mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-27 11:28:11 +08:00
Ontologies (#1110)
* add sample ontologies file * add ontologies reducer * Move select category to own component * Dialog and Input factored out * refactoring categorical, partway * validationn * anno * suggest populates input * frontend for ontology working * initial implementation of back-end support for ontologies * edit is now dialog again * autosuggest working on edit * part way through create arbitrary label * handle choice in function * pass duplicate cat prop * editing works * update test to match new CLI params * fix occupancy alignment * edit category as dialogue * secondary button * remove stubbed out ontologies * add label setting upon new label creation * Update legal characters for labels (#1119) * Allow any term in the ontology (bypass legal name check) * Add hyphens and parens to legal characters in names * improve performance for large ontologies * correctly handle case where ontologies are disabled * fix logic error in CLI Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com> * PR cleanup 1 * lint * validate user generated labels * finish hooking up connected suggest component * protect against undefined callbacks * Fix illegal characters error message * break out npm run commands * fix error detection on label edit Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com> Co-authored-by: Sidney Bell <sidneymbell@users.noreply.github.com>
This commit is contained in:
Colin Megill
co-authored by
Bruce Martin
Sidney Bell
Bruce Martin
Sidney Bell
parent
8d725b1ad9
commit
d48647a655
@@ -0,0 +1,91 @@
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import React from "react";
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import { connect } from "react-redux";
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import { Button, Tooltip, Dialog, Classes, Colors } from "@blueprintjs/core";
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@connect(state => ({
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colorAccessor: state.colors.colorAccessor,
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categoricalSelection: state.categoricalSelection,
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annotations: state.annotations,
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universe: state.universe,
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ontology: state.ontology,
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ontologyLoading: state.ontology?.loading
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}))
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class AnnoDialog extends React.Component {
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constructor(props) {
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super(props);
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this.state = {};
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}
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render() {
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const {
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isActive,
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text,
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title,
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instruction,
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cancelTooltipContent,
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errorMessage,
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validationError,
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annoSelect,
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annoInput,
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handleCancel,
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handleSubmit,
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primaryButtonText,
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secondaryButtonText,
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handleSecondaryButtonSubmit
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} = this.props;
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return (
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<Dialog icon="tag" title={title} isOpen={isActive} onClose={handleCancel}>
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<form
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onSubmit={e => {
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e.preventDefault();
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}}
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>
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<div className={Classes.DIALOG_BODY}>
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<div style={{ marginBottom: 20 }}>
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<p>{instruction}</p>
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{annoInput || null}
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<p
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style={{
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marginTop: 7,
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visibility: validationError ? "visible" : "hidden",
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color: Colors.ORANGE3
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}}
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>
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{errorMessage}
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</p>
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</div>
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{annoSelect || null}
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</div>
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<div className={Classes.DIALOG_FOOTER}>
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<div className={Classes.DIALOG_FOOTER_ACTIONS}>
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<Tooltip content={cancelTooltipContent}>
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<Button onClick={handleCancel}>Cancel</Button>
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</Tooltip>
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{handleSecondaryButtonSubmit && secondaryButtonText ? (
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<Button
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onClick={handleSecondaryButtonSubmit}
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disabled={!text || validationError}
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intent="none"
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type="submit"
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>
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{secondaryButtonText}
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</Button>
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) : null}
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<Button
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onClick={handleSubmit}
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disabled={!text || validationError}
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intent="primary"
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type="submit"
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>
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{primaryButtonText}
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</Button>
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</div>
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</div>
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</form>
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</Dialog>
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);
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}
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}
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export default AnnoDialog;
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@@ -0,0 +1,159 @@
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import React from "react";
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import { connect } from "react-redux";
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import { InputGroup, MenuItem } from "@blueprintjs/core";
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import { Suggest } from "@blueprintjs/select";
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import fuzzysort from "fuzzysort";
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const filterOntology = (query, ontology) =>
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/* fires on load, once, and then for each character typed into the input */
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fuzzysort.go(query, ontology, {
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limit: 100,
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threshold: -10000 // don't return bad results
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});
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const renderListItem = (fuzzySortResult, { handleClick, modifiers }) => {
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if (!modifiers.matchesPredicate) {
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return null;
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}
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/* the fuzzysort wraps the object with other properties, like a score */
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const geneName = fuzzySortResult.target;
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return (
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<MenuItem
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active={modifiers.active}
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disabled={modifiers.disabled}
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data-testid={`suggest-menu-item-${geneName}`}
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// Use of annotations in this way is incorrect and dataset specific.
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// See https://github.com/chanzuckerberg/cellxgene/issues/483
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// label={gene.n_counts}
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key={geneName}
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onClick={g =>
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/* this fires when user clicks a menu item */
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handleClick(g)
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}
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text={geneName}
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/>
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);
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};
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const AnnoSuggest = props => {
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const {
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ontologyLoading,
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handleItemChange,
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handleChoice,
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ontology,
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handleCreateArbitraryLabel,
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handleTextChange,
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isTextInvalid,
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isTextInvalidErrorMessage
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} = props;
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return (
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<Suggest
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fill
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resetOnSelect
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closeOnSelect
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resetOnClose
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createNewItemFromQuery={() => {}}
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createNewItemRenderer={userInputStr => {
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return isTextInvalid?.(userInputStr) ? (
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<MenuItem disabled text={isTextInvalidErrorMessage(userInputStr)} />
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) : (
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<MenuItem
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icon="add"
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text="Create a label not in the ontology"
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active
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onClick={() => {
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handleCreateArbitraryLabel(userInputStr);
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}}
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shouldDismissPopover={false}
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/>
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);
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}}
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itemDisabled={ontologyLoading ? () => true : () => false}
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noResults={<MenuItem disabled text="No matching ontology identifier" />}
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onItemSelect={handleChoice}
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initialContent={
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<MenuItem disabled text="Enter an ontology identifier…" />
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}
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inputProps={{ "data-testid": "gene-search" }}
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inputValueRenderer={t => t.target}
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itemListPredicate={filterOntology}
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onActiveItemChange={handleItemChange}
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itemRenderer={renderListItem.bind(this)}
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items={!ontologyLoading && ontology ? ontology : ["No ontology loaded"]}
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popoverProps={{ minimal: true }}
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onQueryChange={(s, e) => {
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// undefined event means resetOnSelect
