Co-authored-by: ts-migrate <>

* [ts-migrate][.] Run TS Migrate

Co-authored-by: ts-migrate <>

* Corrected files mangled by ts-migrate.

* Updated lint config, minor linting.

* Re-enabled Husky.

* Updated tests and config.

* Reverted webpack devtool config.

* Removed obsolete snapshots.

* Added annotations snap.

* Updated tsconfig includes wrt linting.

* Removed ts-migrate.

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
This commit is contained in:
Mim Hastie
2021-07-26 20:18:17 +00:00
committed by GitHub
co-authored by ts-migrate Timmy Huang
parent 7328cbdbd5
commit 934cc5c69b
206 changed files with 4719 additions and 2085 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/annoMatrix/annoMatrix.js → client/src/annoMatrix/annoMatrix.ts
+82 -26
View File
@@ -17,6 +17,28 @@ import { _queryValidate, _queryCacheKey } from "./query";
const _dataframeCache = dataframeMemo(128);
export default class AnnoMatrix {
public isView: any;
public nObs: any;
public nVar: any;
public rowIndex: any;
public schema: any;
public userFlags: any;
public viewOf: any;
protected _cache: any;
private _pendingLoad: any;
private _whereCache: any;
private _gcInfo: any;
/*
Abstract base class for all AnnoMatrix objects. This class provides a proxy
to the annotated matrix data authoritatively served by the server/back-end.
@@ -54,7 +76,7 @@ export default class AnnoMatrix {
return ["obs", "var", "emb", "X"];
}
constructor(schema, nObs, nVar, rowIndex = null) {
constructor(schema: any, nObs: any, nVar: any, rowIndex = null) {
/*
Private constructor - this is an abstract base class. Do not use.
*/
@@ -83,13 +105,13 @@ export default class AnnoMatrix {
this.userFlags = {};
/*
Private instance variables.
Private instance variables.
These are caches - lazily loaded. The only guarantee is that if they
are loaded, they will conform to the schema & dimensionality constraints.
These are caches - lazily loaded. The only guarantee is that if they
are loaded, they will conform to the schema & dimensionality constraints.
Do NOT use directly - instead, use the fetch() and preload() API.
*/
Do NOT use directly - instead, use the fetch() and preload() API.
*/
this._cache = {
obs: Dataframe.empty(this.rowIndex),
var: Dataframe.empty(this.rowIndex),
@@ -109,6 +131,7 @@ export default class AnnoMatrix {
/**
** Schema helper/accessors
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
getMatrixColumns(field) {
/*
Return array of column names in the field. ONLY supported on the
@@ -132,6 +155,7 @@ export default class AnnoMatrix {
return AnnoMatrix.fields();
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
getColumnSchema(field, col) {
/*
Return the schema for the field & column ,eg,
@@ -144,6 +168,7 @@ 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, col) {
/*
Return the dimensions on this field / column. For most fields, which are 1D,
@@ -174,6 +199,7 @@ export default class AnnoMatrix {
/**
** Load / read interfaces
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
fetch(field, q) {
/*
Return the given query on a single matrix field as a single dataframe.
@@ -231,6 +257,7 @@ 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, q) {
/*
Start a data fetch & cache fill. Identical to fetch() except it does
@@ -261,7 +288,8 @@ export default class AnnoMatrix {
** The actual implementation is in the sub-classes, which MUST override these.
**/
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
addObsAnnoCategory(col, category) {
/*
Add a new category value (aka "label") to a writable obs column, and return the new AnnoMatrix.
@@ -278,7 +306,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
async removeObsAnnoCategory(col, category, unassignedCategory) {
/*
Remove a category value from an obs column, reassign any obs having that value
@@ -299,7 +328,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
dropObsColumn(col) {
/*
Drop an entire writable column, eg a user-created obs annotation. Typical use
@@ -315,7 +345,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
addObsColumn(colSchema, Ctor, value) {
/*
Add a new writable OBS annotation column, with the caller-specified schema, initial value
@@ -344,7 +375,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
renameObsColumn(oldCol, newCol) {
/*
Rename the obs column 'oldCol' to have name 'newCol' and returns new AnnoMatrix.
