Merge branch 'master' into colinmegill/geneset-prototype

client/__tests__/e2e/config.js

@@ -1,9 +1,9 @@
-export const jest_env = process.env.JEST_ENV;
+export const jestEnv = process.env.JEST_ENV;
 export const appPort = process.env.CXG_SERVER_PORT;
 export const appUrlBase =
   process.env.CXG_URL_BASE || `http://localhost:${appPort}`;
-export const DEV = jest_env === "dev";
+export const DEV = jestEnv === "dev";
-export const DEBUG = jest_env === "debug";
+export const DEBUG = jestEnv === "debug";
 export const DATASET = "pbmc3k";
 
 if (DEBUG) jest.setTimeout(100000);

client/__tests__/e2e/e2e.test.js

@@ -7,7 +7,10 @@ import { appUrlBase, DATASET } from "./config";
 import { setupTestBrowser } from "./testBrowser";
 import { datasets } from "./data";
 
-let browser, page, utils, cxgActions;
+let browser;
+let page;
+let utils;
+let cxgActions;
 const data = datasets[DATASET];
 
 beforeAll(async () => {
@@ -29,6 +32,17 @@ describe("did launch", () => {
     );
     expect(element).toBe(data.title);
   });
+
+  test("terms of service, if they are there", async () => {
+    try {
+      await utils.clickOn("tos-cookies-accept", { timeout: 500 });
+    } catch {
+      console.warn("No terms of service footer detected.");
+    }
+    page.waitFor(50); // give the footer a chance to disappear
+    const result = await page.$("[data-testid='tos-cookies-accept']");
+    expect(result).toBeNull();
+  });
 });
 
 describe("metadata loads", () => {
@@ -119,7 +133,7 @@ describe("gene entry", () => {
       testGenes
     );
     expect(allHistograms).toEqual(expect.arrayContaining(testGenes));
-    expect(allHistograms.length).toEqual(testGenes.length);
+    expect(allHistograms).toHaveLength(testGenes.length);
   });
 });
 
@@ -133,7 +147,7 @@ describe("differential expression", () => {
     expect(allHistograms).toEqual(
       expect.arrayContaining(data.diffexp["gene-results"])
     );
-    expect(allHistograms.length).toEqual(data.diffexp["gene-results"].length);
+    expect(allHistograms).toHaveLength(data.diffexp["gene-results"].length);
   });
 });
 

client/__tests__/e2e/e2eAnnotations.test.js

@@ -5,7 +5,10 @@ import { appUrlBase, DATASET } from "./config";
 import { setupTestBrowser } from "./testBrowser";
 import { datasets } from "./data";
 
-let browser, page, utils, actions;
+let browser;
+let page;
+let utils;
+let actions;
 const data = datasets[DATASET];
 
 beforeAll(async () => {

client/__tests__/e2e/feature.test.js

@@ -12,9 +12,13 @@ import { appUrlBase, DEBUG, DEV, DATASET } from "./config";
 import { puppeteerUtils, cellxgeneActions } from "./puppeteerUtils";
 import { datasets } from "./data";
 
-let browser, page, utils, cxgActions, spy;
+let browser;
+let page;
+let utils;
+let cxgActions;
+let spy;
 const browserViewport = { width: 1280, height: 960 };
-let data = datasets[DATASET].features;
+const data = datasets[DATASET].features;
 
 if (DEBUG) jest.setTimeout(100000);
 if (DEV) jest.setTimeout(10000);

client/__tests__/e2e/puppeteerUtils.js

@@ -44,8 +44,8 @@ export const puppeteerUtils = (page) => ({
   },
 
   async clickOn(testid, options = {}) {
-    await this.waitByID(testid);
+    await this.waitByID(testid, options);
-    const click = await page.click(`[data-testid='${testid}']`, options);
+    const click = await page.click(`[data-testid='${testid}']`);
     await page.waitFor(50);
     return click;
   },

client/__tests__/e2e/testBrowser.js

@@ -36,6 +36,10 @@ export async function setupTestBrowser() {
     page.on("console", async (msg) => {
       // If there is a console.error but an error is not thrown, this will ensure the test fails
       if (msg.type() === "error") {
+        // TODO: chromium does not currently support the CSP directive on the
+        // line below, so we swallow this error. Remove this when the test
+        // suite uses a browser version that supports this directive.
+        if (msg.text() === "Unrecognized Content-Security-Policy directive 'require-trusted-types-for'.\n") return;
         const errorMsgText = await Promise.all(
           // TODO can we do this without internal properties?
           msg.args().map((arg) => arg._remoteObject.description)

client/__tests__/util/promiseLimit.test.js

@@ -1,4 +1,4 @@
-import { PromiseLimit } from "../../src/util/promiseLimit";
+import PromiseLimit from "../../src/util/promiseLimit";
 import { range } from "../../src/util/range";
 
 const delay = (t) => new Promise((resolve, reject) => setTimeout(resolve, t));

client/configuration/webpack/cspHashPlugin.js

@@ -54,7 +54,7 @@ class CspHashPlugin {
       .createHash("sha256")
       .update(str, "utf8")
       .digest("base64");
-    return "sha256-" + hash;
+    return `sha256-${hash}`;
   }
 }
 

client/src/actions/index.js

@@ -7,7 +7,7 @@ import {
   doBinaryRequest,
   dispatchNetworkErrorMessageToUser,
 } from "../util/actionHelpers";
-import { PromiseLimit } from "../util/promiseLimit";
+import PromiseLimit from "../util/promiseLimit";
 import { requestReembed, reembedResetWorldToUniverse } from "./reembed";
 import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
 

client/src/components/autosave/filenameDialog.js

@@ -18,7 +18,7 @@ import {
   saveInProgress: state.autosave?.saveInProgress ?? false,
   lastSavedObsAnnotations: state.autosave?.lastSavedObsAnnotations,
   error: state.autosave?.error,
-  writableCategoriesEnabled: state.config?.parameters?.["annotations"] ?? false,
+  writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
 }))
 class FilenameDialog extends React.Component {
   constructor(props) {

client/src/components/autosave/index.js

@@ -1,6 +1,5 @@
 import React from "react";
 import { connect } from "react-redux";
-import * as globals from "../../globals";
 import actions from "../../actions";
 import FilenameDialog from "./filenameDialog";
 
@@ -11,7 +10,7 @@ import FilenameDialog from "./filenameDialog";
   saveInProgress: state.autosave?.saveInProgress ?? false,
   lastSavedObsAnnotations: state.autosave?.lastSavedObsAnnotations,
   error: state.autosave?.error,
-  writableCategoriesEnabled: state.config?.parameters?.["annotations"] ?? false,
+  writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
   initialDataLoadComplete: state.autosave?.initialDataLoadComplete,
 }))
 class Autosave extends React.Component {

client/src/components/categorical/category/index.js

@@ -64,7 +64,7 @@ class Category extends React.Component {
       } else if (categoryCount.selectedCatCount < categoryCount.totalCatCount) {
         /* to be explicit... */
         this.checkbox.indeterminate = true;
-        this.setState({ isChecked: false });
+        this.setState({ isChecked: false }); // eslint-disable-line react/no-did-update-set-state
       }
     }
   }
@@ -77,14 +77,15 @@ class Category extends React.Component {
     });
   };
 