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if (e !== undefined) handleTextChange?.(s);
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}}
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/>
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);
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};
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const VanillaInput = props => {
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const { text, handleTextChange } = props;
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return (
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<InputGroup
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autoFocus
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value={text}
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intent="none"
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onChange={e => handleTextChange?.(e.target.value)}
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leftIcon="tag"
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/>
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);
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};
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@connect(state => ({
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colorAccessor: state.colors.colorAccessor,
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categoricalSelection: state.categoricalSelection,
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annotations: state.annotations,
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universe: state.universe,
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world: state.world,
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ontology: state.ontology?.terms,
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ontologyLoading: state.ontology?.loading
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}))
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class AnnoInputs extends React.Component {
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constructor(props) {
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super(props);
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this.state = {};
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}
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render() {
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const {
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useSuggest,
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handleTextChange,
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text,
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ontologyLoading,
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world,
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handleChoice,
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handleItemChange,
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handleCreateArbitraryLabel,
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ontology,
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isTextInvalid,
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isTextInvalidErrorMessage
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} = this.props;
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return (
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<div>
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{/* Le sigh https://github.com/palantir/blueprint/issues/2864 */}
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{useSuggest ? (
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<AnnoSuggest
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world={world}
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text={text}
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handleChoice={handleChoice}
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ontologyLoading={ontologyLoading}
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handleCreateArbitraryLabel={handleCreateArbitraryLabel}
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handleItemChange={handleItemChange}
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ontology={ontology}
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handleTextChange={handleTextChange}
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isTextInvalid={isTextInvalid}
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isTextInvalidErrorMessage={isTextInvalidErrorMessage}
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/>
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) : (
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<VanillaInput text={text} handleTextChange={handleTextChange} />
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)}
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</div>
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);
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}
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}
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export default AnnoInputs;
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@@ -0,0 +1,57 @@
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import React from "react";
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import { connect } from "react-redux";
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import { Button, MenuItem } from "@blueprintjs/core";
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import { Select } from "@blueprintjs/select";
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@connect(state => ({
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colorAccessor: state.colors.colorAccessor,
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categoricalSelection: state.categoricalSelection,
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annotations: state.annotations,
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universe: state.universe,
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ontology: state.ontology,
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ontologyLoading: state.ontology?.loading
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}))
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class DuplicateCategorySelect extends React.Component {
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constructor(props) {
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super(props);
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this.state = {};
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}
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render() {
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const {
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allCategoryNames,
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categoryToDuplicate,
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handleModalDuplicateCategorySelection
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} = this.props;
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return (
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<div>
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<p>
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Optionally duplicate all labels & cell assignments from existing
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category into new category:
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</p>
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<Select
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items={
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allCategoryNames ||
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[] /* this is a placeholder, could be a subcomponent to avoid this */
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}
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filterable={false}
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itemRenderer={(d, { handleClick }) => {
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return <MenuItem onClick={handleClick} key={d} text={d} />;
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}}
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noResults={<MenuItem disabled text="No results." />}
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onItemSelect={d => {
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handleModalDuplicateCategorySelection(d);
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}}
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>
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{/* children become the popover target; render value here */}
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<Button
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text={categoryToDuplicate || "None (all cells 'unassigned')"}
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rightIcon="double-caret-vertical"
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/>
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</Select>
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</div>
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);
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}
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}
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export default DuplicateCategorySelect;
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@@ -1,20 +1,13 @@
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// jshint esversion: 6
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import React from "react";
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import _ from "lodash";
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import {
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Button,
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Tooltip,
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InputGroup,
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Dialog,
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Classes,
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MenuItem,
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Colors
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} from "@blueprintjs/core";
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import { Select } from "@blueprintjs/select";
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import { Button } from "@blueprintjs/core";
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import { connect } from "react-redux";
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import * as globals from "../../globals";
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import Category from "./category";
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import { AnnotationsHelpers } from "../../util/stateManager";
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import AnnoDialog from "./annoDialog";
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import AnnoInputs from "./annoInputs";
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import AnnoSelect from "./annoSelect";
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@connect(state => ({
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categoricalSelection: state.categoricalSelection,
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@@ -71,7 +64,7 @@ class Categories extends React.Component {
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/* allow empty string */
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if (name === "") return false;
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/*
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/*
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test for uniqueness against *all* annotation names, not just the subset
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we render as categorical.
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*/
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@@ -102,13 +95,25 @@ class Categories extends React.Component {
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"empty-string": "Blank names not allowed",
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duplicate: "Name must be unique",
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"trim-spaces": "Leading and trailing spaces not allowed",
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"illegal-characters": "Only alphanumeric, underscore and period allowed",
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"illegal-characters":
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"Only alphanumeric and special characters (-_.) allowed",
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"multi-space-run": "Multiple consecutive spaces not allowed"
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};
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const errorMessage = errorMessageMap[err] ?? "error";
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return <span>{errorMessage}</span>;
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};
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handleNewCategoryText = txt => {
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this.setState({ newCategoryText: txt });
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};
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handleChoice = e => {
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/* Blueprint Suggest format */
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this.setState({ newCategoryText: e.target });
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};
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handleSuggestActiveItemChange = () => {};
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render() {
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const {
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createAnnoModeActive,
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@@ -131,9 +136,39 @@ class Categories extends React.Component {
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padding: globals.leftSidebarSectionPadding
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}}
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>
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<AnnoDialog
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isActive={createAnnoModeActive}
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title="Create new category"
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instruction="New, unique category name:"
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cancelTooltipContent="Close this dialog without creating a category."
