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/annoMatrix/annoMatrix.ts

@@ -219,7 +219,7 @@ export default class AnnoMatrix {
    **/
   // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  fetch(field, q) {
+  fetch(field, q): Dataframe {
     /*
 		Return the given query on a single matrix field as a single dataframe.
 		Currently supports ONLY full column query.
@@ -248,7 +248,7 @@ export default class AnnoMatrix {
     1. Fetch the "n_genes" column the "obs":
 
 			const df = await fetch("obs", "n_genes")
-      console.log("Largest number of genes is: ", df.summarize().max);
+      console.log("Largest number of genes is: ", df.summarizeContinuous().max);
 
     2. Fetch two separate columns from obs.  Returns a single dataframe containing
        the columns:
@@ -278,7 +278,7 @@ export default class AnnoMatrix {
 
   // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  prefetch(field, q) {
+  prefetch(field, q): void {
     /*
 		Start a data fetch & cache fill.  Identical to fetch() except it does
 		not return a value.
@@ -287,7 +287,6 @@ export default class AnnoMatrix {
     overall component rendering latency.
 		*/
     this._fetch(field, q);
-    return undefined;
   }
 
   /**
@@ -494,8 +493,8 @@ Return cache keys for columns associated with this query.  May return
 
   // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  async _fetch(field, q) {
-    if (!AnnoMatrix.fields().includes(field)) return undefined;
+  async _fetch(field, q): Dataframe {
+    if (!AnnoMatrix.fields().includes(field)) return Dataframe.empty();
     const queries = Array.isArray(q) ? q : [q];
     queries.forEach(_queryValidate);
 

client/src/annoMatrix/loader.ts

@@ -196,7 +196,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     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");
+      if (idx === -1) throw new Error("Unknown row label");
       data[idx] = value;
     }
 
@@ -299,8 +299,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
       default:
         throw new Error("Unknown field name");
     }
-
     const buffer = await promiseThrottle.priorityAdd(priority, doRequest);
+    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'unknown' is not assignable to parameter of type 'ArrayBuffer | ArrayBuffer[]'.... Remove this comment to see the full error message
     let result = matrixFBSToDataframe(buffer);
     if (!result || result.isEmpty()) throw Error("Unknown field/col");
 

client/src/annoMatrix/normalize.ts

@@ -1,3 +1,4 @@
+import { Schema } from "../common/types/schema";
 import { _getColumnSchema, _isIndex } from "./schema";
 import catLabelSort from "../util/catLabelSort";
 import {
@@ -5,12 +6,11 @@ import {
   overflowCategoryLabel,
   globalConfig,
 } from "../globals";
-import { Dataframe } from "../util/dataframe";
+import { Dataframe, LabelType, DataframeColumn } from "../util/dataframe";
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
 export function normalizeResponse(
   field: string,
-  schema: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  schema: Schema,
   response: Dataframe
 ): Dataframe {
   /**
@@ -65,8 +65,7 @@ export function normalizeResponse(
   return response;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-function castColumnToBoolean(df: Dataframe, label: any): Dataframe {
+function castColumnToBoolean(df: Dataframe, label: LabelType): Dataframe {
   const colData = df.col(label).asArray();
   const newColData = new Array(colData.length);
   for (let i = 0; i < colData.length; i += 1) newColData[i] = !!colData[i];
@@ -75,7 +74,10 @@ function castColumnToBoolean(df: Dataframe, label: any): Dataframe {
 }
 
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function normalizeWritableCategoricalSchema(colSchema: any, col: any) {
+export function normalizeWritableCategoricalSchema(
+  colSchema: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  col: DataframeColumn
+) {
   /*
   Ensure all enum writable / categorical schema have a categories array, that
   the categories array contains all unique values in the data array, AND that 
@@ -91,12 +93,11 @@ export function normalizeWritableCategoricalSchema(colSchema: any, col: any) {
   return colSchema;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
 export function normalizeCategorical(
   df: Dataframe,
-  colLabel: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  colLabel: LabelType,
   colSchema: any // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) {
+): Dataframe {
   /*
   If writable, ensure schema matches data and we have an unassigned label
 

client/src/annoMatrix/views.ts

@@ -197,7 +197,7 @@ function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) {
   if (qmax > 1) qmax = 1;
   if (qmin === 0 && qmax === 1) return colData;
 
-  const quantiles = df.col(colLabel).summarize().percentiles;
+  const quantiles = df.col(colLabel).summarizeContinuous().percentiles;
   const lower = quantiles[100 * qmin];
   const upper = quantiles[100 * qmax];
   const clippedData = clip(colData.slice(), lower, upper, Number.NaN);