-  toggleAll() {
+  handleCategoryClick = () => {
-    const { dispatch, metadataField } = this.props;
+    const { annotations, metadataField, onExpansionChange } = this.props;
-    dispatch({
+    const editingCategory =
-      type: "categorical metadata filter all of these",
+      annotations.isEditingCategoryName &&
-      metadataField,
+      annotations.categoryBeingEdited === metadataField;
-    });
+    if (!editingCategory) {
-    this.setState({ isChecked: true });
+      onExpansionChange(metadataField);
-  }
+    }
+  };
 
   toggleNone() {
     const { dispatch, metadataField } = this.props;
@@ -95,6 +96,15 @@ class Category extends React.Component {
     this.setState({ isChecked: false });
   }
 
+  toggleAll() {
+    const { dispatch, metadataField } = this.props;
+    dispatch({
+      type: "categorical metadata filter all of these",
+      metadataField,
+    });
+    this.setState({ isChecked: true });
+  }
+
   handleToggleAllClick() {
     const { isChecked } = this.state;
     // || this.checkbox.indeterminate === false
@@ -115,6 +125,8 @@ class Category extends React.Component {
       globals.categoryDisplayStringMaxLength
     );
 
+    const checkboxID = `category-select-${metadataField}`;
+
     return (
       <div
         style={{
@@ -135,8 +147,8 @@ class Category extends React.Component {
               alignItems: "flex-start",
             }}
           >
-            <label className="bp3-control bp3-checkbox">
+            <label htmlFor={checkboxID} className="bp3-control bp3-checkbox">
-              <input disabled checked type="checkbox" />
+              <input disabled id={checkboxID} checked type="checkbox" />
               <span className="bp3-control-indicator" />
             </label>
             <Tooltip
@@ -174,9 +186,7 @@ class Category extends React.Component {
       metadataField,
       categoricalSelection,
       isColorAccessor,
-      annotations,
       isExpanded,
-      onExpansionChange,
       schema,
     } = this.props;
 
@@ -185,6 +195,8 @@ class Category extends React.Component {
       return this.renderIsStillLoading();
     }
 
+    const checkboxID = `category-select-${metadataField}`;
+
     const isUserAnno =
       schema?.annotations?.obsByName[metadataField]?.writable ?? false;
     const isTruncated = _.get(
@@ -225,8 +237,9 @@ class Category extends React.Component {
             alignItems: "flex-start",
           }}
         >
-          <label className="bp3-control bp3-checkbox">
+          <label className="bp3-control bp3-checkbox" htmlFor={checkboxID}>
             <input
+              id={checkboxID}
               data-testclass="category-select"
               data-testid={`${metadataField}:category-select`}
               onChange={this.handleToggleAllClick.bind(this)}
@@ -251,19 +264,19 @@ class Category extends React.Component {
             }}
           >
             <span
+              role="menuitem"
+              tabIndex="0"
               data-testid={`${metadataField}:category-expand`}
+              onKeyPress={(e) => {
+                if (e.key === "Enter") {
+                  this.handleCategoryClick();
+                }
+              }}
               style={{
                 cursor: "pointer",
                 display: "inline-block",
               }}
-              onClick={() => {
+              onClick={this.handleCategoryClick}
-                const editingCategory =
-                  annotations.isEditingCategoryName &&
-                  annotations.categoryBeingEdited === metadataField;
-                if (!editingCategory) {
-                  onExpansionChange(metadataField);
-                }
-              }}
             >
               {isUserAnno ? (
                 <Icon style={{ marginRight: 5 }} icon="tag" iconSize={16} />

client/src/components/categorical/index.js

@@ -11,7 +11,7 @@ import LabelInput from "./labelInput";
 import { labelPrompt } from "./labelUtil";
 
 @connect((state) => ({
-  writableCategoriesEnabled: state.config?.parameters?.["annotations"] ?? false,
+  writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
   schema: state.world?.schema,
   config: state.config,
   ontology: state.ontology,

client/src/components/categorical/labelInput.js

@@ -23,6 +23,9 @@ export default class LabelInput extends React.PureComponent {
   * popoverProps -- will be passed to <Suggest>
   */
 
+  /* maxinum number of suggestions */
+  static QueryResultLimit = 100;
+
   constructor(props) {
     super(props);
 
@@ -103,9 +106,6 @@ export default class LabelInput extends React.PureComponent {
     );
   };
 
-  /* maxinum number of suggestions */
-  static QueryResultLimit = 100;
-
   filterLabels(query) {
     const { labelSuggestions } = this.props;
     if (!labelSuggestions) return [];

client/src/components/categorical/value/index.js

@@ -62,6 +62,8 @@ class CategoryValue extends React.Component {
       prevProps.metadataField !== metadataField ||
       prevProps.categoryIndex !== categoryIndex
     ) {
+      // adequately checked to prevent looping
+      // eslint-disable-next-line react/no-did-update-set-state
       this.setState({
         editedLabelText: this.currentLabel(),
       });
@@ -327,6 +329,8 @@ class CategoryValue extends React.Component {
       annotations.isEditingLabelName &&
       annotations.labelEditable.label === categoryIndex;
 
+    const valueToggleLabel = `value-toggle-checkbox-${displayString}`;
+
     return (
       <div
         key={i}
@@ -360,8 +364,13 @@ class CategoryValue extends React.Component {
           }}
         >
           <div style={{ display: "flex", alignItems: "baseline" }}>
-            <label className="bp3-control bp3-checkbox" style={{ margin: 0 }}>
+            <label
+              htmlFor={valueToggleLabel}
+              className="bp3-control bp3-checkbox"
+              style={{ margin: 0 }}
+            >
               <input
+                id={valueToggleLabel}
                 onChange={selected ? this.toggleOff : this.toggleOn}
                 data-testclass="categorical-value-select"
                 data-testid={`categorical-value-select-${metadataField}-${displayString}`}

client/src/components/framework/toasters.js

@@ -7,11 +7,6 @@ const ToastTopCenter = Toaster.create({
   position: Position.TOP,
 });
 
-const ToastBottomCenter = Toaster.create({
-  className: "recipe-toaster",
-  position: Position.BOTTOM,
-});
-
 /*
 A "user" error - eg, bad input
 */

client/src/components/geneExpression/addGenes.js

@@ -262,7 +262,7 @@ class AddGenes extends React.Component {
               }}
               itemListPredicate={filterGenes}
               onActiveItemChange={(item) => this.setState({ activeItem: item })}
-              itemRenderer={renderGene.bind(this)}
+              itemRenderer={renderGene}
               items={varIndex || ["No genes"]}
               popoverProps={{ minimal: true }}
             />

client/src/components/graph/graph.js

@@ -10,7 +10,6 @@ import setupSVGandBrushElements from "./setupSVGandBrush";
 import _camera from "../../util/camera";
 import _drawPoints from "./drawPointsRegl";
 import { isTypedArray } from "../../util/typeHelpers";
-import styles from "./graph.css";
 
 import GraphOverlayLayer from "./overlays/graphOverlayLayer";
 import CentroidLabels from "./overlays/centroidLabels";
@@ -190,7 +189,7 @@ class Graph extends React.Component {
       tool: null,
       container: null,
       cameraRender: 0,
-      viewport
+      viewport,
     };
   }
 
@@ -209,7 +208,10 @@ class Graph extends React.Component {
 
     // create all default rendering transformations
     const modelTF = createModelTF();
-    const projectionTF = createProjectionTF(this.reglCanvas.width, this.reglCanvas.height);
+    const projectionTF = createProjectionTF(
+      this.reglCanvas.width,
+      this.reglCanvas.height
+    );
 