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primaryButtonText="Create new category"
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text={newCategoryText}
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validationError={this.categoryNameError(newCategoryText)}
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errorMessage={this.categoryNameErrorMessage(newCategoryText)}
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handleSubmit={this.handleCreateUserAnno}
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handleCancel={this.handleDisableAnnoMode}
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annoInput={
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<AnnoInputs
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text={newCategoryText}
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handleItemChange={this.handleSuggestActiveItemChange}
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handleChoice={this.handleChoice}
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handleTextChange={this.handleNewCategoryText}
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/>
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}
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annoSelect={
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<AnnoSelect
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handleModalDuplicateCategorySelection={
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this.handleModalDuplicateCategorySelection
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}
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categoryToDuplicate={categoryToDuplicate}
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allCategoryNames={allCategoryNames}
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/>
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}
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/>
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{/* READ ONLY CATEGORICAL FIELDS */}
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{/* this is duplicative but flat, could be abstracted */}
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{_.map(allCategoryNames, catName =>
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{allCategoryNames.map(catName =>
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!schema.annotations.obsByName[catName].writable ? (
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<Category
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key={catName}
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@@ -144,7 +179,7 @@ class Categories extends React.Component {
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) : null
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)}
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{/* WRITEABLE FIELDS */}
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{_.map(allCategoryNames, catName =>
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{allCategoryNames.map(catName =>
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schema.annotations.obsByName[catName].writable ? (
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<Category
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key={catName}
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@@ -156,94 +191,6 @@ class Categories extends React.Component {
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)}
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{writableCategoriesEnabled ? (
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<div>
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<Dialog
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icon="tag"
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title="Create new category"
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isOpen={createAnnoModeActive}
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onClose={this.handleDisableAnnoMode}
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>
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<form
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onSubmit={e => {
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e.preventDefault();
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}}
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>
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<div className={Classes.DIALOG_BODY}>
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<div style={{ marginBottom: 20 }}>
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<p>New, unique category name:</p>
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<InputGroup
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autoFocus
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value={newCategoryText}
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intent={
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this.categoryNameError(newCategoryText)
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? "warning"
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: "none"
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}
|
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onChange={e =>
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this.setState({ newCategoryText: e.target.value })
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}
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leftIcon="tag"
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/>
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<p
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style={{
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marginTop: 7,
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visibility: this.categoryNameError(newCategoryText)
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? "visible"
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: "hidden",
|
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color: Colors.ORANGE3
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}}
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>
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{this.categoryNameErrorMessage(newCategoryText)}
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</p>
|
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</div>
|
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|
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<p>
|
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Optionally duplicate all labels & cell assignments from
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existing category into new category:
|
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</p>
|
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<Select
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items={allCategoryNames}
|
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filterable={false}
|
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itemRenderer={(d, { handleClick }) => {
|
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return (
|
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<MenuItem onClick={handleClick} key={d} text={d} />
|
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);
|
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}}
|
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noResults={<MenuItem disabled text="No results." />}
|
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onItemSelect={d => {
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this.handleModalDuplicateCategorySelection(d);
|
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}}
|
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>
|
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{/* children become the popover target; render value here */}
|
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<Button
|
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text={
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categoryToDuplicate || "None (all cells 'unassigned')"
|
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}
|
||||
rightIcon="double-caret-vertical"
|
||||
/>
|
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</Select>
|
||||
</div>
|
||||
<div className={Classes.DIALOG_FOOTER}>
|
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<div className={Classes.DIALOG_FOOTER_ACTIONS}>
|
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<Tooltip content="Close this dialog without creating a category.">
|
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<Button onClick={this.handleDisableAnnoMode}>
|
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Cancel
|
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</Button>
|
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</Tooltip>
|
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<Button
|
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onClick={this.handleCreateUserAnno}
|
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disabled={
|
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!newCategoryText ||
|
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this.categoryNameError(newCategoryText)
|
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}
|
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intent="primary"
|
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type="submit"
|
||||
>
|
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Create new category
|
||||
</Button>
|
||||
</div>
|
||||
</div>
|
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</form>
|
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</Dialog>
|
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<Button onClick={this.handleEnableAnnoMode} intent="primary">
|
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Create new category
|
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</Button>
|
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|
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@@ -6,28 +6,30 @@ import { Flipper, Flipped } from "react-flip-toolkit";
|
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import {
|
||||
Button,
|
||||
Tooltip,
|
||||
InputGroup,
|
||||
Menu,
|
||||
Dialog,
|
||||
MenuItem,
|
||||
Popover,
|
||||
Classes,
|
||||
Icon,
|
||||
Position,
|
||||
PopoverInteractionKind,
|
||||
Colors
|
||||
} from "@blueprintjs/core";
|
||||
import AnnoDialog from "./annoDialog";
|
||||
import AnnoInputs from "./annoInputs";
|
||||
|
||||
import * as globals from "../../globals";
|
||||
import Value from "./value";
|
||||
import sortedCategoryLabels from "../../util/catLabelSort";
|
||||
import { AnnotationsHelpers } from "../../util/stateManager";
|
||||
import { labelErrorMessage, isLabelErroneous } from "./labelUtil";
|
||||
|
||||
@connect(state => ({
|
||||
colorAccessor: state.colors.colorAccessor,
|
||||
categoricalSelection: state.categoricalSelection,
|
||||
annotations: state.annotations,
|
||||
universe: state.universe
|
||||
universe: state.universe,
|
||||
ontology: state.ontology,
|
||||
ontologyLoading: state.ontology?.loading,
|
||||
ontologyEnabled: state.ontology?.enabled
|
||||
}))
|
||||
class Category extends React.Component {
|
||||
constructor(props) {
|
||||
@@ -91,14 +93,48 @@ class Category extends React.Component {
|
||||
handleAddNewLabelToCategory = () => {
|
||||
const { dispatch, metadataField } = this.props;
|
||||
const { newLabelText } = this.state;
|
||||
|
||||
dispatch({
|
||||
type: "annotation: add new label to category",
|
||||
metadataField,
|
||||
newLabelText
|
||||
newLabelText,
|
||||
assignSelectedCells: false
|
||||
});
|
||||
this.setState({ newLabelText: "" });
|
||||
};
|
||||
|
||||
addLabelAndAssignCells = () => {
|
||||
const { dispatch, metadataField } = this.props;
|
||||
const { newLabelText } = this.state;
|
||||
|
||||
dispatch({
|
||||
type: "annotation: add new label to category",
|
||||
metadataField,
|
||||
newLabelText,
|
||||
assignSelectedCells: true
|
||||
});
|
||||
|
||||
this.setState({ newLabelText: "" });
|
||||
};
|
||||
|
||||
handleCreateArbitraryLabel = newLabelTextNotInOntology => {
|
||||
const { dispatch, metadataField } = this.props;
|
||||
|
||||
dispatch({
|
||||
type: "annotation: add new label to category",
|
||||
metadataField,
|
||||
newLabelText: newLabelTextNotInOntology,
|
||||
assignSelectedCells: false
|
||||
});
|
||||
this.setState({ newLabelText: "" });
|
||||
};
|
||||
|
||||
handleCategoryEditTextChange = txt => {
|
||||
this.setState({
|
||||
newCategoryText: txt
|
||||
});
|
||||
};
|
||||
|
||||
activateEditCategoryMode = () => {
|
||||
const { dispatch, metadataField } = this.props;
|
||||
|
||||
@@ -154,63 +190,16 @@ class Category extends React.Component {
|
||||
};
|
||||
|
||||
labelNameError = name => {
|
||||
/*
|
||||
return false if this is a LEGAL/acceptable category name or NULL/empty string,
|
||||
or return an error type.