@@ -359,7 +391,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
async setObsColumnValues(col, obsLabels, value) {
/*
Set all obs with label in array 'obsLabels' to have 'value'. Typical use would be
@@ -377,7 +410,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
async resetObsColumnValues(col, oldValue, newValue) {
/*
Set by value - all elements in the column with value 'oldValue' are set to 'newValue'.
@@ -394,7 +428,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @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 -- make sure subclass implements
addEmbedding(colSchema) {
/*
Add a new obs embedding to the AnnoMatrix, with provided schema.
@@ -407,28 +442,35 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
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).
*/
Return cache keys for columns associated with this query. May return
[unknown] if no keys are known (ie, nothing is or was cached).
*/
return _whereCacheGet(this._whereCache, this.schema, field, query);
}
/**
** Private interfaces below.
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_resolveCachedQueries(field, queries) {
return queries
.map((query) =>
_whereCacheGet(this._whereCache, this.schema, field, query).filter(
(cacheKey) =>
cacheKey !== undefined && this._cache[field].hasCol(cacheKey)
return (
queries
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'query' implicitly has an 'any' type.
.map((query) =>
_whereCacheGet(this._whereCache, this.schema, field, query).filter(
// @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, q) {
if (!AnnoMatrix.fields().includes(field)) return undefined;
const queries = Array.isArray(q) ? q : [q];
@@ -441,6 +483,7 @@ export default class AnnoMatrix {
/* 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) =>
cacheKey === undefined || !this._cache[field].hasCol(cacheKey)
)
@@ -450,8 +493,10 @@ export default class AnnoMatrix {
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(field, query, async (_field, _query) => {
/* fetch, then index. _doLoad is subclass interface */
// @ts-expect-error ts-migrate(2488) FIXME: Type 'void' must have a '[Symbol.iterator]()' meth... Remove this comment to see the full error message
const [whereCacheUpdate, df] = await this._doLoad(_field, _query);
this._cache[_field] = this._cache[_field].withColsFrom(df);
this._whereCache = _whereCacheMerge(
@@ -472,6 +517,7 @@ export default class AnnoMatrix {
return response;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
async _getPendingLoad(field, query, fetchFn) {
/*
Given a query on a field, ensure that we only have a single outstanding
@@ -527,19 +573,21 @@ export default class AnnoMatrix {
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, isHot, pinnedColumns) {
const maxColumns = isHot ? 256 : 10; // maybe to aggressive?
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.
.filter((col) => !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, b) => {
let atime = _gcInfo.get(_columnCacheKey(field, a));
if (atime === undefined) atime = 0;
@@ -558,13 +606,16 @@ export default class AnnoMatrix {
// )}]`
// );
this._cache[field] = toDrop.reduce(
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type.
(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) => _gcInfo.delete(_columnCacheKey(field, col)));
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_gcFetchCleanup(field, pinnedColumns) {
/*
Called during data load/fetch. By definition, this is 'hot', so we
@@ -579,6 +630,7 @@ export default class AnnoMatrix {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'hints' implicitly has an 'any' type.
_gc(hints) {
/*
Called from middleware, or elsewhere. isHot is true if we are in the active store,
@@ -591,6 +643,7 @@ export default class AnnoMatrix {
);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_gcUpdateStats(field, dataframe) {
/*
called each time a query is performed, allowing the gc to update any bookkeeping
@@ -600,6 +653,7 @@ export default class AnnoMatrix {
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) => {
_gcInfo.set(_columnCacheKey(field, c), now);
});
@@ -617,6 +671,7 @@ export default class AnnoMatrix {
Do not override _clone();
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'clone' implicitly has an 'any' type.