     // initial draw to canvas
     this.renderPoints(
@@ -250,7 +252,8 @@ class Graph extends React.Component {
     } = this.props;
     const { regl, toolSVG, camera, modelTF, viewport } = this.state;
     let { projectionTF } = this.state;
-    const hasResized = prevState.viewport.height !== this.reglCanvas.height ||
+    const hasResized =
+      prevState.viewport.height !== this.reglCanvas.height ||
       prevState.viewport.width !== this.reglCanvas.width;
     let stateChanges = {};
     let needsRepaint = hasResized;
@@ -261,7 +264,10 @@ class Graph extends React.Component {
       const { drawPoints, pointBuffer, colorBuffer, flagBuffer } = this.state;
 
       if (hasResized) {
-        projectionTF = createProjectionTF(this.reglCanvas.width, this.reglCanvas.height);
+        projectionTF = createProjectionTF(
+          this.reglCanvas.width,
+          this.reglCanvas.height
+        );
         stateChanges = {
           ...stateChanges,
           projectionTF,
@@ -322,7 +328,10 @@ class Graph extends React.Component {
         ...stateChanges,
         ...this.createToolSVG(),
       };
-    } else if ((viewport.height && viewport.width && !toolSVG) || selectionTool !== prevProps.selectionTool ) {
+    } else if (
+      (viewport.height && viewport.width && !toolSVG) ||
+      selectionTool !== prevProps.selectionTool
+    ) {
       // first time or change of selection tool
       stateChanges = { ...stateChanges, ...this.createToolSVG() };
     } else if (prevProps.graphInteractionMode !== graphInteractionMode) {
@@ -349,6 +358,7 @@ class Graph extends React.Component {
       );
     }
     if (Object.keys(stateChanges).length > 0) {
+      // Preventing update loop via stateChanges and diff checks
       // eslint-disable-next-line react/no-did-update-set-state
       this.setState(stateChanges);
     }
@@ -371,12 +381,11 @@ class Graph extends React.Component {
     const { viewportRef } = this.props;
     return {
       height: viewportRef.clientHeight,
-      width: viewportRef.clientWidth
+      width: viewportRef.clientWidth,
     };
   };
 
-
+  handleCanvasEvent = (e) => {
-  handleCanvasEvent = e => {
     const { camera, projectionTF } = this.state;
     if (e.type !== "wheel") e.preventDefault();
     if (camera.handleEvent(e, projectionTF)) {
@@ -547,12 +556,8 @@ class Graph extends React.Component {
     vec2.transformMat3(xy, xy, projectionTF);
 
     return [
-      Math.round(
+      Math.round(((xy[0] + 1) * viewport.width) / 2),
-        (xy[0] + 1) * viewport.width / 2
+      Math.round(-((xy[1] + 1) / 2 - 1) * viewport.height),
-      ),
-      Math.round(
-        -((xy[1] + 1) / 2 - 1) * viewport.height
-      )
     ];
   }
 
@@ -698,7 +703,7 @@ class Graph extends React.Component {
       count: this.count,
       projView,
       nPoints: universe.nObs,
-      minViewportDimension: Math.min(width, height)
+      minViewportDimension: Math.min(width, height),
     });
     regl._gl.flush();
   }
@@ -744,9 +749,11 @@ class Graph extends React.Component {
           cameraTF={cameraTF}
           modelTF={modelTF}
           projectionTF={projectionTF}
-          handleCanvasEvent={graphInteractionMode === "zoom" ? this.handleCanvasEvent : undefined}
+          handleCanvasEvent={
+            graphInteractionMode === "zoom" ? this.handleCanvasEvent : undefined
+          }
         >
-          <CentroidLabels/>
+          <CentroidLabels />
         </GraphOverlayLayer>
         <svg
           id="lasso-layer"
@@ -756,13 +763,11 @@ class Graph extends React.Component {
             position: "absolute",
             top: 0,
             left: 0,
-            zIndex: 1
+            zIndex: 1,
           }}
           width={viewport.width}
           height={viewport.height}
-          pointerEvents={
+          pointerEvents={graphInteractionMode === "select" ? "auto" : "none"}
-            graphInteractionMode === "select" ? "auto" : "none"
-          }
         />
         <canvas
           width={viewport.width}
@@ -777,7 +782,9 @@ class Graph extends React.Component {
           }}
           className="graph-canvas"
           data-testid="layout-graph"
-          ref={canvas => { this.reglCanvas = canvas; }}
+          ref={(canvas) => {
+            this.reglCanvas = canvas;
+          }}
           onMouseDown={this.handleCanvasEvent}
           onMouseUp={this.handleCanvasEvent}
           onMouseMove={this.handleCanvasEvent}

client/src/components/graph/overlays/centroidLabels.js

@@ -1,5 +1,3 @@
-/* eslint-disable max-classes-per-file */
-/* eslint-disable jsx-a11y/mouse-events-have-key-events */
 import React, { PureComponent } from "react";
 import { connect } from "react-redux";
 
@@ -26,7 +24,7 @@ class CentroidLabels extends PureComponent {
       // Notify overlay layer of display change
       overlayToggled("centroidLabels", displayChangeOn);
     }
-  };
+  }
 
   render() {
     const {
@@ -59,6 +57,7 @@ class CentroidLabels extends PureComponent {
 
       labelSVGS.push(
         <g
+          // label is unique so disabling eslint rule
           // eslint-disable-next-line react/no-array-index-key
           key={label}
           className="centroid-label"
@@ -66,6 +65,8 @@ class CentroidLabels extends PureComponent {
           data-testclass="centroid-label"
           data-testid={`${label}-centroid-label`}
         >
+          {/* The mouse actions for centroid labels do not have a screen reader alternative */}
+          {/* eslint-disable-next-line jsx-a11y/mouse-events-have-key-events */}
           <text
             transform={inverseTransform}
             textAnchor="middle"

client/src/components/graph/overlays/graphOverlayLayer.js

@@ -2,8 +2,7 @@ import React, { PureComponent, cloneElement } from "react";
 
 import styles from "../graph.css";
 
-export default
+export default class GraphOverlayLayer extends PureComponent {
-class GraphOverlayLayer extends PureComponent {
   /*
     This component takes its children (assumed in the data coordinate space ([0, 1] range, origin in bottom left corner))
     and transforms itself multiple times resulting in screen space ([0, screenWidth/Height] range, origin in top left corner)
@@ -49,7 +48,6 @@ class GraphOverlayLayer extends PureComponent {
       handleCanvasEvent,
       width,
       height,
-      style
     } = this.props;
     const { display } = this.state;
 
@@ -63,7 +61,7 @@ class GraphOverlayLayer extends PureComponent {
       cameraTF
     )} ${this.reverseMatrixScaleTransformString(
       projectionTF
-    )} scale(1 2) scale(1 ${1 / (-height)}) scale(2 1) scale(${1 / width} 1)`;
+    )} scale(1 2) scale(1 ${1 / -height}) scale(2 1) scale(${1 / width} 1)`;
 
     // Copy the children passed with the overlay and add the inverse transform and onDisplayChange props
     const newChildren = React.Children.map(children, (child) =>

client/src/components/leftSidebar/topLeftLogoAndTitle.js

@@ -4,7 +4,7 @@ import { connect } from "react-redux";
 import * as globals from "../../globals";
 import Logo from "../framework/logo";
 
