TS typing for Dataframe (#2382)

* initial TS typing

* first cut at Dataframe TS typing

* more Dataframe typing

* comments

* more Dataframe cleanup

* PR review fixes and improvements

client/src/util/stateManager/annotationsHelpers.ts

@@ -4,6 +4,7 @@ See also reducers/annotations.js
 */
 
 import { Schema } from "../../common/types/schema";
+import { Dataframe, LabelType } from "../dataframe";
 
 /*
 There are a number of state constraints assumed throughout the
@@ -57,9 +58,12 @@ export function isUserAnnotation(annoMatrix, name) {
   return _isUserAnnotation(annoMatrix.schema, name);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type.
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export function allHaveLabelByMask(df, colName, label, mask) {
+export function allHaveLabelByMask(
+  df: Dataframe,
+  colName: LabelType,
+  label: string,
+  mask: Uint8Array
+): boolean {
   // return true if all rows as indicated by mask have the colname set to label.
   // False if not.
   const col = df.col(colName);

client/src/util/stateManager/colorHelpers.ts

@@ -7,6 +7,7 @@ import memoize from "memoize-one";
 import * as globals from "../../globals";
 import parseRGB from "../parseRGB";
 import { range } from "../range";
+import { Dataframe, LabelType } from "../dataframe";
 
 /*
 given a color mode & accessor, generate an annoMatrix query that will
@@ -95,18 +96,19 @@ Returns:
   }
 */
 function _createColorTable(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  colorMode: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  colorByAccessor: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  colorByData: any,
+  colorMode: string | null,
+  colorByAccessor: LabelType | null,
+  colorByData: Dataframe | null,
   // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
   schema: any,
   userColors = null
 ) {
+  if (colorMode === null || colorByData === null)
+    return defaultColors(schema.dataframe.nObs);
+
   switch (colorMode) {
     case "color by categorical metadata": {
+      if (colorByAccessor === null) return defaultColors(schema.dataframe.nObs);
       const data = colorByData.col(colorByAccessor).asArray();
       // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
       if (userColors && colorByAccessor in userColors) {
@@ -115,18 +117,19 @@ function _createColorTable(
       return createColorsByCategoricalMetadata(data, colorByAccessor, schema);
     }
     case "color by continuous metadata": {
+      if (colorByAccessor === null) return defaultColors(schema.dataframe.nObs);
       const col = colorByData.col(colorByAccessor);
-      const { min, max } = col.summarize();
+      const { min, max } = col.summarizeContinuous();
       return createColorsByContinuousMetadata(col.asArray(), min, max);
     }
     case "color by expression": {
       const col = colorByData.icol(0);
-      const { min, max } = col.summarize();
+      const { min, max } = col.summarizeContinuous();
       return createColorsByContinuousMetadata(col.asArray(), min, max);
     }
     case "color by geneset mean expression": {
       const col = colorByData.icol(0);
-      const { min, max } = col.summarize();
+      const { min, max } = col.summarizeContinuous();
       return createColorsByContinuousMetadata(col.asArray(), min, max);
     }
     default: {

client/src/util/stateManager/matrix.ts

@@ -1,6 +1,10 @@
 import { flatbuffers } from "flatbuffers";
 import { NetEncoding } from "./matrix_generated";
-import { isTypedArray, isFloatTypedArray } from "../../common/types/arraytypes";
+import {
+  TypedArray,
+  isTypedArray,
+  isFloatTypedArray,
+} from "../../common/types/arraytypes";
 import {
   Dataframe,
   IdentityInt32Index,
@@ -94,14 +98,13 @@ function encodeTypedArray(builder: any, uType: any, uData: any) {
   return builder.endObject();
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function encodeMatrixFBS(df: any) {
+export function encodeMatrixFBS(df: Dataframe): Uint8Array {
   /*
   encode the dataframe as an FBS Matrix
   */
 
   /* row indexing not supported currently */
-  if (df.rowIndex.constructor !== IdentityInt32Index) {
+  if (!(df.rowIndex instanceof IdentityInt32Index)) {
     throw new Error("FBS does not support row index encoding at this time");
   }
 
@@ -115,11 +118,9 @@ export function encodeMatrixFBS(df: any) {
   let encColumns;
 
   if (shape[0] > 0 && shape[1] > 0) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const columns = df.columns().map((col: any) => col.asArray());
+    const columns = df.columns().map((col) => col.asArray());
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const cols = columns.map((carr: any) => {
+    const cols = columns.map((carr) => {
       let uType;
       let tarr;
       if (isTypedArray(carr)) {
@@ -179,8 +180,7 @@ export function encodeMatrixFBS(df: any) {
   return builder.asUint8Array();
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function promoteTypedArray(o: any) {
+function promoteTypedArray(o: TypedArray) {
   /*
   Decide what internal data type to use for the data returned from
   the server.
@@ -212,8 +212,9 @@ function promoteTypedArray(o: any) {
   return new TypedArrayCtor(o);
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function matrixFBSToDataframe(arrayBuffers: any) {
+export function matrixFBSToDataframe(
+  arrayBuffers: ArrayBuffer | ArrayBuffer[]
+): Dataframe {
   /*
   Convert array of Matrix FBS to a Dataframe.
 