_cloneDeeper(clone) {
clone._cache = _shallowClone(this._cache);
clone._gcInfo = new Map();
@@ -640,6 +695,7 @@ export default class AnnoMatrix {
/*
private utility functions below
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _columnCacheKey(field, column) {
return `${field}/${column}`;
}
client/src/annoMatrix/clone.js → client/src/annoMatrix/clone.ts
+1 -1
View File
@@ -1,6 +1,6 @@
/*
Shallow clone an object, correctly handling prototype
*/
export default function _shallowClone(orig) {
export default function _shallowClone(orig: any) {
return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig);
}
client/src/annoMatrix/crossfilter.js → client/src/annoMatrix/crossfilter.ts
+81 -31
View File
@@ -10,26 +10,31 @@ AnnoMatrix stay in sync:
import Crossfilter from "../util/typedCrossfilter";
import { _getColumnSchema } from "./schema";
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _dimensionNameFromDf(field, df) {
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(field, colNames) {
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
constructor(annoMatrix, _obsCrossfilter = null) {
this.annoMatrix = annoMatrix;
this.obsCrossfilter =
(this as any).annoMatrix = annoMatrix;
(this as any).obsCrossfilter =
_obsCrossfilter || new Crossfilter(annoMatrix._cache.obs);
this.obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
(this as any).obsCrossfilter = (this as any).obsCrossfilter.setData(
annoMatrix._cache.obs
);
}
size() {
return this.obsCrossfilter.size();
return (this as any).obsCrossfilter.size();
}
/**
@@ -39,14 +44,23 @@ 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(colSchema, Ctor, value) {
const annoMatrix = this.annoMatrix.addObsColumn(colSchema, Ctor, value);
const obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
const annoMatrix = (this as any).annoMatrix.addObsColumn(
colSchema,
Ctor,
value
);
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) {
const annoMatrix = this.annoMatrix.dropObsColumn(col);
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);
if (obsCrossfilter.hasDimension(dimName)) {
@@ -55,10 +69,12 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
renameObsColumn(oldCol, newCol) {
const annoMatrix = this.annoMatrix.renameObsColumn(oldCol, newCol);
const annoMatrix = (this as any).annoMatrix.renameObsColumn(oldCol, newCol);
const oldDimName = _dimensionName("obs", oldCol);
const newDimName = _dimensionName("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);
@@ -66,9 +82,14 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
addObsAnnoCategory(col, category) {
const annoMatrix = this.annoMatrix.addObsAnnoCategory(col, category);
const annoMatrix = (this as any).annoMatrix.addObsAnnoCategory(
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);
@@ -76,13 +97,15 @@ 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(col, category, unassignedCategory) {
const annoMatrix = await this.annoMatrix.removeObsAnnoCategory(
const annoMatrix = await (this as any).annoMatrix.removeObsAnnoCategory(
col,
category,
unassignedCategory
);
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);
@@ -90,13 +113,15 @@ 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(col, rowLabels, value) {
const annoMatrix = await this.annoMatrix.setObsColumnValues(
const annoMatrix = await (this as any).annoMatrix.setObsColumnValues(
col,
rowLabels,
value
);
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);
@@ -104,13 +129,15 @@ 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(col, oldValue, newValue) {
const annoMatrix = await this.annoMatrix.resetObsColumnValues(
const annoMatrix = await (this as any).annoMatrix.resetObsColumnValues(
col,
oldValue,
newValue
);
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);
@@ -118,9 +145,13 @@ 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) {
const annoMatrix = this.annoMatrix.addEmbedding(colSchema);
return new AnnoMatrixObsCrossfilter(annoMatrix, this.obsCrossfilter);
const annoMatrix = (this as any).annoMatrix.addEmbedding(colSchema);
return new AnnoMatrixObsCrossfilter(
annoMatrix,
(this as any).obsCrossfilter
);
}
/**
@@ -128,11 +159,15 @@ export default class AnnoMatrixObsCrossfilter {
* want to stop trackin 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, 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.