-@connect(state => ({
+@connect((state) => ({
   datasetTitle: state.config?.displayNames?.dataset ?? "",
   aboutURL: state.config?.links?.["about-dataset"],
   scatterplotXXaccessor: state.controls.scatterplotXXaccessor,
@@ -75,7 +75,7 @@ class LeftSideBar extends React.Component {
           title={datasetTitle}
         >
           {aboutURL ? (
-            <a href={aboutURL} target="_blank">
+            <a href={aboutURL} target="_blank" rel="noopener noreferrer">
               {displayTitle}
             </a>
           ) : (

client/src/components/menubar/cellSetButtons.js

@@ -45,7 +45,9 @@ class CellSetButton extends React.PureComponent {
         <AnchorButton
           type="button"
           disabled={differential.diffExp}
-          onClick={this.set.bind(this)}
+          onClick={() => {
+            this.set();
+          }}
           data-testid={`cellset-button-${eitherCellSetOneOrTwo}`}
         >
           {eitherCellSetOneOrTwo}

client/src/components/menubar/diffexpButtons.js

@@ -1,14 +1,7 @@
 // jshint esversion: 6
 import React from "react";
 import { connect } from "react-redux";
-import {
+import { Button, ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core";
-  Popover,
-  Button,
-  ButtonGroup,
-  AnchorButton,
-  Tooltip,
-  Position,
-} from "@blueprintjs/core";
 import * as globals from "../../globals";
 import styles from "./menubar.css";
 import actions from "../../actions";
@@ -21,16 +14,9 @@ import CellSetButton from "./cellSetButtons";
   celllist1: state.differential?.celllist1,
   celllist2: state.differential?.celllist2,
   diffexpMayBeSlow: state.config?.parameters?.["diffexp-may-be-slow"] ?? false,
-  diffexpCellcountMax: state.config?.limits?.diffexp_cellcount_max,
+  diffexpCellcountMax: state.config?.limits?.["diffexp_cellcount_max"],
 }))
 class DiffexpButtons extends React.Component {
-  constructor(props) {
-    super(props);
-    this.state = {
-      userDismissedPopover: false,
-    };
-  }
-
   computeDiffExp = () => {
     const { dispatch, differential } = this.props;
     if (differential.celllist1 && differential.celllist2) {
@@ -54,16 +40,9 @@ class DiffexpButtons extends React.Component {
     });
   };
 
-  handlePopoverDismiss = () => {
-    this.setState({
-      userDismissedPopover: true,
-    });
-  };
-
   render() {
     /* diffexp-related buttons may be disabled */
     const { differential, diffexpMayBeSlow, diffexpCellcountMax } = this.props;
-    const { userDismissedPopover } = this.state;
 
     const haveBothCellSets =
       !!differential.celllist1 && !!differential.celllist2;
@@ -86,7 +65,7 @@ class DiffexpButtons extends React.Component {
         diffexpCellcountMax;
 
     return (
-      <ButtonGroup className={styles.menubarButton} >
+      <ButtonGroup className={styles.menubarButton}>
         <CellSetButton
           {...this.props} // eslint-disable-line react/jsx-props-no-spreading
           eitherCellSetOneOrTwo={1}

client/src/components/menubar/embedding.js

@@ -69,9 +69,7 @@ class Embedding extends React.PureComponent {
     const { layoutChoice } = this.props;
 
     return (
-      <ButtonGroup
+      <ButtonGroup className={styles.menubarButton}>
-        className={styles.menubarButton}
-      >
         <Popover
           target={
             <Tooltip

client/src/components/menubar/index.js

@@ -1,7 +1,7 @@
 // jshint esversion: 6
 import React from "react";
 import { connect } from "react-redux";
-import { Button, ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core";
+import { ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core";
 
 import * as globals from "../../globals";
 import styles from "./menubar.css";
@@ -28,7 +28,7 @@ import DiffexpButtons from "./diffexpButtons";
   scatterplotYYaccessor: state.controls.scatterplotYYaccessor,
   celllist1: state.differential.celllist1,
   celllist2: state.differential.celllist2,
-  libraryVersions: state.config?.library_versions, // eslint-disable-line camelcase
+  libraryVersions: state.config?.["library_versions"],
   undoDisabled: state["@@undoable/past"].length === 0,
   redoDisabled: state["@@undoable/future"].length === 0,
   aboutLink: state.config?.links?.["about-dataset"],
@@ -207,9 +207,10 @@ class MenuBar extends React.Component {
     const { pendingClipPercentiles } = this.state;
 
     // constants used to create selection tool button
-    const [selectionTooltip, selectionButtonIcon] = selectionTool === "brush"
+    const [selectionTooltip, selectionButtonIcon] =
-      ? ["Brush selection", "Lasso selection"]
+      selectionTool === "brush"
-      : ["select", "polygon-filter"];
+        ? ["Brush selection", "Lasso selection"]
+        : ["select", "polygon-filter"];
 
     return (
       <div
@@ -245,80 +246,82 @@ class MenuBar extends React.Component {
           handleClipCommit={this.handleClipCommit}
           isClipDisabled={this.isClipDisabled}
           handleClipOnKeyPress={this.handleClipOnKeyPress}
-          handleClipPercentileMaxValueChange={this.handleClipPercentileMaxValueChange}
+          handleClipPercentileMaxValueChange={
-          handleClipPercentileMinValueChange={this.handleClipPercentileMinValueChange}
+            this.handleClipPercentileMaxValueChange
+          }
+          handleClipPercentileMinValueChange={
+            this.handleClipPercentileMinValueChange
+          }
         />
-    <Embedding />
+        <Embedding />
-    <Tooltip
+        <Tooltip
-      content="When a category is colored by, show labels on the graph"
+          content="When a category is colored by, show labels on the graph"
-      position="bottom"
+          position="bottom"
-      disabled={graphInteractionMode === "zoom"}
+          disabled={graphInteractionMode === "zoom"}
-    >
+        >
-      <AnchorButton
+          <AnchorButton
-        className={styles.menubarButton}
+            className={styles.menubarButton}
-        type="button"
+            type="button"
-        data-testid="centroid-label-toggle"
+            data-testid="centroid-label-toggle"
-        icon="property"
+            icon="property"
-        onClick={this.handleCentroidChange}
+            onClick={this.handleCentroidChange}
-        active={showCentroidLabels}
+            active={showCentroidLabels}
-        intent={showCentroidLabels ? "primary" : "none"}
+            intent={showCentroidLabels ? "primary" : "none"}
-      />
+          />
-    </Tooltip>
+        </Tooltip>
-    <ButtonGroup
+        <ButtonGroup className={styles.menubarButton}>
-      className={styles.menubarButton}
+          <Tooltip
-    >
+            content={selectionTooltip}
-      <Tooltip
+            position="bottom"
-        content={selectionTooltip}
+            hoverOpenDelay={globals.tooltipHoverOpenDelay}
-        position="bottom"
+          >
-        hoverOpenDelay={globals.tooltipHoverOpenDelay}
+            <AnchorButton
-      >
+              type="button"
-        <AnchorButton
+              data-testid="mode-lasso"
-          type="button"
+              icon={selectionButtonIcon}
-          data-testid="mode-lasso"
+              active={graphInteractionMode === "select"}
-          icon={selectionButtonIcon}
+              onClick={() => {
-          active={graphInteractionMode === "select"}
+                dispatch({
-          onClick={() => {
+                  type: "change graph interaction mode",
-            dispatch({
+                  data: "select",
-              type: "change graph interaction mode",
+                });
-              data: "select"
+              }}
-            });
+            />
+          </Tooltip>
+          <Tooltip
+            content="Drag to pan, scroll to zoom"
+            position="bottom"
+            hoverOpenDelay={globals.tooltipHoverOpenDelay}
+          >
+            <AnchorButton
+              type="button"
+              data-testid="mode-pan-zoom"
+              icon="zoom-in"
+              active={graphInteractionMode === "zoom"}
+              onClick={() => {
+                dispatch({
+                  type: "change graph interaction mode",
+                  data: "zoom",
+                });
+              }}
+            />
+          </Tooltip>
+        </ButtonGroup>
+        <Subset
+          subsetPossible={this.subsetPossible()}
+          subsetResetPossible={this.subsetResetPossible()}
+          handleSubset={() => {
+            dispatch(actions.setWorldToSelection());
+            dispatch({ type: "increment graph render counter" });
+          }}
+          handleSubsetReset={() => {
+            dispatch(actions.resetWorldToUniverse());
+            dispatch({ type: "increment graph render counter" });
           }}
         />
-      </Tooltip>
+        {disableDiffexp ? null : <DiffexpButtons />}
-      <Tooltip
+      </div>
-        content="Drag to pan, scroll to zoom"
+    );
-        position="bottom"
-        hoverOpenDelay={globals.tooltipHoverOpenDelay}
-      >
-        <AnchorButton
-          type="button"
-          data-testid="mode-pan-zoom"
-          icon="zoom-in"
-          active={graphInteractionMode === "zoom"}
-          onClick={() => {
-            dispatch({
-              type: "change graph interaction mode",
-              data: "zoom"
-            });
-          }}
-        />
-      </Tooltip>
-    </ButtonGroup>
-    <Subset
-      subsetPossible={this.subsetPossible()}
-      subsetResetPossible={this.subsetResetPossible()}
-      handleSubset={() => {
-        dispatch(actions.setWorldToSelection());
-        dispatch({ type: "increment graph render counter" });
-      }}
-      handleSubsetReset={() => {
-        dispatch(actions.resetWorldToUniverse());
-        dispatch({ type: "increment graph render counter" });
-      }}
-    />
-    {disableDiffexp ? null : <DiffexpButtons/>}
-    </div>
-  );
   }
 }
 