@@ -229,37 +230,30 @@ export function matrixFBSToDataframe(arrayBuffers: any) {
     arrayBuffers = [arrayBuffers];
   }
   if (arrayBuffers.length === 0) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (Dataframe as any).Dataframe.empty();
+    return Dataframe.empty();
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const fbs = arrayBuffers.map((ab: any) => decodeMatrixFBS(ab, true)); // leave in place
+  const fbs = arrayBuffers.map((ab) => decodeMatrixFBS(ab, true)); // leave in place
   /* check that all FBS have same row dimensionality */
   const { nRows } = fbs[0];
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  fbs.forEach((b: any) => {
+  fbs.forEach((b) => {
     if (b.nRows !== nRows)
       throw new Error("FBS with inconsistent dimensionality");
   });
-  const columns = fbs // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    .map((fb: any) =>
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      fb.columns.map((c: any) => {
+  const columns = fbs
+    .map((fb) =>
+      fb.columns.map((c) => {
         if (isFloatTypedArray(c) || Array.isArray(c)) return c;
         return promoteTypedArray(c);
       })
     )
     .flat();
   // colIdx may be TypedArray or Array
-  const colIdx = fbs // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    .map((b: any) =>
-      Array.isArray(b.colIdx) ? b.colIdx : Array.from(b.colIdx)
-    )
+  const colIdx = fbs
+    .map((b) => (Array.isArray(b.colIdx) ? b.colIdx : Array.from(b.colIdx)))
     .flat();
   const nCols = columns.length;
 
-  // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
   const df = new Dataframe([nRows, nCols], columns, null, new KeyIndex(colIdx));
   return df;
 }

client/src/util/stateManager/viewStackHelpers.ts

@@ -37,6 +37,7 @@ Views can be interogated for their type with the following:
 
 import { clip, isubsetMask, isubset } from "../../annoMatrix";
 import { memoize } from "../dataframe/util";
+import { Dataframe, LabelIndex } from "../dataframe";
 
 // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
@@ -101,7 +102,7 @@ export function _userResetSubsetAnnoMatrix(annoMatrix) {
 
 // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export function _setEmbeddingSubset(annoMatrix, embeddingDf) {
+export function _setEmbeddingSubset(annoMatrix, embeddingDf: Dataframe) {
   /*
   Set the embedding subset view.  Only create a subset view for the embedding
   when it is needed, ie, there are NaN values in the embeddings.
@@ -141,8 +142,10 @@ export function _setEmbeddingSubset(annoMatrix, embeddingDf) {
   return annoMatrix;
 }
 
-// @ts-expect-error ts-migrate(6133) FIXME: 'baseRowIndex' is declared but its value is never ... Remove this comment to see the full error message
-function _getEmbeddingRowOffsets(baseRowIndex, embeddingDf) {
+function _getEmbeddingRowOffsets(
+  _baseRowIndex: LabelIndex,
+  embeddingDf: Dataframe
+) {
   /*
   given a dataframe containing an embedding:
     - if the embedding contains no NaN coordinates, return null
@@ -167,17 +170,16 @@ function _getEmbeddingRowOffsets(baseRowIndex, embeddingDf) {
   return offsets.subarray(0, numOffsets);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'embeddingDf' implicitly has an 'any' ty... Remove this comment to see the full error message
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export function _getDiscreteCellEmbeddingRowIndex(embeddingDf) {
+export function _getDiscreteCellEmbeddingRowIndex(
+  embeddingDf: Dataframe
+): LabelIndex {
   const idx = _getEmbeddingRowOffsets(embeddingDf.rowIndex, embeddingDf);
   if (idx === null) return embeddingDf.rowIndex;
   return embeddingDf.rowIndex.isubset(idx);
 }
 export const getDiscreteCellEmbeddingRowIndex = memoize(
   _getDiscreteCellEmbeddingRowIndex,
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type.
-  (df) => df.__id
+  (df: Dataframe) => df.__id
 );
 
 // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message