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Merge branch 'master' into colinmegill/geneset-prototype

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This commit is contained in:
Colin Megill
2020-05-19 15:58:36 -04:00
parent 7551118800 c34a68304e
commit 708499c1fd
47 changed files with 314 additions and 294 deletions
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client/__tests__/e2e/config.js
+3 -3
View File
@@ -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:${appPort}`;
export const DEV = jest_env === "dev";
export const DEBUG = jest_env === "debug";
export const DEV = jestEnv === "dev";
export const DEBUG = jestEnv === "debug";
export const DATASET = "pbmc3k";
if (DEBUG) jest.setTimeout(100000);
client/__tests__/e2e/e2e.test.js
+17 -3
View File
@@ -7,7 +7,10 @@ import { appUrlBase, DATASET } from "./config";
import { setupTestBrowser } from "./testBrowser";
import { datasets } from "./data";
let browser, page, utils, cxgActions;
let browser;
let page;
let utils;
let cxgActions;
const data = datasets[DATASET];
beforeAll(async () => {
@@ -29,6 +32,17 @@ describe("did launch", () => {
);
expect(element).toBe(data.title);
});
test("terms of service, if they are there", async () => {
try {
await utils.clickOn("tos-cookies-accept", { timeout: 500 });
} catch {
console.warn("No terms of service footer detected.");
}
page.waitFor(50); // give the footer a chance to disappear
const result = await page.$("[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
+4 -1
View File
@@ -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
+6 -2
View File
@@ -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
+2 -2
View File
@@ -44,8 +44,8 @@ export const puppeteerUtils = (page) => ({
},
async clickOn(testid, options = {}) {
await this.waitByID(testid);
const click = await page.click(`[data-testid='${testid}']`, options);
await this.waitByID(testid, options);
const click = await page.click(`[data-testid='${testid}']`);
await page.waitFor(50);
return click;
},
client/__tests__/e2e/testBrowser.js
+4
View File
@@ -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 -1
View File
@@ -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
+1 -1
View File
@@ -54,7 +54,7 @@ class CspHashPlugin {
.createHash("sha256")
.update(str, "utf8")
.digest("base64");
return "sha256-" + hash;
return `sha256-${hash}`;
}
}
client/src/actions/index.js
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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 -2
View File
@@ -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
+35 -22
View File
@@ -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() {
const { dispatch, metadataField } = this.props;
dispatch({
type: "categorical metadata filter all of these",
metadataField,
});
this.setState({ isChecked: true });
}
handleCategoryClick = () => {
const { annotations, metadataField, onExpansionChange } = this.props;
const editingCategory =
annotations.isEditingCategoryName &&
annotations.categoryBeingEdited === metadataField;
if (!editingCategory) {
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">
<input disabled checked type="checkbox" />
<label htmlFor={checkboxID} className="bp3-control bp3-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={() => {
const editingCategory =
annotations.isEditingCategoryName &&
annotations.categoryBeingEdited === metadataField;
if (!editingCategory) {
onExpansionChange(metadataField);
}
}}
onClick={this.handleCategoryClick}
>
{isUserAnno ? (
<Icon style={{ marginRight: 5 }} icon="tag" iconSize={16} />
client/src/components/categorical/index.js
+1 -1
View File
@@ -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
+3 -3
View File
@@ -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
+10 -1
View File
@@ -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
-5
View File
@@ -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
+1 -1
View File
@@ -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
+30 -23
View File
@@ -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(
(xy[0] + 1) * viewport.width / 2
),
Math.round(
-((xy[1] + 1) / 2 - 1) * viewport.height
)
Math.round(((xy[0] + 1) * viewport.width) / 2),
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={
graphInteractionMode === "select" ? "auto" : "none"
}
pointerEvents={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
+4 -3
View File
@@ -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 -4
View File
@@ -2,8 +2,7 @@ import React, { PureComponent, cloneElement } from "react";
import styles from "../graph.css";
export default
class GraphOverlayLayer extends PureComponent {
export default 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
+2 -2
View File
@@ -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
+3 -1
View File
@@ -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
+3 -24
View File
@@ -1,14 +1,7 @@
// jshint esversion: 6
import React from "react";
import { connect } from "react-redux";
import {
Popover,
Button,
ButtonGroup,
AnchorButton,
Tooltip,
Position,
} from "@blueprintjs/core";
import { Button, ButtonGroup, AnchorButton, Tooltip } 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
+1 -3
View File
@@ -69,9 +69,7 @@ class Embedding extends React.PureComponent {
const { layoutChoice } = this.props;
return (
<ButtonGroup
className={styles.menubarButton}
>
<ButtonGroup className={styles.menubarButton}>
<Popover
target={
<Tooltip
client/src/components/menubar/index.js
+79 -76
View File
@@ -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"
? ["Brush selection", "Lasso selection"]
: ["select", "polygon-filter"];
const [selectionTooltip, selectionButtonIcon] =
selectionTool === "brush"
? ["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}
handleClipPercentileMinValueChange={this.handleClipPercentileMinValueChange}
handleClipPercentileMaxValueChange={
this.handleClipPercentileMaxValueChange
}
handleClipPercentileMinValueChange={
this.handleClipPercentileMinValueChange
}
/>
<Embedding />
<Tooltip