client/src/components/scatterplot/scatterplot.js

@@ -141,7 +141,7 @@ class Scatterplot extends React.PureComponent {
       viewport: {
         height: null,
         width: null,
-      }
+      },
     };
   }
 
@@ -190,7 +190,7 @@ class Scatterplot extends React.PureComponent {
       svg,
       drawPoints,
       projectionTF,
-      viewport
+      viewport,
     });
   }
 
@@ -286,20 +286,11 @@ class Scatterplot extends React.PureComponent {
     return {
       viewport: {
         height: window.height,
-        width: window.width
+        width: window.width,
-      }
+      },
     };
   };
 
-  handleResize = () => {
-    const { state } = this.state;
-    const viewport = this.getViewportDimensions();
-    this.setState({
-      ...state,
-      viewport,
-    });
-  };
-
   static setupScales(expressionX, expressionY) {
     const xScale = d3
       .scaleLinear()
@@ -316,6 +307,15 @@ class Scatterplot extends React.PureComponent {
     };
   }
 
+  handleResize = () => {
+    const { state } = this.state;
+    const viewport = this.getViewportDimensions();
+    this.setState({
+      ...state,
+      viewport,
+    });
+  };
+
   updateViewportDimensions = () => {
     this.setState(this.getViewportDimensions());
   };
@@ -390,7 +390,7 @@ class Scatterplot extends React.PureComponent {
       minViewportDimension: Math.min(
         viewport.width - globals.leftSidebarWidth || width,
         viewport.height || height
-      )
+      ),
     });
     regl._gl.flush();
   }

client/src/components/termsPrompt/index.js

@@ -8,8 +8,6 @@ import {
   Colors,
   Icon,
 } from "@blueprintjs/core";
-import * as globals from "../../globals";
-import { termsOfServiceToast } from "../framework/toasters";
 
 const CookieDecision = "cxg.cookieDecision";
 
@@ -26,12 +24,14 @@ function storageGet(key, defaultValue = null) {
 function storageSet(key, value) {
   try {
     window.localStorage.setItem(key, value);
-  } catch {}
+  } catch {
+    // continue
+  }
 }
 
 @connect((state) => ({
-  tosURL: state.config?.parameters?.about_legal_tos,
+  tosURL: state.config?.parameters?.["about_legal_tos"],
-  privacyURL: state.config?.parameters?.about_legal_privacy,
+  privacyURL: state.config?.parameters?.["about_legal_privacy"],
 }))
 class TermsPrompt extends React.PureComponent {
   constructor(props) {
@@ -59,7 +59,9 @@ class TermsPrompt extends React.PureComponent {
     if (window.cookieDecisionCallback instanceof Function) {
       try {
         window.cookieDecisionCallback();
-      } catch (e) {}
+      } catch (e) {
+        // continue
+      }
     }
   };
 
@@ -82,6 +84,7 @@ class TermsPrompt extends React.PureComponent {
           }}
           href={tosURL}
           target="_blank"
+          rel="noopener noreferrer"
         >
           terms of service
         </a>
@@ -103,6 +106,7 @@ class TermsPrompt extends React.PureComponent {
           }}
           href={privacyURL}
           target="_blank"
+          rel="noopener noreferrer"
         >
           privacy policy
         </a>
@@ -118,12 +122,10 @@ class TermsPrompt extends React.PureComponent {
       <Drawer
         onclose={this.drawerClose}
         isOpen={isOpen}
-        size={"120px"}
+        size="120px"
         position={Position.BOTTOM}
         canOutsideClickClose={false}
-        hasBackdrop={
+        hasBackdrop /* if the user can't use the app or click outside to dismiss, that should be visually represented with a backdrop */
-          true /* if the user can't use the app or click outside to dismiss, that should be visually represented with a backdrop */
-        }
         enforceFocus={false}
         autoFocus={false}
         portal={false}
@@ -149,12 +151,9 @@ class TermsPrompt extends React.PureComponent {
               onClick={this.handleOK}
               data-testid="tos-cookies-accept"
             >
-              I'm OK with cookies!
+              I&apos;m OK with cookies!
             </Button>{" "}
-            <Button
+            <Button onClick={this.handleNo} data-testid="tos-cookies-reject">
-              onClick={this.handleNo}
-              data-testid="tos-cookies-reject"
-            >
               No thanks
             </Button>
           </div>

client/src/index.js

@@ -1,5 +1,4 @@
 // jshint esversion: 6
-/* eslint-disable no-console */
 import React from "react";
 import ReactDOM from "react-dom";
 import { Provider } from "react-redux";

client/src/reducers/colors.js

@@ -150,7 +150,7 @@ const ColorsReducer = (
     case "annotation: delete label": {
       const { world } = nextSharedState;
       const { colorMode, colorAccessor } = state;
-      const { metadataField, colors } = action;
+      const { metadataField } = action;
       if (
         colorMode !== "color by categorical metadata" ||
         colorAccessor !== metadataField

client/src/reducers/layoutChoice.js

@@ -49,7 +49,7 @@ const LayoutChoice = (
     }
 
     case "reembed: add reembedding": {
-      const name = action.schema.name;
+      const { name } = action.schema;
       const available = Array.from(new Set(state.available).add(name));
       return {
         ...state,

client/src/reducers/ontology.js

@@ -9,11 +9,12 @@ const Ontology = (
 ) => {
   switch (action.type) {
     case "configuration load complete": {
-      /* eslint-disable camelcase */
       const enabled =
-        action.config?.parameters?.annotations_cell_ontology_enabled ?? false;
+        action.config?.parameters?.["annotations_cell_ontology_enabled"] ??
-      const terms = action.config?.parameters?.annotations_cell_ontology_terms;
+        false;
-      /* eslint-enable camelcase */
+      const terms =
+        action.config?.parameters?.["annotations_cell_ontology_terms"];
+
       const termSet = new Set(terms);
       return {
         ...state,

client/src/reducers/world.js

@@ -41,8 +41,8 @@ const WorldReducer = (
       const { dim } = action;
 