|
||||
*/
|
||||
|
||||
/* allow empty string */
|
||||
if (name === "") return false;
|
||||
|
||||
/* check for label syntax errors */
|
||||
const error = AnnotationsHelpers.annotationNameIsErroneous(name);
|
||||
if (error) return error;
|
||||
|
||||
/* disallow duplicates */
|
||||
const { metadataField, universe } = this.props;
|
||||
const { obsByName } = universe.schema.annotations;
|
||||
if (obsByName[metadataField].categories.indexOf(name) !== -1)
|
||||
return "duplicate";
|
||||
|
||||
/* otherwise, no error */
|
||||
return false;
|
||||
const { metadataField, ontology, universe } = this.props;
|
||||
return isLabelErroneous(name, metadataField, ontology, universe.schema);
|
||||
};
|
||||
|
||||
labelNameErrorMessage = name => {
|
||||
const { metadataField } = this.props;
|
||||
const err = this.labelNameError(name);
|
||||
|
||||
if (err === "duplicate") {
|
||||
/* duplicate error is special cased because it has special formatting */
|
||||
return (
|
||||
<span>
|
||||
<span style={{ fontStyle: "italic" }}>{name}</span> already exists
|
||||
already exists within{" "}
|
||||
<span style={{ fontStyle: "italic" }}>{metadataField}</span>{" "}
|
||||
</span>
|
||||
);
|
||||
}
|
||||
|
||||
if (err) {
|
||||
/* all other errors - map code to human error message */
|
||||
const errorMessageMap = {
|
||||
"empty-string": "Blank names not allowed",
|
||||
duplicate: "Name must be unique",
|
||||
"trim-spaces": "Leading and trailing spaces not allowed",
|
||||
"illegal-characters":
|
||||
"Only alphanumeric, underscore and period allowed",
|
||||
"multi-space-run": "Multiple consecutive spaces not allowed"
|
||||
};
|
||||
const errorMessage = errorMessageMap[err] ?? "error";
|
||||
return <span>{errorMessage}</span>;
|
||||
}
|
||||
|
||||
/* no error, no message generated */
|
||||
return null;
|
||||
const { metadataField, ontology, universe } = this.props;
|
||||
return labelErrorMessage(name, metadataField, ontology, universe.schema);
|
||||
};
|
||||
|
||||
categoryNameErrorMessage = () => {
|
||||
const { newCategoryText } = this.state;
|
||||
const err = this.editedCategoryNameError();
|
||||
if (err === false) return null;
|
||||
|
||||
@@ -219,7 +208,8 @@ class Category extends React.Component {
|
||||
"empty-string": "Blank names not allowed",
|
||||
duplicate: "Category name must be unique",
|
||||
"trim-spaces": "Leading and trailing spaces not allowed",
|
||||
"illegal-characters": "Only alphanumeric, underscore and period allowed",
|
||||
"illegal-characters":
|
||||
"Only alphanumeric and special characters (-_.) allowed",
|
||||
"multi-space-run": "Multiple consecutive spaces not allowed"
|
||||
};
|
||||
const errorMessage = errorMessageMap[err] ?? "error";
|
||||
@@ -261,6 +251,15 @@ class Category extends React.Component {
|
||||
return false;
|
||||
};
|
||||
|
||||
/* leaky to have both of these in multiple components */
|
||||
handleChoice = e => {
|
||||
this.setState({ newLabelText: e.target });
|
||||
};
|
||||
|
||||
handleTextChange = text => {
|
||||
this.setState({ newLabelText: text });
|
||||
};
|
||||
|
||||
toggleAll() {
|
||||
const { dispatch, metadataField } = this.props;
|
||||
dispatch({
|
||||
@@ -318,13 +317,13 @@ class Category extends React.Component {
|
||||
colorAccessor,
|
||||
categoricalSelection,
|
||||
isUserAnno,
|
||||
annotations
|
||||
annotations,
|
||||
ontologyEnabled
|
||||
} = this.props;
|
||||
const { isTruncated } = categoricalSelection[metadataField];
|
||||
const cat = categoricalSelection[metadataField];
|
||||
const optTuples = [...cat.categoryValueIndices];
|
||||
const optTuplesAsKey = _.map(optTuples, t => t[0]).join(""); // animation
|
||||
const allCategoryNames = _.keys(categoricalSelection);
|
||||
|
||||
return (
|
||||
<div
|
||||
@@ -381,46 +380,30 @@ class Category extends React.Component {
|
||||
<Icon style={{ marginRight: 5 }} icon="tag" iconSize={16} />
|
||||
) : null}
|
||||
|
||||
{annotations.isEditingCategoryName &&
|
||||
annotations.categoryBeingEdited === metadataField ? (
|
||||
<form
|
||||
style={{ display: "inline-block" }}
|
||||
onSubmit={e => {
|
||||
e.preventDefault();
|
||||
this.handleEditCategory();
|
||||
}}
|
||||
>
|
||||
<InputGroup
|
||||
style={{ position: "relative", top: -1 }}
|
||||
ref={input => {
|
||||
this.editableCategoryInput = input;
|
||||
}}
|
||||
small
|
||||
autoFocus
|
||||
onChange={e => {
|
||||
this.setState({
|
||||
newCategoryText: e.target.value
|
||||
});
|
||||
}}
|
||||
defaultValue={metadataField}
|
||||
rightElement={
|
||||
<Button
|
||||
minimal
|
||||
disabled={this.editedCategoryNameError()}
|
||||
style={{ position: "relative", top: -1 }}
|
||||
type="button"
|
||||
icon="small-tick"
|
||||
data-testclass="submitCategoryNameEdit"
|
||||
data-testid="submitCategoryNameEdit"
|
||||
onClick={this.handleEditCategory}
|
||||
/>
|
||||
}
|
||||
{metadataField}
|
||||
|
||||
<AnnoDialog
|
||||
isActive={
|
||||
annotations.isEditingCategoryName &&
|
||||
annotations.categoryBeingEdited === metadataField
|
||||
}
|
||||
title="Edit category name"
|
||||
instruction="New, unique category name:"
|
||||
cancelTooltipContent="Close this dialog without editing this category."
