mirror of
https://github.com/chanzuckerberg/cellxgene.git
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Added @typescript-eslint/recommended config with suppressions (#2345)
* Disabled @blueprintjs/classes-constants. #2288. * thuang-eslint-bp-off (#2344) * Disabled @blueprintjs/classes-constants on webpack dev and shared. #2288. * Added TS recommended, suppress lint errors codemod. * Added per-error/warning ignore for tests. * Added per-error/warning ignore for configuration. * Added per-error/warning ignore for src. Removed suppress package. * Minor linting. Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
This commit is contained in:
Mim Hastie
co-authored by
Timmy Huang
Timmy Huang
parent
32f60a1547
commit
27575b8d86
@@ -23,6 +23,7 @@ import {
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const promiseThrottle = new PromiseLimit(5);
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export default class AnnoMatrixLoader extends AnnoMatrix {
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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baseURL: any;
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/*
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@@ -35,6 +36,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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new AnnoMatrixLoader(serverBaseURL, schema) -> instance
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*/
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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constructor(baseURL: any, schema: any) {
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const { nObs, nVar } = schema.dataframe;
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super(schema, nObs, nVar);
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@@ -50,6 +52,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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/**
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** Public. API described in base class.
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**/
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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addObsAnnoCategory(col: any, category: any) {
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/*
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Add a new category (aka label) to the schema for an obs column.
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@@ -62,9 +65,13 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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return newAnnoMatrix;
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}
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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async removeObsAnnoCategory(
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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col: any,
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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category: any,
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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unassignedCategory: any
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) {
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/*
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@@ -86,6 +93,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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return newAnnoMatrix;
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}
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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dropObsColumn(col: any) {
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/*
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drop column from field
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@@ -94,12 +102,14 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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_writableCheck(colSchema); // throws on error
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const newAnnoMatrix = this._clone();
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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newAnnoMatrix._cache.obs = (this as any)._cache.obs.dropCol(col);
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newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col);
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return newAnnoMatrix;
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}
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// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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addObsColumn(colSchema, Ctor, value) {
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/*
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add a column to field, initializing with value. Value may
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@@ -112,6 +122,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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const colName = colSchema.name;
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if (
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_getColumnSchema(this.schema, "obs", colName) ||
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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(this as any)._cache.obs.hasCol(colName)
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) {
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throw new Error("column already exists");
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@@ -128,6 +139,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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} else {
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data = new Ctor(this.nObs).fill(value);
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}
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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newAnnoMatrix._cache.obs = (this as any)._cache.obs.withCol(colName, data);
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_normalizeCategoricalSchema(
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colSchema,
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@@ -138,14 +150,17 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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}
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// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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renameObsColumn(oldCol, newCol) {
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/*
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Rename the obs oldColName to newColName. oldCol must be writable.
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*/
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const oldColSchema = _getColumnSchema(this.schema, "obs", oldCol);
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_writableCheck(oldColSchema);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const value = (this as any)._cache.obs.hasCol(oldCol)
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? (this as any)._cache.obs.col(oldCol).asArray()
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? // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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(this as any)._cache.obs.col(oldCol).asArray()
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: undefined;
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return this.dropObsColumn(oldCol).addObsColumn(
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{
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@@ -158,6 +173,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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}
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// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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async setObsColumnValues(col, rowLabels, value) {
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/*
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Set all rows identified by rowLabels to value.
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@@ -167,10 +183,12 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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// ensure that we have the data in cache before we manipulate it
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await this.fetch("obs", col);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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if (!(this as any)._cache.obs.hasCol(col))
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throw new Error("Internal error - user annotation data missing");
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const rowIndices = this.rowIndex.getOffsets(rowLabels);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const data = (this as any)._cache.obs.col(col).asArray().slice();
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for (let i = 0, len = rowIndices.length; i < len; i += 1) {
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const idx = rowIndices[i];
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@@ -179,6 +197,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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}
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const newAnnoMatrix = this._clone();
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
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col,
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data
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@@ -191,6 +210,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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}
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// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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async resetObsColumnValues(col, oldValue, newValue) {
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/*
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Set all rows with value 'oldValue' to 'newValue'.
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@@ -204,15 +224,18 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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// ensure that we have the data in cache before we manipulate it
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await this.fetch("obs", col);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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if (!(this as any)._cache.obs.hasCol(col))
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throw new Error("Internal error - user annotation data missing");
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const data = (this as any)._cache.obs.col(col).asArray().slice();
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for (let i = 0, l = data.length; i < l; i += 1) {
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if (data[i] === oldValue) data[i] = newValue;
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}
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const newAnnoMatrix = this._clone();
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
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col,
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data
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@@ -225,6 +248,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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}
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// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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addEmbedding(colSchema) {
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/*
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add new layout to the obs embeddings
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@@ -243,6 +267,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
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** Private below
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**/
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// @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixLoader' is n... Remove this comment to see the full error message
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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async _doLoad(field, query) {
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/*
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_doLoad - evaluates the query against the field. Returns:
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