       // we don't clip anything except for varData and obsAnnotations
-      let unclipped = state.unclipped;
+      let { unclipped } = state;
-      if (dim == "varData" || dim == "obsAnnotations") {
+      if (dim === "varData" || dim === "obsAnnotations") {
         unclipped = {
           ...unclipped,
           [dim]: universe[dim].clone(),
@@ -298,7 +298,7 @@ const WorldReducer = (
       const { obsLayout: origObsLayout, schema: origSchema } = state;
       const { embedding, schema: embeddingSchema } = action;
 
-      const { dims, name } = embeddingSchema;
+      const { dims } = embeddingSchema;
       let obsLayout = origObsLayout;
       let schema = origSchema;
 

client/src/util/dataframe/labelIndex.js

@@ -1,3 +1,4 @@
+/* eslint-disable max-classes-per-file */
 /**
 Label indexing - map a label to & from an integer offset.  See Dataframe
 for how this is used.
@@ -23,7 +24,6 @@ function extent(tarr) {
   return [min, max];
 }
 
-/* eslint-disable class-methods-use-this */
 class IdentityInt32Index {
   /*
   identity/noop index, with small assumptions that labels are int32
@@ -41,11 +41,13 @@ class IdentityInt32Index {
     return k;
   }
 
+  // eslint-disable-next-line class-methods-use-this
   getOffset(i) {
     // label to offset
     return i;
   }
 
+  // eslint-disable-next-line class-methods-use-this
   getLabel(i) {
     // offset to label
     return i;
@@ -93,9 +95,6 @@ class IdentityInt32Index {
     return this.__promote(labelArray);
   }
 }
-/* eslint-enable class-methods-use-this */
-
-/* eslint-disable class-methods-use-this */
 class DenseInt32Index {
   /*
   DenseInt32Index indexes integer labels, and uses Int32Array typed arrays
@@ -177,9 +176,7 @@ class DenseInt32Index {
     return this.__promote(labelArray);
   }
 }
-/* eslint-enable class-methods-use-this */
 
-/* eslint-disable class-methods-use-this */
 class KeyIndex {
   /*
   KeyIndex indexes arbitrary JS primitive types, and uses a Map()
@@ -223,6 +220,7 @@ class KeyIndex {
     return this.rindex.length;
   }
 
+  // eslint-disable-next-line class-methods-use-this
   subsetLabels(labelArray) {
     return new KeyIndex(labelArray);
   }

client/src/util/promiseLimit.js

@@ -13,7 +13,7 @@ return Promise.all([
 	plimit.add(() => fetch('/baz'))
 ])
 */
-export class PromiseLimit {
+export default class PromiseLimit {
   constructor(maxConcurrency) {
     this.queue = new Set();
     this.maxConcurrency = maxConcurrency;

client/src/util/significantDigits.js

@@ -5,6 +5,6 @@
 export default (n) => {
   return n
     .toExponential()
-    .replace(/e[\+\-0-9]*$/, "")
+    .replace(/e[+\-0-9]*$/, "")
     .replace(/^0\.?0*|\./, "").length;
 };

client/src/util/typedCrossfilter/crossfilter.js

@@ -1,3 +1,4 @@
+// eslint-disable-next-line max-classes-per-file
 import PositiveIntervals from "./positiveIntervals";
 import BitArray from "./bitArray";
 import {
@@ -409,7 +410,7 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension {
     this.index = makeSortIndex(array);
   }
 
-  /* eslint-disable class-methods-use-this */
+  // eslint-disable-next-line class-methods-use-this
   _createValueArray(data, mapf, array) {
     // create dimension value array
     const len = data.length;
@@ -419,7 +420,6 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension {
     }
     return larray;
   }
-  /* eslint-enable class-methods-use-this */
 
   select(spec) {
     const { mode } = spec;
@@ -466,7 +466,7 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension {
     const ranges = [];
     const r = [
       lowerBoundIndirect(value, index, lo, 0, value.length),
-      !!inclusive
+      inclusive
         ? upperBoundIndirect(value, index, hi, 0, value.length)
         : lowerBoundIndirect(value, index, hi, 0, value.length),
     ];
@@ -514,11 +514,10 @@ class ImmutableEnumDimension extends ImmutableScalarDimension {
     });
   }
 
-  /* eslint-disable class-methods-use-this */
+  // eslint-disable-next-line class-methods-use-this
   selectRange() {
     throw new Error("range selection unsupported on Enumerated dimension");
   }
-  /* eslint-enable class-methods-use-this */
 }
 
 class ImmutableSpatialDimension extends _ImmutableBaseDimension {

server/app/app.py

@@ -105,7 +105,7 @@ def get_data_adaptor(dataset=None):
             raise DatasetAccessError("Invalid dataset {dataset}")
 
     if datapath is None:
-        return common_rest.abort_and_log(HTTPStatus.BAD_REQUEST, f"Invalid dataset NONE", loglevel=logging.INFO)
+        return common_rest.abort_and_log(HTTPStatus.BAD_REQUEST, "Invalid dataset NONE", loglevel=logging.INFO)
 
     cache_manager = current_app.matrix_data_cache_manager
     return cache_manager.data_adaptor(datapath, config)

server/common/app_config.py

@@ -279,13 +279,13 @@ class AppConfig(object):
         if self.server__csp_directives is not None:
             for k, v in self.server__csp_directives.items():
                 if not isinstance(k, str):
-                    raise ConfigurationError(f"CSP directive names must be a string.")
+                    raise ConfigurationError("CSP directive names must be a string.")
                 if isinstance(v, list):
                     for policy in v:
                         if not isinstance(policy, str):
-                            raise ConfigurationError(f"CSP directive value must be a string or list of strings.")
+                            raise ConfigurationError("CSP directive value must be a string or list of strings.")
                 elif not isinstance(v, str):
-                    raise ConfigurationError(f"CSP directive value must be a string or list of strings.")
+                    raise ConfigurationError("CSP directive value must be a string or list of strings.")
 
         # scripts can be string (filename) or dict (attributes).   Convert string to dict.
         scripts = []
@@ -476,8 +476,8 @@ class AppConfig(object):
             with self.matrix_data_cache_manager.data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
                 if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
                     context["messagefn"](
-                        f"CAUTION: due to the size of your dataset, "
+                        "CAUTION: due to the size of your dataset, "
-                        f"running differential expression may take longer or fail."
+                        "running differential expression may take longer or fail."
                     )
 
         max_workers = self.diffexp__alg_cxg__max_workers

server/data_anndata/anndata_adaptor.py

@@ -183,13 +183,13 @@ class AnndataAdaptor(DataAdaptor):
     def _validate_and_initialize(self):
         if anndata_version_is_pre_070() and self.config.adaptor__anndata_adaptor__backed:
             warnings.warn(
-                f"Use of --backed mode with anndata versions older than 0.7 will have serious "
+                "Use of --backed mode with anndata versions older than 0.7 will have serious "
                 "performance issues. Please update to at least anndata 0.7 or later."
             )
 
         # var and obs column names must be unique
         if not self.data.obs.columns.is_unique or not self.data.var.columns.is_unique:
-            raise KeyError(f"All annotation column names must be unique.")
+            raise KeyError("All annotation column names must be unique.")
 
         self._alias_annotation_names()
         self._validate_data_types()
@@ -222,8 +222,8 @@ class AnndataAdaptor(DataAdaptor):
         X0 = self.data.X[0, 0:1]
         if sparse.isspmatrix(X0) and not sparse.isspmatrix_csc(X0):
             warnings.warn(
-                f"Anndata data matrix is sparse, but not a CSC (columnar) matrix.  "
+                "Anndata data matrix is sparse, but not a CSC (columnar) matrix.  "
-                f"Performance may be improved by using CSC."
+                "Performance may be improved by using CSC."
             )
         if self.data.X.dtype != "float32":
             warnings.warn(
@@ -295,7 +295,7 @@ class AnndataAdaptor(DataAdaptor):
                 valid_layouts.append(layout)
 
         if len(valid_layouts) == 0:
-            raise PrepareError(f"No valid layout data.")
+            raise PrepareError("No valid layout data.")
 
