Merge branch 'main' into colinmegill/#632

client/__tests__/util/annoMatrix/serverMocks/schema.ts

@@ -1,4 +1,6 @@
-export const schema = {
+import { RawSchema } from "../../../../src/common/types/entities";
+
+export const schema: { schema: RawSchema } = {
   schema: {
     annotations: {
       obs: {

client/__tests__/util/stateManager/sampleResponses.ts

@@ -5,6 +5,7 @@ import zip from "lodash.zip";
 import _ from "lodash";
 import { flatbuffers } from "flatbuffers";
 import { NetEncoding } from "../../../src/util/stateManager/matrix_generated";
+import { RawSchema } from "../../../src/common/types/entities";
 
 /*
 test data mocking REST 0.2 API responses.  Used in several tests.
@@ -29,7 +30,7 @@ const aConfigResponse = {
   },
 };
 
-const aSchemaResponse = {
+const aSchemaResponse: { schema: RawSchema } = {
   schema: {
     dataframe: {
       nObs,
@@ -40,28 +41,30 @@ const aSchemaResponse = {
       obs: {
         index: "name",
         columns: [
-          { name: "name", type: "string" },
+          { name: "name", type: "string", writable: false },
-          { name: "field1", type: "int32" },
+          { name: "field1", type: "int32", writable: false },
-          { name: "field2", type: "float32" },
+          { name: "field2", type: "float32", writable: false },
-          { name: "field3", type: "boolean" },
+          { name: "field3", type: "boolean", writable: false },
           {
             name: "field4",
             type: "categorical",
             categories: field4Categories,
+            writable: false,
           },
         ],
       },
       var: {
         index: "name",
         columns: [
-          { name: "name", type: "string" },
+          { name: "name", type: "string", writable: false },
-          { name: "fieldA", type: "int32" },
+          { name: "fieldA", type: "int32", writable: false },
-          { name: "fieldB", type: "float32" },
+          { name: "fieldB", type: "float32", writable: false },
-          { name: "fieldC", type: "boolean" },
+          { name: "fieldC", type: "boolean", writable: false },
           {
             name: "fieldD",
             type: "categorical",
             categories: fieldDCategories,
+            writable: false,
           },
         ],
       },

client/package.json

@@ -12,9 +12,10 @@
     "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.ts",
     "e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts",
     "fmt": "eslint --fix src __tests__",
-    "lint": "eslint --fix src __tests__",
+    "lint": "eslint src __tests__ & npm run type-check",
     "prod": "npm run build -- configuration/webpack/webpack.config.prod.js",
-    "test": "jest --testPathIgnorePatterns e2e"
+    "test": "jest --testPathIgnorePatterns e2e",
+    "type-check": "tsc --noEmit"
   },
   "engineStrict": true,
   "engines": {

client/src/common/types/entities.ts

@@ -1 +1,60 @@
 // If a globally shared type or interface doesn't have a clear owner, put it here
+
+export type Category = number | string | boolean;
+
+export interface AnnotationColumn {
+  categories?: Category[];
+  name: string;
+  type: "string" | "float32" | "int32" | "categorical" | "boolean";
+  writable: boolean;
+}
+
+interface DataFrame {
+  nObs: number;
+  nVar: number;
+  // TODO(thuang): Not sure what other types are available
+  type: "float32";
+}
+
+export interface LayoutColumn {
+  dims: string[];
+  name: string;
+  // TODO(thuang): Not sure what other types are available
+  type: "float32";
+}
+interface RawLayout {
+  obs: LayoutColumn[];
+  var?: LayoutColumn[];
+}
+
+interface RawAnnotations {
+  obs: {
+    columns: AnnotationColumn[];
+    index: string;
+  };
+  var: {
+    columns: AnnotationColumn[];
+    index: string;
+  };
+}
+
+export interface RawSchema {
+  annotations: RawAnnotations;
+  dataframe: DataFrame;
+  layout: RawLayout;
+}
+
+interface Annotations extends RawAnnotations {
+  obsByName: { [name: string]: AnnotationColumn };
+  varByName: { [name: string]: AnnotationColumn };
+}
+
+interface Layout extends RawLayout {
+  obsByName: { [name: string]: LayoutColumn };
+  varByName: { [name: string]: LayoutColumn };
+}
+
+export interface Schema extends RawSchema {
+  annotations: Annotations;
+  layout: Layout;
+}