.filter((k) => k !== undefined);
const dimName = _dimensionName(field, keys);
if (obsCrossfilter.hasDimension(dimName)) {
@@ -146,8 +181,11 @@ 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(field, query, spec) {
// @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;
if (!annoMatrix?._cache?.[field]) {
@@ -180,55 +218,59 @@ export default class AnnoMatrixObsCrossfilter {
/*
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;
const currentDims = this.obsCrossfilter.dimensionNames();
const currentDims = (this as any).obsCrossfilter.dimensionNames();
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'xfltr' implicitly has an 'any' type.
const obsCrossfilter = currentDims.reduce((xfltr, dim) => {
return xfltr.select(dim, { mode: "all" });
}, this.obsCrossfilter);
}, (this as any).obsCrossfilter);
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
countSelected() {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (this.obsCrossfilter.size() === 0) return this.annoMatrix.nObs;
return this.obsCrossfilter.countSelected();
if ((this as any).obsCrossfilter.size() === 0)
return (this as any).annoMatrix.nObs;
return (this as any).obsCrossfilter.countSelected();
}
allSelectedMask() {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (
this.obsCrossfilter.size() === 0 ||
this.obsCrossfilter.dimensionNames().length === 0
(this as any).obsCrossfilter.size() === 0 ||
(this as any).obsCrossfilter.dimensionNames().length === 0
) {
/* fake the mask */
return new Uint8Array(this.annoMatrix.nObs).fill(1);
return new Uint8Array((this as any).annoMatrix.nObs).fill(1);
}
return this.obsCrossfilter.allSelectedMask();
return (this as any).obsCrossfilter.allSelectedMask();
}
allSelectedLabels() {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (
this.obsCrossfilter.size() === 0 ||
this.obsCrossfilter.dimensionNames().length === 0
(this as any).obsCrossfilter.size() === 0 ||
(this as any).obsCrossfilter.dimensionNames().length === 0
) {
return this.annoMatrix.rowIndex.labels();
return (this as any).annoMatrix.rowIndex.labels();
}
const mask = this.obsCrossfilter.allSelectedMask();
const index = this.annoMatrix.rowIndex.isubsetMask(mask);
const mask = (this as any).obsCrossfilter.allSelectedMask();
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(array, selectedValue, deselectedValue) {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (
this.obsCrossfilter.size() === 0 ||
this.obsCrossfilter.dimensionNames().length === 0
(this as any).obsCrossfilter.size() === 0 ||
(this as any).obsCrossfilter.dimensionNames().length === 0
) {
return array.fill(selectedValue);
}
return this.obsCrossfilter.fillByIsSelected(
return (this as any).obsCrossfilter.fillByIsSelected(
array,
selectedValue,
deselectedValue
@@ -239,21 +281,29 @@ 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(annoMatrix, obsCrossfilter, field, df) {
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
obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams);
return obsCrossfilter;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_getColumnBaseType(field, col) {
/* Look up the primitive type for this field/col */
const colSchema = _getColumnSchema(this.annoMatrix.schema, field, col);
const colSchema = _getColumnSchema(
(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(field, df) {
/* return the crossfilter dimensiontype type and params for this field/dataframe */
client/src/annoMatrix/fetchHelpers.js → client/src/annoMatrix/fetchHelpers.ts
+4 -4
View File
@@ -1,19 +1,19 @@
export { doBinaryRequest, doFetch } from "../util/actionHelpers";
/* double URI encode - needed for query-param filters */
export function _dubEncURIComp(s) {
export function _dubEncURIComp(s: any) {
return encodeURIComponent(encodeURIComponent(s));
}
/* currently unused, consider deleting */
export function _fetchResult(promise) {
export function _fetchResult(promise: any) {
let _status = "pending";
const res = promise.then(
(r) => {
(r: any) => {
_status = "success";
return r;
},
(e) => {
(e: any) => {
_status = "error";
throw e;
}
client/src/annoMatrix/index.js → client/src/annoMatrix/index.ts
View File
client/src/annoMatrix/loader.js → client/src/annoMatrix/loader.ts
+39 -17
View File
@@ -23,6 +23,8 @@ import {
const promiseThrottle = new PromiseLimit(5);
export default class AnnoMatrixLoader extends AnnoMatrix {
baseURL: any;
/*
AnnoMatrix implementation which proxies to HTTP server using the CXG REST API.