         # cap layouts to MAX_LAYOUTS
         return layouts[0:MAX_LAYOUTS]

server/data_common/data_adaptor.py

@@ -230,18 +230,19 @@ class DataAdaptor(metaclass=ABCMeta):
 
         # all labels must have a name, which must be unique and not used in obs column names
         if not labels_df.columns.is_unique:
-            raise KeyError(f"All column names specified in user annotations must be unique.")
+            raise KeyError("All column names specified in user annotations must be unique.")
 
         # the label index must be unique, and must have same values the anndata obs index
         if not labels_df.index.is_unique:
-            raise KeyError(f"All row index values specified in user annotations must be unique.")
+            raise KeyError("All row index values specified in user annotations must be unique.")
 
         obs_columns = self.get_obs_columns()
 
         duplicate_columns = list(set(labels_df.columns) & set(obs_columns))
         if len(duplicate_columns) > 0:
             raise KeyError(
-                f"Labels file may not contain column names which overlap " f"with h5ad obs columns {duplicate_columns}"
+                "Labels file may not contain column names which overlap "
+                f"with h5ad obs columns {duplicate_columns}"
             )
 
         # labels must have same count as obs annotations
@@ -351,13 +352,13 @@ class DataAdaptor(metaclass=ABCMeta):
         """
         embeddings = self.get_embedding_names() if fields is None or len(fields) == 0 else fields
         layout_data = []
-        with ServerTiming.time(f"layout.query"):
+        with ServerTiming.time("layout.query"):
             for ename in embeddings:
                 embedding = self.get_embedding_array(ename, 2)
                 normalized_layout = DataAdaptor.normalize_embedding(embedding)
                 layout_data.append(pd.DataFrame(normalized_layout, columns=[f"{ename}_0", f"{ename}_1"]))
 
-        with ServerTiming.time(f"layout.encode"):
+        with ServerTiming.time("layout.encode"):
             if layout_data:
                 df = pd.concat(layout_data, axis=1, copy=False)
             else:

server/data_common/matrix_loader.py

@@ -228,7 +228,7 @@ class MatrixDataLoader(object):
             self.matrix_data_type = self.__matrix_data_type()
 
         if not self.__matrix_data_type_allowed(app_config):
-            raise DatasetAccessError(f"Dataset does not have an allowed type.")
+            raise DatasetAccessError("Dataset does not have an allowed type.")
 
         if self.matrix_data_type == MatrixDataType.H5AD:
             from server.data_anndata.anndata_adaptor import AnndataAdaptor
@@ -272,7 +272,7 @@ class MatrixDataLoader(object):
 
     def pre_load_validation(self):
         if self.matrix_data_type == MatrixDataType.UNKNOWN:
-            raise DatasetAccessError(f"Dataset does not have a recognized type: .h5ad or .cxg")
+            raise DatasetAccessError("Dataset does not have a recognized type: .h5ad or .cxg")
         self.matrix_type.pre_load_validation(self.location)
 
     def file_size(self):

server/data_cxg/cxg_adaptor.py

@@ -264,7 +264,7 @@ class CxgAdaptor(DataAdaptor):
     # function to get the embedding
     # this function to iterate through embeddings.
     def get_embedding_names(self):
-        with ServerTiming.time(f"layout.lsuri"):
+        with ServerTiming.time("layout.lsuri"):
             pemb = self.get_path("emb")
             embeddings = [os.path.basename(p) for (p, t) in self.lsuri(pemb) if t == "array"]
         if len(embeddings) == 0:
@@ -311,7 +311,7 @@ class CxgAdaptor(DataAdaptor):
             A = self.open_array(ax)
             schema_hints = json.loads(A.meta["cxg_schema"]) if "cxg_schema" in A.meta else {}
             if type(schema_hints) is not dict:
-                raise TypeError(f"Array schema was malformed.")
+                raise TypeError("Array schema was malformed.")
 
             cols = []
             for attr in A.schema:

server/eb/app.py

@@ -156,7 +156,7 @@ try:
 
     dataroot = os.getenv("CXG_DATAROOT")
     if dataroot:
-        logging.info(f"Configuration from CXG_DATAROOT")
+        logging.info("Configuration from CXG_DATAROOT")
         app_config.update(multi_dataset__dataroot=dataroot)
 
     secret_name = os.getenv("CXG_AWS_SECRET_NAME")
@@ -171,7 +171,7 @@ try:
             if not secret_region_name:
                 secret_region_name = discover_s3_region_name(config_file)
         if not secret_region_name:
-            logging.error(f"Could not determine the AWS Secret Manager region")
+            logging.error("Could not determine the AWS Secret Manager region")
             sys.exit(1)
 
         flask_secret_key = get_flask_secret_key(secret_region_name, secret_name)
@@ -188,7 +188,7 @@ try:
 
     if not app_config.server__flask_secret_key:
         logging.critical(
-            f"flask_secret_key is not provided.  Either set in config file, CXG_SECRET_KEY environment variable, "
+            "flask_secret_key is not provided.  Either set in config file, CXG_SECRET_KEY environment variable, "
             "or in AWS Secret Manager"
         )
         sys.exit(1)

server/eb/check_requirements.py

@@ -29,16 +29,12 @@ def check(expected, custom):
     # cdict must only have exact requirements (==)
     for cname, cspecs in cdict.items():
         if len(cspecs) != 1 or cspecs[0][0] != "==":
-            print(
+            print(f"Error, spec must be an exact requirement {custom}: {cname} {str(cspecs)}")
-                f"Error, spec must be an exact requirement {custom}: {cname} {str(cspecs)}"
-            )
             okay = False
 
     for ename, especs in edict.items():
         if ename not in cdict:
-            print(
+            print(f"Error, missing requirement from {custom}: {ename} {str(especs)}")
-                f"Error, missing requirement from {custom}: {ename} {str(especs)}"
-            )
             okay = False
             continue
 