content="When a category is colored by, show labels on the graph"
position="bottom"
disabled={graphInteractionMode === "zoom"}
>
<AnchorButton
className={styles.menubarButton}
type="button"
data-testid="centroid-label-toggle"
icon="property"
onClick={this.handleCentroidChange}
active={showCentroidLabels}
intent={showCentroidLabels ? "primary" : "none"}
/>
</Tooltip>
<ButtonGroup
className={styles.menubarButton}
>
<Tooltip
content={selectionTooltip}
position="bottom"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<AnchorButton
type="button"
data-testid="mode-lasso"
icon={selectionButtonIcon}
active={graphInteractionMode === "select"}
onClick={() => {
dispatch({
type: "change graph interaction mode",
data: "select"
});
<Embedding />
<Tooltip
content="When a category is colored by, show labels on the graph"
position="bottom"
disabled={graphInteractionMode === "zoom"}
>
<AnchorButton
className={styles.menubarButton}
type="button"
data-testid="centroid-label-toggle"
icon="property"
onClick={this.handleCentroidChange}
active={showCentroidLabels}
intent={showCentroidLabels ? "primary" : "none"}
/>
</Tooltip>
<ButtonGroup className={styles.menubarButton}>
<Tooltip
content={selectionTooltip}
position="bottom"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<AnchorButton
type="button"
data-testid="mode-lasso"
icon={selectionButtonIcon}
active={graphInteractionMode === "select"}
onClick={() => {
dispatch({
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>
<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" });
}}
/>
{disableDiffexp ? null : <DiffexpButtons/>}
</div>
);
{disableDiffexp ? null : <DiffexpButtons />}
</div>
);
}
}
client/src/components/scatterplot/scatterplot.js
+14 -14
View File
@@ -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
+14 -15
View File
@@ -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,
privacyURL: state.config?.parameters?.about_legal_privacy,
tosURL: state.config?.parameters?.["about_legal_tos"],
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={
true /* if the user can't use the app or click outside to dismiss, that should be visually represented with a backdrop */
}
hasBackdrop /* 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
onClick={this.handleNo}
data-testid="tos-cookies-reject"
>
<Button onClick={this.handleNo} data-testid="tos-cookies-reject">
No thanks
</Button>
</div>
client/src/index.js
-1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+5 -4
View File
@@ -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;
const terms = action.config?.parameters?.annotations_cell_ontology_terms;
/* eslint-enable camelcase */
action.config?.parameters?.["annotations_cell_ontology_enabled"] ??
false;
const terms =
action.config?.parameters?.["annotations_cell_ontology_terms"];
const termSet = new Set(terms);
return {
...state,
client/src/reducers/world.js
+3 -3
View File
@@ -41,8 +41,8 @@ const WorldReducer = (
const { dim } = action;
// we don't clip anything except for varData and obsAnnotations
let unclipped = state.unclipped;
if (dim == "varData" || dim == "obsAnnotations") {
let { unclipped } = state;
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
+4 -6
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+4 -5
View File
@@ -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
+1 -1
View File
@@ -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
+5 -5
View File
@@ -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, "
f"running differential expression may take longer or fail."
"CAUTION: due to the size of your dataset, "
"running differential expression may take longer or fail."
)
max_workers = self.diffexp__alg_cxg__max_workers
server/data_anndata/anndata_adaptor.py
+5 -5
View File
@@ -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. "
f"Performance may be improved by using CSC."
"Anndata data matrix is sparse, but not a CSC (columnar) matrix. "
"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
+6 -5
View File
@@ -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
+2 -2
View File
@@ -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
+2 -2
View File
@@ -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
+3 -3
View File
@@ -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
+3 -9
View File
@@ -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(
f"Error, spec must be an exact requirement {custom}: {cname} {str(cspecs)}"
)
print(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(
f"Error, missing requirement from {custom}: {ename} {str(especs)}"
)
print(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(
f"Error, failed requirement from {custom}: {ename} {espec}, {cver}"
)
print(f"Error, failed requirement from {custom}: {ename} {espec}, {cver}")
okay = False
if okay:
server/requirements.txt
+1 -1
View File
@@ -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
+8 -8
View File
@@ -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
+15 -15
View File
@@ -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_B": pd.Series(["label_B" 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"] * 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_B"] == ["label_B" 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"] * 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_C": pd.Series(["label_C" 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"] * 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_C"] == ["label_C" 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"] * 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_B": pd.Series(["label_B" 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"] * 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_B": pd.Series(["label_B" 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"] * 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_B")], ["label_B" 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"] * n_rows)
# verify the schema was updated
all_col_schema = {c["name"]: c for c in schema["annotations"]["obs"]["columns"]}