client/src/util/fromEntries.ts

@@ -1,15 +1,17 @@
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export default function fromEntries<T = unknown>(
-export default function fromEntries(arr: any) {
+  arr: [string | number, T][]
+): { [key: string]: T } {
   /*
 	Similar to Object.fromEntries, but only handles array.
-	This could be replaced with the standard fucnction once it
+	This could be replaced with the standard function once it
 	is widely available.   As of 3/20/2019, it has not yet
 	been released in the Chrome stable channel.
 	*/
-  const obj = {};
+  const obj: { [key: string]: T } = {};
-  for (let i = 0, l = arr.length; i < l; i += 1) {
+
-    // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+  for (let i = 0; i < arr.length; i += 1) {
     obj[arr[i][0]] = arr[i][1];
   }
+
   return obj;
 }

client/src/util/stateManager/annotationsHelpers.ts

@@ -3,6 +3,8 @@ Helper functions for user-editable annotations state management.
 See also reducers/annotations.js
 */
 
+import { Schema } from "../../common/types/entities";
+
 /*
 There are a number of state constraints assumed throughout the
 application:
@@ -16,34 +18,36 @@ application:
 In addition, the current state management only allows for
 categorical annotations to be writable.
 */
-
+export function isCategoricalAnnotation(
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
+  schema: Schema,
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  name: string
-export function isCategoricalAnnotation(schema, name) {
+): boolean | undefined {
   /*
   we treat any string, categorical or boolean as a categorical.
-  Return true/false/undefined (for unkonwn fields)
   */
   const colSchema = schema.annotations.obsByName[name];
+
   if (colSchema === undefined) return undefined;
+
   const { type } = colSchema;
+
   return type === "string" || type === "boolean" || type === "categorical";
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
+export function isContinuousAnnotation(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  schema: Schema,
-export function isContinuousAnnotation(schema, name) {
+  name: string
-  /*
+): boolean | undefined {
-  Return true/false/undefined
-  */
   const colSchema = schema.annotations.obsByName[name];
+
   if (colSchema === undefined) return undefined;
+
   const { type } = colSchema;
+
   return !(type === "string" || type === "boolean" || type === "categorical");
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
+function _isUserAnnotation(schema: Schema, name: string): boolean {
-function _isUserAnnotation(schema, name) {
   return schema.annotations.obsByName[name]?.writable || false;
 }
 
@@ -72,9 +76,8 @@ export function allHaveLabelByMask(df, colName, label, mask) {
 }
 
 const legalCharacters = /^(\w|[ .()-])+$/;
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'name' implicitly has an 'any' type.
+
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+export function annotationNameIsErroneous(name: string): boolean | string {
-export function annotationNameIsErroneous(name) {
   /*
 	Validate the name - return:
 	* false - a valid name
@@ -101,6 +104,6 @@ export function annotationNameIsErroneous(name) {
     }
   }
 
-  /* all is well!  Indicte not erroneous with a false */
+  /* all is well! Indicate not erroneous with a false */
   return false;
 }

client/src/util/stateManager/schemaHelpers.ts

@@ -8,6 +8,12 @@ import cloneDeep from "lodash.clonedeep";
 
 import fromEntries from "../fromEntries";
 import catLabelSort from "../catLabelSort";
+import {
+  RawSchema,
+  Schema,
+  LayoutColumn,
+  AnnotationColumn,
+} from "../../common/types/entities";
 
 /*
 System wide schema assumptions:
@@ -15,31 +21,25 @@ System wide schema assumptions:
   - schema will be internally self-consistent (eg, index matches columns)
 */
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function indexEntireSchema(schema: RawSchema): Schema {
-export function indexEntireSchema(schema: any) {
   /* Index schema for ease of use */
-  schema.annotations.obsByName = fromEntries(
+  (schema as Schema).annotations.obsByName = fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.annotations?.obs?.columns?.map((v) => [v.name, v]) || []
-    schema.annotations?.obs?.columns?.map((v: any) => [v.name, v]) ?? []
   );
-  schema.annotations.varByName = fromEntries(
+  (schema as Schema).annotations.varByName = fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.annotations?.var?.columns?.map((v) => [v.name, v]) || []
-    schema.annotations?.var?.columns?.map((v: any) => [v.name, v]) ?? []
   );
-  schema.layout.obsByName = fromEntries(
+  (schema as Schema).layout.obsByName = fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.layout?.obs?.map((v) => [v.name, v]) || []
-    schema.layout?.obs?.map((v: any) => [v.name, v]) ?? []
   );
-  schema.layout.varByName = fromEntries(
+  (schema as Schema).layout.varByName = fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.layout?.var?.map((v) => [v.name, v]) || []
-    schema.layout?.var?.map((v: any) => [v.name, v]) ?? []
   );
 