Used as the base (non-view) instance.
@@ -33,7 +35,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
new AnnoMatrixLoader(serverBaseURL, schema) -> instance
*/
constructor(baseURL, schema) {
constructor(baseURL: any, schema: any) {
const { nObs, nVar } = schema.dataframe;
super(schema, nObs, nVar);
@@ -48,7 +50,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
/**
** Public. API described in base class.
**/
addObsAnnoCategory(col, category) {
addObsAnnoCategory(col: any, category: any) {
/*
Add a new category (aka label) to the schema for an obs column.
*/
@@ -60,7 +62,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
async removeObsAnnoCategory(
col: any,
category: any,
unassignedCategory: any
) {
/*
Remove a single "category" (aka "label") from the data & schema of an obs column.
*/
@@ -80,7 +86,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
dropObsColumn(col) {
dropObsColumn(col: any) {
/*
drop column from field
*/
@@ -88,11 +94,12 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
_writableCheck(colSchema); // throws on error
const newAnnoMatrix = this._clone();
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(colSchema, Ctor, value) {
/*
add a column to field, initializing with value. Value may
@@ -105,7 +112,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colName = colSchema.name;
if (
_getColumnSchema(this.schema, "obs", colName) ||
this._cache.obs.hasCol(colName)
(this as any)._cache.obs.hasCol(colName)
) {
throw new Error("column already exists");
}
@@ -121,7 +128,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
} else {
data = new Ctor(this.nObs).fill(value);
}
newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data);
newAnnoMatrix._cache.obs = (this as any)._cache.obs.withCol(colName, data);
_normalizeCategoricalSchema(
colSchema,
newAnnoMatrix._cache.obs.col(colName)
@@ -130,15 +137,15 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
renameObsColumn(oldCol, newCol) {
/*
Rename the obs oldColName to newColName. oldCol must be writable.
*/
const oldColSchema = _getColumnSchema(this.schema, "obs", oldCol);
_writableCheck(oldColSchema); // throws on error
const value = this._cache.obs.hasCol(oldCol)
? this._cache.obs.col(oldCol).asArray()
_writableCheck(oldColSchema);
const value = (this as any)._cache.obs.hasCol(oldCol)
? (this as any)._cache.obs.col(oldCol).asArray()
: undefined;
return this.dropObsColumn(oldCol).addObsColumn(
{
@@ -150,6 +157,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async setObsColumnValues(col, rowLabels, value) {
/*
Set all rows identified by rowLabels to value.
@@ -159,11 +167,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
// ensure that we have the data in cache before we manipulate it
await this.fetch("obs", col);
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);
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 === undefined) throw new Error("Unknown row label");
@@ -171,7 +179,10 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
}
const newAnnoMatrix = this._clone();
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);
@@ -179,6 +190,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async resetObsColumnValues(col, oldValue, newValue) {
/*
Set all rows with value 'oldValue' to 'newValue'.
@@ -192,16 +204,19 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
// ensure that we have the data in cache before we manipulate it
await this.fetch("obs", col);
if (!this._cache.obs.hasCol(col))
if (!(this as any)._cache.obs.hasCol(col))
throw new Error("Internal error - user annotation data missing");
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();
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);
@@ -209,6 +224,7 @@ 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) {
/*
add new layout to the obs embeddings
@@ -226,6 +242,7 @@ 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(field, query) {
/*
_doLoad - evaluates the query against the field. Returns:
@@ -280,12 +297,14 @@ 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 _writableCheck(colSchema) {
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 _writableCategoryTypeCheck(colSchema) {
_writableCheck(colSchema);
if (colSchema.type !== "categorical") {
@@ -293,6 +312,7 @@ function _writableCategoryTypeCheck(colSchema) {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
function _embLoader(baseURL, _field, query) {
_expectSimpleQuery(query);
@@ -302,6 +322,7 @@ function _embLoader(baseURL, _field, query) {
return () => doBinaryRequest(url);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
function _obsOrVarLoader(baseURL, field, query) {
_expectSimpleQuery(query);
@@ -311,6 +332,7 @@ function _obsOrVarLoader(baseURL, field, query) {
return () => doBinaryRequest(url);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
function _XLoader(baseURL, field, query) {
_expectComplexQuery(query);
client/src/annoMatrix/middleware.js → client/src/annoMatrix/middleware.ts
+8 -6
View File
@@ -11,7 +11,7 @@ Undoable metareducer and the AnnoMatrix private API. It would be helpful
to make the Undoable interface better factored.