|
||||
primaryButtonText="Edit category name"
|
||||
text={newCategoryText}
|
||||
validationError={this.editedCategoryNameError(newCategoryText)}
|
||||
errorMessage={this.categoryNameErrorMessage(newCategoryText)}
|
||||
handleSubmit={this.handleEditCategory}
|
||||
handleCancel={this.disableEditCategoryMode}
|
||||
annoInput={
|
||||
<AnnoInputs
|
||||
useSuggest={false}
|
||||
text={newCategoryText}
|
||||
handleTextChange={this.handleCategoryEditTextChange}
|
||||
/>
|
||||
{this.categoryNameErrorMessage()}
|
||||
</form>
|
||||
) : (
|
||||
metadataField
|
||||
)}
|
||||
}
|
||||
/>
|
||||
|
||||
{isExpanded ? (
|
||||
<FaChevronDown
|
||||
@@ -438,71 +421,37 @@ class Category extends React.Component {
|
||||
<div>
|
||||
{isUserAnno ? (
|
||||
<>
|
||||
<Dialog
|
||||
icon="tag"
|
||||
title="Add new label"
|
||||
isOpen={
|
||||
<AnnoDialog
|
||||
isActive={
|
||||
annotations.isAddingNewLabel &&
|
||||
annotations.categoryAddingNewLabel === metadataField
|
||||
}
|
||||
onClose={this.disableAddNewLabelMode}
|
||||
>
|
||||
<form
|
||||
onSubmit={e => {
|
||||
e.preventDefault();
|
||||
this.handleAddNewLabelToCategory();
|
||||
}}
|
||||
>
|
||||
<div className={Classes.DIALOG_BODY}>
|
||||
<div style={{ marginBottom: 20 }}>
|
||||
<p>New, unique label name:</p>
|
||||
<InputGroup
|
||||
autoFocus
|
||||
value={newLabelText}
|
||||
intent={
|
||||
this.labelNameError(newLabelText)
|
||||
? "warning"
|
||||
: "none"
|
||||
}
|
||||
onChange={e =>
|
||||
this.setState({ newLabelText: e.target.value })
|
||||
}
|
||||
leftIcon="tag"
|
||||
/>
|
||||
<p
|
||||
style={{
|
||||
marginTop: 7,
|
||||
visibility: this.labelNameError(newLabelText)
|
||||
? "visible"
|
||||
: "hidden",
|
||||
color: Colors.ORANGE3
|
||||
}}
|
||||
>
|
||||
{this.labelNameErrorMessage(newLabelText)}
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
<div className={Classes.DIALOG_FOOTER}>
|
||||
<div className={Classes.DIALOG_FOOTER_ACTIONS}>
|
||||
<Tooltip content="Close this dialog without adding a label.">
|
||||
<Button onClick={this.disableAddNewLabelMode}>
|
||||
Cancel
|
||||
</Button>
|
||||
</Tooltip>
|
||||
<Button
|
||||
disabled={
|
||||
!newLabelText || this.labelNameError(newLabelText)
|
||||
}
|
||||
onClick={this.handleAddNewLabelToCategory}
|
||||
intent="primary"
|
||||
type="submit"
|
||||
>
|
||||
Add new label to category
|
||||
</Button>
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
</Dialog>
|
||||
title="Add new label to category"
|
||||
instruction="New, unique label name:"
|
||||
cancelTooltipContent="Close this dialog without adding a label."
|
||||
primaryButtonText="Add"
|
||||
secondaryButtonText="Add label & assign currently selected cells"
|
||||
handleSecondaryButtonSubmit={this.addLabelAndAssignCells}
|
||||
text={newLabelText}
|
||||
validationError={this.labelNameError(newLabelText)}
|
||||
errorMessage={this.labelNameErrorMessage(newLabelText)}
|
||||
handleSubmit={this.handleAddNewLabelToCategory}
|
||||
handleCancel={this.disableAddNewLabelMode}
|
||||
annoInput={
|
||||
<AnnoInputs
|
||||
useSuggest={ontologyEnabled}
|
||||
text={newLabelText}
|
||||
handleCreateArbitraryLabel={
|
||||
this.handleCreateArbitraryLabel
|
||||
}
|
||||
handleItemChange={this.handleSuggestActiveItemChange}
|
||||
handleChoice={this.handleChoice}
|
||||
handleTextChange={this.handleTextChange}
|
||||
isTextInvalid={this.labelNameError}
|
||||
isTextInvalidErrorMessage={this.labelNameErrorMessage}
|
||||
/>
|
||||
}
|
||||
/>
|
||||
<Popover
|
||||
interactionKind={PopoverInteractionKind.HOVER}
|
||||
boundary="window"
|
||||
|
||||
@@ -0,0 +1,57 @@
|
||||
import React from "react";
|
||||
import { AnnotationsHelpers } from "../../util/stateManager";
|
||||
|
||||
export function isLabelErroneous(label, metadataField, ontology, schema) {
|
||||
/*
|
||||
return false if this is a LEGAL/acceptable category name or NULL/empty string,
|
||||
or return an error type.