-  return schema;
+  return schema as Schema;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _copyObsAnno(schema: Schema): Schema {
-function _copyObsAnno(schema: any) {
   /* redux copy conventions - WARNING, only for modifying obs annotations */
   return {
     ...schema,
@@ -50,8 +50,7 @@ function _copyObsAnno(schema: any) {
   };
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _copyObsLayout(schema: Schema): Schema {
-function _copyObsLayout(schema: any) {
   return {
     ...schema,
     layout: {
@@ -61,57 +60,62 @@ function _copyObsLayout(schema: any) {
   };
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _reindexObsAnno(schema: Schema): Schema {
-function _reindexObsAnno(schema: any) {
   /* reindex obs annotations ONLY */
   schema.annotations.obsByName = fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.annotations.obs.columns.map((v) => [v.name, v])
-    schema.annotations.obs.columns.map((v: any) => [v.name, v])
   );
   return schema;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _reindexObsLayout(schema: Schema) {
-function _reindexObsLayout(schema: any) {
   schema.layout.obsByName = fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.layout.obs.map((v) => [v.name, v])
-    schema.layout.obs.map((v: any) => [v.name, v])
   );
   return schema;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function removeObsAnnoColumn(schema: Schema, name: string): Schema {
-export function removeObsAnnoColumn(schema: any, name: any) {
   const newSchema = _copyObsAnno(schema);
   newSchema.annotations.obs.columns = schema.annotations.obs.columns.filter(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    (v) => v.name !== name
-    (v: any) => v.name !== name
   );
   return _reindexObsAnno(newSchema);
 }
 
-// @ts-expect-error ts-migrate(6133) FIXME: 'name' is declared but its value is never read.
+export function addObsAnnoColumn(
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  schema: Schema,
-export function addObsAnnoColumn(schema: any, name: any, defn: any) {
+  _: string,
+  defn: AnnotationColumn
+): Schema {
   const newSchema = _copyObsAnno(schema);
+
   newSchema.annotations.obs.columns.push(defn);
+
   return _reindexObsAnno(newSchema);
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function removeObsAnnoCategory(
-export function removeObsAnnoCategory(schema: any, name: any, category: any) {
+  schema: Schema,
+  name: string,
+  category: string
+): Schema {
   /* remove a category from a categorical annotation */
   const categories = schema.annotations.obsByName[name]?.categories;
-  if (!categories)
+
+  if (!categories) {
     throw new Error("column does not exist or is not categorical");
+  }
 
   const idx = categories.indexOf(category);
+
   if (idx === -1) throw new Error("category does not exist");
 
   const newSchema = _reindexObsAnno(_copyObsAnno(schema));
 
   /* remove category.  Do not need to resort as this can't change presentation order */
-  newSchema.annotations.obsByName[name].categories.splice(idx, 1);
+  newSchema.annotations.obsByName[name].categories?.splice(idx, 1);
+
   return newSchema;
 }
 
@@ -129,26 +133,27 @@ export function addObsAnnoCategory(schema: any, name: any, category: any) {
 
   /* add category, retaining presentation sort order */
   const catAnno = newSchema.annotations.obsByName[name];
+
   catAnno.categories = catLabelSort(catAnno.writable, [
-    ...catAnno.categories,
+    ...(catAnno.categories || []),
     category,
   ]);
+
   return newSchema;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function addObsLayout(schema: Schema, layout: LayoutColumn): Schema {
-export function addObsLayout(schema: any, layout: any) {
   /* add or replace a layout */
   const newSchema = _copyObsLayout(schema);
   newSchema.layout.obs.push(layout);
   return _reindexObsLayout(newSchema);
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function removeObsLayout(schema: Schema, name: string): Schema {
-export function removeObsLayout(schema: any, name: any) {
   /* remove a layout */
   const newSchema = _copyObsLayout(schema);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+
-  newSchema.layout.obs = schema.layout.obs.filter((v: any) => v.name !== name);
+  newSchema.layout.obs = schema.layout.obs.filter((v) => v.name !== name);
+
   return _reindexObsLayout(newSchema);
 }

client/tsconfig.json

@@ -31,5 +31,5 @@
     "__tests__/**/*",
     "jest-puppeteer.config.js"
   ],
-  "exclude": ["__tests__/e2e/__snapshots__/**/*"]
+  "exclude": ["node_modules", "__tests__/e2e/__snapshots__/**/*"]
 }