*/
const annoMatrixGC = (store) => (next) => (action) => {
const annoMatrixGC = (store: any) => (next: any) => (action: any) => {
if (_itIsTimeForGC()) {
_doGC(store);
}
@@ -34,7 +34,7 @@ function _itIsTimeForGC() {
return false;
}
function _doGC(store) {
function _doGC(store: any) {
const state = store.getState();
// these should probably be a function imported from undoable.js, etc, as
@@ -43,8 +43,8 @@ function _doGC(store) {
const undoableFuture = state["@@undoable/future"];
const undoableStack = undoablePast
.concat(undoableFuture)
.flatMap((snapshot) =>
snapshot.filter((v) => v[0] === "annoMatrix").map((v) => v[1])
.flatMap((snapshot: any) =>
snapshot.filter((v: any) => v[0] === "annoMatrix").map((v: any) => v[1])
);
const currentAnnoMatrix = state.annoMatrix;
@@ -53,14 +53,16 @@ function _doGC(store) {
as our current gc algo is more aggressive with those not hot.
*/
const allAnnoMatrices = new Map(
undoableStack.map((m) => [m, { isHot: false }])
undoableStack.map((m: any) => [m, { isHot: false }])
);
let am = currentAnnoMatrix;
while (am) {
allAnnoMatrices.set(am, { isHot: true });
am = am.viewOf;
}
allAnnoMatrices.forEach((hints, annoMatrix) => annoMatrix._gc(hints));
allAnnoMatrices.forEach((hints, annoMatrix) =>
(annoMatrix as any)._gc(hints)
);
}
export default annoMatrixGC;
client/src/annoMatrix/query.js → client/src/annoMatrix/query.ts
+10 -10
View File
@@ -10,7 +10,7 @@ import { _dubEncURIComp } from "./fetchHelpers";
* @param {object | string} query - the query
* @returns {object | string} - the normalized query
*/
export function _queryValidate(query) {
export function _queryValidate(query: any) {
if (typeof query !== "object") return query;
if (query.where && query.summarize)
@@ -40,11 +40,11 @@ export function _queryValidate(query) {
throw new Error("query must specify one of where or summarize");
}
export function _expectSimpleQuery(query) {
export function _expectSimpleQuery(query: any) {
if (typeof query === "object") throw new Error("expected simple query");
}
export function _expectComplexQuery(query) {
export function _expectComplexQuery(query: any) {
if (typeof query !== "object") throw new Error("expected complex query");
}
@@ -55,7 +55,7 @@ export function _expectComplexQuery(query) {
* @param {string|object} query
* @returns the key
*/
export function _queryCacheKey(field, query) {
export function _queryCacheKey(field: any, query: any) {
if (typeof query === "object") {
// complex query
if (query.where) {
@@ -84,22 +84,22 @@ export function _queryCacheKey(field, query) {
return `${field}/${query}`;
}
function _urlEncodeWhereQuery(q) {
function _urlEncodeWhereQuery(q: any) {
const { field: queryField, column: queryColumn, value: queryValue } = q;
return `${_dubEncURIComp(queryField)}:${_dubEncURIComp(
queryColumn
)}=${_dubEncURIComp(queryValue)}`;
}
function _urlEncodeSummarizeQuery(q) {
function _urlEncodeSummarizeQuery(q: any) {
const { method, field, column, values } = q;
const filter = values
.map((value) => _urlEncodeWhereQuery({ field, column, value }))
.map((value: any) => _urlEncodeWhereQuery({ field, column, value }))
.join("&");
return `method=${method}&${filter}`;
}
export function _urlEncodeComplexQuery(q) {
export function _urlEncodeComplexQuery(q: any) {
if (typeof q === "object") {
if (q.where) {
return _urlEncodeWhereQuery(q.where);
@@ -111,7 +111,7 @@ export function _urlEncodeComplexQuery(q) {
throw new Error("Unrecognized complex query type");
}
export function _urlEncodeLabelQuery(colKey, q) {
export function _urlEncodeLabelQuery(colKey: any, q: any) {
if (!colKey) throw new Error("Unsupported query by name");
if (typeof q !== "string") throw new Error("Query must be a simple label.");
return `${colKey}=${encodeURIComponent(q)}`;
@@ -120,7 +120,7 @@ export function _urlEncodeLabelQuery(colKey, q) {
/**
* Generate the column key the server will send us for this query.