@@ -46,9 +42,7 @@ def check(expected, custom):
         for espec in especs:
             rokay = check_version(cver, espec[0], Version(espec[1]))
             if not rokay:
-                print(
+                print(f"Error, failed requirement from {custom}: {ename} {espec}, {cver}")
-                    f"Error, failed requirement from {custom}: {ename} {espec}, {cver}"
-                )
                 okay = False
 
     if okay:

server/requirements.txt

@@ -1,6 +1,6 @@
 anndata>=0.6.20
 boto3>=1.12.18
-click>=6.7
+click>=7.1.2
 fastobo>=0.6.1
 Flask>=1.0.2
 Flask-Compress>=1.4.0

server/test/test_api.py

@@ -185,14 +185,14 @@ class EndPoints(object):
         self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
 
     def test_data_mimetype_error(self):
-        endpoint = f"data/var"
+        endpoint = "data/var"
         header = {"Accept": "xxx"}
         url = f"{self.URL_BASE}{endpoint}"
         result = self.session.put(url, headers=header)
         self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
 
     def test_fbs_default(self):
-        endpoint = f"data/var"
+        endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
         result = self.session.put(url)
         self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
@@ -202,21 +202,21 @@ class EndPoints(object):
         self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
 
     def test_data_put_fbs(self):
-        endpoint = f"data/var"
+        endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
         header = {"Accept": "application/octet-stream"}
         result = self.session.put(url, headers=header)
         self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
 
     def test_data_get_fbs(self):
-        endpoint = f"data/var"
+        endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
         header = {"Accept": "application/octet-stream"}
         result = self.session.get(url, headers=header)
         self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
 
     def test_data_put_filter_fbs(self):
-        endpoint = f"data/var"
+        endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
         header = {"Accept": "application/octet-stream"}
         filter = {"filter": {"var": {"index": [0, 1, 4]}}}
@@ -233,8 +233,8 @@ class EndPoints(object):
 
     def test_data_get_filter_fbs(self):
         index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
+        endpoint = "data/var"
         query = f"var:{index_col_name}=SIK1"
-        endpoint = f"data/var"
         url = f"{self.URL_BASE}{endpoint}?{query}"
         header = {"Accept": "application/octet-stream"}
         result = self.session.get(url, headers=header)
@@ -245,7 +245,7 @@ class EndPoints(object):
         self.assertEqual(df["n_cols"], 1)
 
     def test_data_put_single_var(self):
-        endpoint = f"data/var"
+        endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
         header = {"Accept": "application/octet-stream"}
         index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
@@ -306,7 +306,7 @@ class EndPointsAnnotations(EndPoints):
         query = "annotation-collection-name=test_annotations"
         url = f"{self.URL_BASE}{endpoint}?{query}"
         n_rows = self.data.get_shape()[0]
-        fbs = make_fbs({"cat_A": pd.Series(["label_A" for l in range(0, n_rows)], dtype="category")})
+        fbs = make_fbs({"cat_A": pd.Series(["label_A"] * n_rows, dtype="category")})
         result = self.session.put(url, data=fbs)
         self.assertEqual(result.status_code, HTTPStatus.OK)
         self.assertEqual(result.headers["Content-Type"], "application/json")

server/test/test_writable_annotation.py

@@ -27,7 +27,7 @@ class WritableAnnotationTest(unittest.TestCase):
     def test_error_checks(self):
         # verify that the expected errors are generated
         n_rows = self.data.get_shape()[0]
-        fbs_bad = make_fbs({"louvain": pd.Series(["undefined" for l in range(0, n_rows)], dtype="category")})
+        fbs_bad = make_fbs({"louvain": pd.Series(["undefined"] * n_rows, dtype="category")})
 
         # ensure we catch attempt to overwrite non-writable data
         with self.assertRaises(KeyError):
@@ -38,8 +38,8 @@ class WritableAnnotationTest(unittest.TestCase):
         n_rows = self.data.get_shape()[0]
         fbs = make_fbs(
             {
-                "cat_A": pd.Series(["label_A" for l in range(0, n_rows)], dtype="category"),
+                "cat_A": pd.Series(["label_A"] * n_rows, dtype="category"),
-                "cat_B": pd.Series(["label_B" for l in range(0, n_rows)], dtype="category"),
+                "cat_B": pd.Series(["label_B"] * n_rows, dtype="category"),
             }
         )
         res = self.annotation_put_fbs(fbs)
@@ -49,14 +49,14 @@ class WritableAnnotationTest(unittest.TestCase):
         self.assertEqual(df.shape, (n_rows, 2))
         self.assertEqual(set(df.columns), {"cat_A", "cat_B"})
         self.assertTrue(self.data.original_obs_index.equals(df.index))
-        self.assertTrue(np.all(df["cat_A"] == ["label_A" for l in range(0, n_rows)]))
+        self.assertTrue(np.all(df["cat_A"] == ["label_A"] * n_rows))
-        self.assertTrue(np.all(df["cat_B"] == ["label_B" for l in range(0, n_rows)]))
+        self.assertTrue(np.all(df["cat_B"] == ["label_B"] * n_rows))
 
         # verify complete overwrite on second attempt, AND rotation occurs
         fbs = make_fbs(
             {
-                "cat_A": pd.Series(["label_A1" for l in range(0, n_rows)], dtype="category"),
+                "cat_A": pd.Series(["label_A1"] * n_rows, dtype="category"),
-                "cat_C": pd.Series(["label_C" for l in range(0, n_rows)], dtype="category"),
+                "cat_C": pd.Series(["label_C"] * n_rows, dtype="category"),
             }
         )
         res = self.annotation_put_fbs(fbs)
@@ -64,8 +64,8 @@ class WritableAnnotationTest(unittest.TestCase):
         self.assertTrue(path.exists(self.annotations.output_file))
         df = pd.read_csv(self.annotations.output_file, index_col=0, header=0, comment="#")
         self.assertEqual(set(df.columns), {"cat_A", "cat_C"})
-        self.assertTrue(np.all(df["cat_A"] == ["label_A1" for l in range(0, n_rows)]))
+        self.assertTrue(np.all(df["cat_A"] == ["label_A1"] * n_rows))
-        self.assertTrue(np.all(df["cat_C"] == ["label_C" for l in range(0, n_rows)]))
+        self.assertTrue(np.all(df["cat_C"] == ["label_C"] * n_rows))
 
         # rotation
         name, ext = path.splitext(self.annotations.output_file)
@@ -79,8 +79,8 @@ class WritableAnnotationTest(unittest.TestCase):
         n_rows = self.data.get_shape()[0]
         fbs = make_fbs(
             {
-                "cat_A": pd.Series(["label_A" for l in range(0, n_rows)], dtype="category"),
+                "cat_A": pd.Series(["label_A"] * n_rows, dtype="category"),
-                "cat_B": pd.Series(["label_B" for l in range(0, n_rows)], dtype="category"),
+                "cat_B": pd.Series(["label_B"] * n_rows, dtype="category"),
             }
         )
         for i in range(0, 11):
@@ -100,8 +100,8 @@ class WritableAnnotationTest(unittest.TestCase):
         n_rows = self.data.get_shape()[0]
         fbs = make_fbs(
             {
-                "cat_A": pd.Series(["label_A" for l in range(0, n_rows)], dtype="category"),
+                "cat_A": pd.Series(["label_A"] * n_rows, dtype="category"),
-                "cat_B": pd.Series(["label_B" for l in range(0, n_rows)], dtype="category"),
+                "cat_B": pd.Series(["label_B"] * n_rows, dtype="category"),
             }
         )
 
@@ -123,8 +123,8 @@ class WritableAnnotationTest(unittest.TestCase):
             [obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain", "cat_A", "cat_B"],
         )
         col_idx = annotations["col_idx"]
-        self.assertEqual(annotations["columns"][col_idx.index("cat_A")], ["label_A" for l in range(0, n_rows)])
+        self.assertEqual(annotations["columns"][col_idx.index("cat_A")], ["label_A"] * n_rows)
-        self.assertEqual(annotations["columns"][col_idx.index("cat_B")], ["label_B" for l in range(0, n_rows)])
+        self.assertEqual(annotations["columns"][col_idx.index("cat_B")], ["label_B"] * n_rows)
 
         # verify the schema was updated
         all_col_schema = {c["name"]: c for c in schema["annotations"]["obs"]["columns"]}