|
||||
*/
|
||||
|
||||
/* allow empty string */
|
||||
if (label === "") return false;
|
||||
|
||||
/* check for label syntax errors, but allow terms in ontology */
|
||||
const termInOntology = ontology?.termSet.has(label) ?? false;
|
||||
const error = AnnotationsHelpers.annotationNameIsErroneous(label);
|
||||
if (error && !termInOntology) return error;
|
||||
|
||||
/* disallow duplicates */
|
||||
const { obsByName } = schema.annotations;
|
||||
if (obsByName[metadataField].categories.indexOf(label) !== -1)
|
||||
return "duplicate";
|
||||
|
||||
/* otherwise, no error */
|
||||
return false;
|
||||
}
|
||||
|
||||
export function labelErrorMessage(label, metadataField, ontology, schema) {
|
||||
const err = isLabelErroneous(label, metadataField, ontology, schema);
|
||||
|
||||
if (err === "duplicate") {
|
||||
/* duplicate error is special cased because it has special formatting */
|
||||
return (
|
||||
<span>
|
||||
<span style={{ fontStyle: "italic" }}>{label}</span> already
|
||||
exists already exists within{" "}
|
||||
<span style={{ fontStyle: "italic" }}>{metadataField}</span>{" "}
|
||||
</span>
|
||||
);
|
||||
}
|
||||
|
||||
if (err) {
|
||||
/* all other errors - map code to human error message */
|
||||
const errorMessageMap = {
|
||||
"empty-string": "Blank names not allowed",
|
||||
duplicate: "Name must be unique",
|
||||
"trim-spaces": "Leading and trailing spaces not allowed",
|
||||
"illegal-characters":
|
||||
"Only alphanumeric and special characters (-_.) allowed",
|
||||
"multi-space-run": "Multiple consecutive spaces not allowed"
|
||||
};
|
||||
const errorMessage = errorMessageMap[err] ?? "error";
|
||||
return <span>{errorMessage}</span>;
|
||||
}
|
||||
|
||||
/* no error, no message generated */
|
||||
return null;
|
||||
}
|
||||
@@ -4,7 +4,6 @@ import React from "react";
|
||||
|
||||
import {
|
||||
Button,
|
||||
InputGroup,
|
||||
Menu,
|
||||
MenuItem,
|
||||
Popover,
|
||||
@@ -16,8 +15,11 @@ import {
|
||||
import Occupancy from "./occupancy";
|
||||
import * as globals from "../../globals";
|
||||
import styles from "./categorical.css";
|
||||
import AnnoDialog from "./annoDialog";
|
||||
import AnnoInputs from "./annoInputs";
|
||||
|
||||
import { AnnotationsHelpers } from "../../util/stateManager";
|
||||
import { labelErrorMessage, isLabelErroneous } from "./labelUtil";
|
||||
|
||||
@connect(state => ({
|
||||
categoricalSelection: state.categoricalSelection,
|
||||
@@ -27,7 +29,10 @@ import { AnnotationsHelpers } from "../../util/stateManager";
|
||||
pointDilation: state.pointDilation,
|
||||
schema: state.world?.schema,
|
||||
world: state.world,
|
||||
crossfilter: state.crossfilter
|
||||
crossfilter: state.crossfilter,
|
||||
ontology: state.ontology,
|
||||
ontologyLoading: state.ontology?.loading,
|
||||
ontologyEnabled: state.ontology?.enabled
|
||||
}))
|
||||
class CategoryValue extends React.Component {
|
||||
constructor(props) {
|
||||
@@ -41,13 +46,20 @@ class CategoryValue extends React.Component {
|
||||
};
|
||||
}
|
||||
|
||||
getLabel = () => {
|
||||
const { metadataField, categoryIndex, categoricalSelection } = this.props;
|
||||
const category = categoricalSelection[metadataField];
|
||||
const label = category.categoryValues[categoryIndex];
|
||||
|
||||
return label;
|
||||
};
|
||||
componentDidUpdate(prevProps) {
|
||||
const { categoricalSelection, metadataField, categoryIndex } = this.props;
|
||||
if (
|
||||
prevProps.categoricalSelection !== categoricalSelection ||
|
||||
prevProps.metadataField !== metadataField ||
|
||||
prevProps.categoryIndex !== categoryIndex
|
||||
) {
|
||||
this.setState({
|
||||
editedLabelText: String(
|
||||
categoricalSelection[metadataField].categoryValues[categoryIndex]
|
||||
).valueOf()
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
handleDeleteValue = () => {
|
||||
const { dispatch, metadataField } = this.props;
|
||||
@@ -84,60 +96,49 @@ class CategoryValue extends React.Component {
|
||||
});
|
||||
};
|
||||
|
||||
valueNameErrorMessage = () => {
|
||||
const err = this.valueNameError();
|
||||
if (err === false) return null;
|
||||
handleCreateArbitraryLabel = editedLabelTextNotInOntology => {
|
||||
const { dispatch, metadataField, categoryIndex } = this.props;
|
||||
const label = this.getLabel();
|
||||
|
||||
const errorMessageMap = {
|
||||
/* map error code to human readable error message */
|
||||
"empty-string": "Blank names not allowed",
|
||||
duplicate: "Label must be unique",
|
||||
"trim-spaces": "Leading and trailing spaces not allowed",
|
||||
"illegal-characters": "Only alphanumeric, underscore and period allowed",
|
||||
"multi-space-run": "Multiple consecutive spaces not allowed"
|
||||
};
|
||||
const errorMessage = errorMessageMap[err] ?? "error";
|
||||
return (
|
||||
<span
|
||||
style={{
|
||||
fontStyle: "italic",
|
||||
fontSize: 12,
|
||||
marginTop: 5,
|
||||
color: Colors.ORANGE3
|
||||
}}
|
||||
>
|
||||
{errorMessage}
|
||||
</span>
|
||||
);
|
||||
dispatch({
|
||||
type: "annotation: label edited",
|
||||
metadataField,
|
||||
editedLabel: editedLabelTextNotInOntology,
|
||||
categoryIndex,
|
||||
label
|
||||
});
|
||||
};
|
||||
|
||||
valueNameError = () => {
|
||||
const { editedLabelText } = this.state;
|
||||
const { categoricalSelection, metadataField, categoryIndex } = this.props;
|
||||
|
||||
/*
|
||||
check label syntax
|
||||
*/
|
||||
const err = AnnotationsHelpers.annotationNameIsErroneous(editedLabelText);
|
||||
if (err) return err;
|
||||
|
||||
/*
|
||||
disallow duplicates
|
||||
*/
|
||||
labelNameError = name => {
|
||||
const {
|
||||
metadataField,
|
||||
ontology,
|
||||
schema,
|
||||
categoricalSelection,
|
||||
categoryIndex
|
||||
} = this.props;
|
||||
const category = categoricalSelection[metadataField];
|
||||
const displayString = String(
|
||||
category.categoryValues[categoryIndex]
|
||||
).valueOf();
|
||||
if (
|
||||
category.categoryValues.indexOf(editedLabelText) > -1 &&
|
||||
editedLabelText !== displayString
|
||||
)
|
||||
return "duplicate";
|
||||
if (name === displayString) return false;
|
||||
return isLabelErroneous(name, metadataField, ontology, schema);
|
||||
};
|
||||
|
||||
/*
|
||||
otherwise, all good!