*/
export function _hashStringValues(arrayOfString) {
export function _hashStringValues(arrayOfString: any) {
const hash = sha1(arrayOfString.join(""));
return hash;
}
client/src/annoMatrix/schema.js → client/src/annoMatrix/schema.ts
+13 -5
View File
@@ -4,7 +4,7 @@ Private helper functions related to schema
import catLabelSort from "../util/catLabelSort";
import { unassignedCategoryLabel } from "../globals";
export function _getColumnSchema(schema, field, col) {
export function _getColumnSchema(schema: any, field: any, col: any) {
/* look up the column definition */
switch (field) {
case "obs":
@@ -26,7 +26,7 @@ export function _getColumnSchema(schema, field, col) {
}
}
export function _getColumnDimensionNames(schema, field, col) {
export function _getColumnDimensionNames(schema: any, field: any, col: any) {
/*
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
@@ -39,6 +39,7 @@ export function _getColumnDimensionNames(schema, field, col) {
return colSchema.dims || [col];
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
export function _schemaColumns(schema, field) {
switch (field) {
case "obs":
@@ -52,18 +53,25 @@ export function _schemaColumns(schema, field) {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
export function _getWritableColumns(schema, field) {
if (field !== "obs") return [];
return schema.annotations.obs.columns
.filter((v) => v.writable)
.map((v) => v.name);
return (
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) {
const { type } = schema;
return !(type === "string" || type === "boolean" || type === "categorical");
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
export function _normalizeCategoricalSchema(colSchema, col) {
const { type, writable } = colSchema;
if (
client/src/annoMatrix/viewCreators.js → client/src/annoMatrix/viewCreators.ts
+6 -1
View File
@@ -5,7 +5,7 @@ instances of AnnoMatrix, implementing common UI functions.
import { AnnoMatrixRowSubsetView, AnnoMatrixClipView } from "./views";
export function isubsetMask(annoMatrix, obsMask) {
export function isubsetMask(annoMatrix: any, obsMask: any) {
/*
Subset annomatrix to contain the rows which have truish value in the mask.
Maks length must equal annoMatrix.nObs (row count).
@@ -13,6 +13,7 @@ export function isubsetMask(annoMatrix, obsMask) {
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(annoMatrix, obsOffsets) {
/*
Subset annomatrix to contain the positions contained in the obsOffsets array
@@ -25,6 +26,7 @@ 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(annoMatrix, obsLabels) {
/*
subset based on labels
@@ -33,6 +35,7 @@ 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(annoMatrix, obsIndex) {
/*
subset based upon the new obs index.
@@ -40,6 +43,7 @@ export function subsetByIndex(annoMatrix, obsIndex) {
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(annoMatrix, qmin, qmax) {
/*
Create a view that clips all continuous data to the [min, max] range.
@@ -53,6 +57,7 @@ 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) {
/* convert masks to lists - method wastes space, but is fast */
if (!mask) {
client/src/annoMatrix/views.js → client/src/annoMatrix/views.ts
+26 -13
View File
@@ -9,21 +9,26 @@ import { _whereCacheCreate } from "./whereCache";
import { _isContinuousType, _getColumnSchema } from "./schema";
class AnnoMatrixView extends AnnoMatrix {
constructor(viewOf, rowIndex = null) {
constructor(viewOf: any, rowIndex = null) {
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const nObs = rowIndex ? rowIndex.size() : viewOf.nObs;
super(viewOf.schema, nObs, viewOf.nVar, rowIndex || viewOf.rowIndex);
this.viewOf = viewOf;
this.isView = true;
}
addObsAnnoCategory(col, category) {
addObsAnnoCategory(col: any, category: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
async removeObsAnnoCategory(
col: any,
category: any,
unassignedCategory: any
) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory(
col,
@@ -34,7 +39,7 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
dropObsColumn(col) {
dropObsColumn(col: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col);
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
@@ -42,21 +47,21 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
addObsColumn(colSchema, Ctor, value) {
addObsColumn(colSchema: any, Ctor: any, value: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
renameObsColumn(oldCol, newCol) {
renameObsColumn(oldCol: any, newCol: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async setObsColumnValues(col, rowLabels, value) {
async setObsColumnValues(col: any, rowLabels: any, value: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues(
col,
@@ -68,7 +73,7 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
async resetObsColumnValues(col, oldValue, newValue) {
async resetObsColumnValues(col: any, oldValue: any, newValue: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues(
col,
@@ -80,7 +85,7 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
addEmbedding(colSchema) {
addEmbedding(colSchema: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
@@ -92,17 +97,20 @@ class AnnoMatrixMapView extends AnnoMatrixView {
/*
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, mapFn) {
super(viewOf);
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(field, query) {
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((colData, colIdx) => {
const colLabel = df.colIndex.getLabel(colIdx);
const colSchema = _getColumnSchema(this.schema, field, colLabel);
return this.mapFn(field, colLabel, colSchema, colData, df);
return (this as any).mapFn(field, colLabel, colSchema, colData, df);
});
const whereCacheUpdate = _whereCacheCreate(
field,
@@ -117,12 +125,14 @@ export class AnnoMatrixClipView extends AnnoMatrixMapView {
/*
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, qmin, qmax) {
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
super(viewOf, (field, colLabel, colSchema, colData, df) =>
_clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax)
);
this.isClipped = true;
this.clipRange = [qmin, qmax];
(this as any).isClipped = true;
(this as any).clipRange = [qmin, qmax];
Object.seal(this);
}
}
@@ -131,11 +141,13 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
/*
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, 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(field, query) {
const df = await this.viewOf._fetch(field, query);
@@ -158,6 +170,7 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
Utility functions below
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) {
/* only clip obs and var scalar columns */
if (field !== "obs" && field !== "X") return colData;
client/src/annoMatrix/whereCache.js → client/src/annoMatrix/whereCache.ts
+12 -2
View File
@@ -51,7 +51,12 @@ creates a cache entry of:
import { _getColumnDimensionNames } from "./schema";
import { _hashStringValues } from "./query";
export function _whereCacheGet(whereCache, schema, field, query) {
export function _whereCacheGet(
whereCache: any,
schema: any,
field: any,
query: any
) {
/*
query will either be an where query (object) or a column name (string).
@@ -85,6 +90,7 @@ export function _whereCacheGet(whereCache, schema, field, query) {
return _getColumnDimensionNames(schema, field, query) ?? [undefined];
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
export function _whereCacheCreate(field, query, columnLabels) {
/*
Create a new whereCache
@@ -131,10 +137,11 @@ export function _whereCacheCreate(field, query, columnLabels) {
return {};
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type.
function __mergeQueries(dst, src) {
for (const [queryField, columnMap] of Object.entries(src)) {
dst[queryField] = dst[queryField] || new Map();
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) {
@@ -144,6 +151,7 @@ function __mergeQueries(dst, src) {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type.
function __whereCacheMerge(dst, src) {
/*
merge src into dst (modifies dst)
@@ -161,6 +169,7 @@ 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] || {};
@@ -171,6 +180,7 @@ 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) {
return caches.reduce(__whereCacheMerge, {});
}