|
||||
*/
|
||||
return false;
|
||||
labelNameErrorMessage = name => {
|
||||
const {
|
||||
metadataField,
|
||||
ontology,
|
||||
schema,
|
||||
categoricalSelection,
|
||||
categoryIndex
|
||||
} = this.props;
|
||||
const category = categoricalSelection[metadataField];
|
||||
const displayString = String(
|
||||
category.categoryValues[categoryIndex]
|
||||
).valueOf();
|
||||
if (name === displayString) return null;
|
||||
return labelErrorMessage(name, metadataField, ontology, schema);
|
||||
};
|
||||
|
||||
activateEditLabelMode = () => {
|
||||
@@ -208,21 +209,6 @@ class CategoryValue extends React.Component {
|
||||
);
|
||||
};
|
||||
|
||||
componentDidUpdate(prevProps) {
|
||||
const { categoricalSelection, metadataField, categoryIndex } = this.props;
|
||||
if (
|
||||
prevProps.categoricalSelection !== categoricalSelection ||
|
||||
prevProps.metadataField !== metadataField ||
|
||||
prevProps.categoryIndex !== categoryIndex
|
||||
) {
|
||||
this.setState({
|
||||
editedLabelText: String(
|
||||
categoricalSelection[metadataField].categoryValues[categoryIndex]
|
||||
).valueOf()
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
toggleOn = () => {
|
||||
const { dispatch, metadataField, categoryIndex } = this.props;
|
||||
dispatch({
|
||||
@@ -250,6 +236,23 @@ class CategoryValue extends React.Component {
|
||||
});
|
||||
};
|
||||
|
||||
handleTextChange = text => {
|
||||
this.setState({ editedLabelText: text });
|
||||
};
|
||||
|
||||
handleChoice = e => {
|
||||
/* Blueprint Suggest format */
|
||||
this.setState({ editedLabelText: e.target });
|
||||
};
|
||||
|
||||
getLabel = () => {
|
||||
const { metadataField, categoryIndex, categoricalSelection } = this.props;
|
||||
const category = categoricalSelection[metadataField];
|
||||
const label = category.categoryValues[categoryIndex];
|
||||
|
||||
return label;
|
||||
};
|
||||
|
||||
isAddCurrentSelectionDisabled(category, value) {
|
||||
/*
|
||||
disable "add current selection to label", if one of the following is true:
|
||||
@@ -289,6 +292,7 @@ class CategoryValue extends React.Component {
|
||||
schema,
|
||||
isUserAnno,
|
||||
annotations,
|
||||
ontologyEnabled,
|
||||
// flippedProps is potentially brittle, their docs want {...flippedProps} on our div,
|
||||
// our lint doesn't like jsx spread, we are version pinned to prevent api change on their part
|
||||
flippedProps,
|
||||
@@ -339,6 +343,12 @@ class CategoryValue extends React.Component {
|
||||
)}`;
|
||||
}
|
||||
|
||||
const editModeActive =
|
||||
isUserAnno &&
|
||||
annotations.labelEditable.category === metadataField &&
|
||||
annotations.isEditingLabelName &&
|
||||
annotations.labelEditable.label === categoryIndex;
|
||||
|
||||
return (
|
||||
<div
|
||||
key={i}
|
||||
@@ -416,66 +426,41 @@ class CategoryValue extends React.Component {
|
||||
verticalAlign: "middle"
|
||||
}}
|
||||
>
|
||||
{annotations.isEditingLabelName &&
|
||||
annotations.labelEditable.category === metadataField &&
|
||||
annotations.labelEditable.label === categoryIndex
|
||||
? null
|
||||
: truncatedString || displayString}
|
||||
{truncatedString || displayString}
|
||||
</span>
|
||||
</Tooltip>
|
||||
{isUserAnno &&
|
||||
annotations.labelEditable.category === metadataField &&
|
||||
annotations.isEditingLabelName &&
|
||||
annotations.labelEditable.label === categoryIndex ? (
|
||||
<form
|
||||
onSubmit={e => {
|
||||
e.preventDefault();
|
||||
if (this.valueNameError()) {
|
||||
return;
|
||||
}
|
||||
this.handleEditValue();
|
||||
}}
|
||||
>
|
||||
<InputGroup
|
||||
style={{ position: "relative", top: -1 }}
|
||||
ref={input => {
|
||||
this.editableInput = input;
|
||||
}}
|
||||
small
|
||||
autoFocus
|
||||
intent={this.valueNameError() ? "warning" : "none"}
|
||||
onChange={e => {
|
||||
this.setState({ editedLabelText: e.target.value });
|
||||
}}
|
||||
defaultValue={displayString}
|
||||
rightElement={
|
||||
<Button
|
||||
minimal
|
||||
style={{ position: "relative", top: -1 }}
|
||||
disabled={this.valueNameError()}
|
||||
type="button"
|
||||
icon="small-tick"
|
||||
data-testclass="submitEdit"
|
||||
data-testid="submitEdit"
|
||||
onClick={this.handleEditValue}
|
||||
{editModeActive ? (
|
||||
<div>
|
||||
<AnnoDialog
|
||||
isActive={editModeActive}
|
||||
title="Edit label"
|
||||
instruction={`New label text must be unique within category ${metadataField}:`}
|
||||
cancelTooltipContent="Close this dialog without editing label text."
|
||||
primaryButtonText="Change label text"
|
||||
text={editedLabelText}
|
||||
categoryToDuplicate={null}
|
||||
validationError={this.labelNameError(editedLabelText)}
|
||||
errorMessage={this.labelNameErrorMessage(editedLabelText)}
|
||||
handleSubmit={this.handleEditValue}
|
||||
handleCancel={this.cancelEdit}
|
||||
annoInput={
|
||||
<AnnoInputs
|
||||
useSuggest={ontologyEnabled}
|
||||
text={editedLabelText}
|
||||
handleCreateArbitraryLabel={
|
||||
this.handleCreateArbitraryLabel
|
||||
}
|
||||
handleItemChange={this.handleSuggestActiveItemChange}
|
||||
handleChoice={this.handleChoice}
|
||||
handleTextChange={this.handleTextChange}
|
||||
isTextInvalid={this.labelNameError}
|
||||
isTextInvalidErrorMessage={this.labelNameErrorMessage}
|
||||
/>
|
||||
}
|
||||
annoSelect={null}
|
||||
/>
|
||||
{this.valueNameErrorMessage()}
|
||||
</form>
|
||||
</div>
|
||||
) : null}
|
||||
{/*
|
||||
CANCEL IT, WITH BUTTON, ESCAPE KEY, CLICK OUT, UNDO?
|
||||
|
||||
<Button
|
||||
minimal
|
||||
style={{ position: "relative", top: -1 }}
|
||||
type="button"
|
||||
icon="cross"
|
||||
data-testclass="submitEdit"
|
||||
data-testid="submitEdit"
|
||||
onClick={this.cancelEdit}
|
||||
/> */}
|
||||
</div>
|
||||
<span style={{ flexShrink: 0 }}>
|
||||
{colorAccessor && !isColorBy && !annotations.isEditingLabelName ? (
|
||||
@@ -483,113 +468,115 @@ class CategoryValue extends React.Component {
|
||||
) : null}
|
||||
</span>
|
||||
</div>
|
||||
<span>
|
||||
<span
|
||||
data-testclass="categorical-value-count"
|
||||
data-testid={`categorical-value-count-${metadataField}-${displayString}`}
|
||||
style={{
|
||||
color:
|
||||
displayString === globals.unassignedCategoryLabel
|
||||
? "#ababab"
|
||||
: "black",
|
||||
fontStyle:
|
||||
displayString === globals.unassignedCategoryLabel
|
||||
? "italic"
|
||||
: "auto"
|
||||
}}
|
||||
>
|
||||
{count}
|
||||
</span>
|
||||
|
||||
<svg
|
||||
display={isColorBy && categories ? "auto" : "none"}
|
||||
style={{
|
||||
marginLeft: 5,
|
||||
width: 11,
|
||||
height: 11,
|
||||
backgroundColor:
|
||||
isColorBy && categories
|
||||
? colorScale(categories.indexOf(value))
|
||||
: "inherit"
|
||||
}}
|
||||
/>
|
||||
{isUserAnno ? (
|
||||
<div>
|
||||
<span>
|
||||
<span
|
||||
onMouseEnter={this.handleMouseExit}
|
||||
onMouseLeave={this.handleMouseEnter}
|
||||
data-testclass="categorical-value-count"
|
||||
data-testid={`categorical-value-count-${metadataField}-${displayString}`}
|
||||
style={{
|
||||
color:
|
||||
displayString === globals.unassignedCategoryLabel
|
||||
? "#ababab"
|
||||
: "black",
|
||||
fontStyle:
|
||||
displayString === globals.unassignedCategoryLabel
|
||||
? "italic"
|
||||
: "auto"
|
||||
}}
|
||||
>
|
||||
<Popover
|
||||
interactionKind={PopoverInteractionKind.HOVER}
|
||||
boundary="window"
|
||||
position={Position.RIGHT_TOP}
|
||||
content={
|
||||
<Menu>
|
||||
<MenuItem
|
||||
icon="plus"
|
||||
data-testclass="handleAddCurrentSelectionToThisLabel"
|
||||
data-testid={`handleAddCurrentSelectionToThisLabel-${metadataField}`}
|
||||
onClick={this.handleAddCurrentSelectionToThisLabel}
|
||||
text={
|
||||
<span>
|
||||
Re-label currently selected cells as
|
||||
<span
|
||||
style={{
|
||||
fontStyle:
|
||||
displayString ===
|
||||
globals.unassignedCategoryLabel
|
||||
? "italic"
|
||||
: "auto"
|
||||
}}
|
||||
>
|
||||
{` ${displayString}`}
|
||||
</span>
|
||||
</span>
|
||||
}
|
||||
disabled={this.isAddCurrentSelectionDisabled(
|
||||
metadataField,
|
||||
value
|
||||
)}
|
||||
/>
|
||||
{displayString !== globals.unassignedCategoryLabel ? (
|
||||
<MenuItem
|
||||
icon="edit"
|
||||
text="Edit this label's name"
|
||||
data-testclass="handleEditValue"
|
||||
data-testid={`handleEditValue-${metadataField}`}
|
||||
onClick={this.activateEditLabelMode}
|
||||
disabled={annotations.isEditingLabelName}
|
||||
/>
|
||||
) : null}
|
||||
{displayString !== globals.unassignedCategoryLabel ? (
|
||||
<MenuItem
|
||||
icon="delete"
|
||||
intent="danger"
|
||||
data-testclass="handleDeleteValue"
|
||||
data-testid={`handleDeleteValue-${metadataField}`}
|
||||
onClick={this.handleDeleteValue}
|
||||
text={`Delete this label, and reassign all cells to type '${globals.unassignedCategoryLabel}'`}
|
||||
/>
|
||||
) : null}
|
||||
</Menu>
|
||||
}
|
||||
>
|
||||
<Button
|
||||
style={{
|
||||
marginLeft: 0,
|
||||
position: "relative",
|
||||
top: -1,
|
||||
minHeight: 16
|
||||
}}
|
||||
data-testclass="seeActions"
|
||||
data-testid={`seeActions-${metadataField}`}
|
||||
icon="more"
|
||||
small
|
||||
minimal
|
||||
/>
|
||||
</Popover>
|
||||
{count}
|
||||
</span>
|
||||
) : null}
|
||||
</span>
|
||||
|
||||
<svg
|
||||
display={isColorBy && categories ? "auto" : "none"}
|
||||
style={{
|
||||
marginLeft: 5,
|
||||
width: 11,
|
||||
height: 11,
|
||||
backgroundColor:
|
||||
isColorBy && categories
|
||||
? colorScale(categories.indexOf(value))
|
||||
: "inherit"
|
||||
}}
|
||||
/>
|
||||
{isUserAnno ? (
|
||||
<span
|
||||
onMouseEnter={this.handleMouseExit}
|
||||
onMouseLeave={this.handleMouseEnter}
|
||||
>
|
||||
<Popover
|
||||
interactionKind={PopoverInteractionKind.HOVER}
|
||||
boundary="window"
|
||||
position={Position.RIGHT_TOP}
|
||||
content={
|
||||
<Menu>
|
||||
<MenuItem
|
||||
icon="plus"
|
||||
data-testclass="handleAddCurrentSelectionToThisLabel"
|
||||
data-testid={`handleAddCurrentSelectionToThisLabel-${metadataField}`}
|
||||
onClick={this.handleAddCurrentSelectionToThisLabel}
|
||||
text={
|
||||
<span>
|
||||
Re-label currently selected cells as
|
||||
<span
|
||||
style={{
|
||||
fontStyle:
|
||||
displayString ===
|
||||
globals.unassignedCategoryLabel
|
||||
? "italic"
|
||||
: "auto"
|
||||
}}
|
||||
>
|
||||
{` ${displayString}`}
|
||||
</span>
|
||||
</span>
|
||||
}
|
||||
disabled={this.isAddCurrentSelectionDisabled(
|
||||
metadataField,
|
||||
value
|
||||
)}
|
||||
/>
|
||||
{displayString !== globals.unassignedCategoryLabel ? (
|
||||
<MenuItem
|
||||
icon="edit"
|
||||
text="Edit this label's name"
|
||||
data-testclass="handleEditValue"
|
||||
data-testid={`handleEditValue-${metadataField}`}
|
||||
onClick={this.activateEditLabelMode}
|
||||
disabled={annotations.isEditingLabelName}
|
||||
/>
|
||||
) : null}
|
||||
{displayString !== globals.unassignedCategoryLabel ? (
|
||||
<MenuItem
|
||||
icon="delete"
|
||||
intent="danger"
|
||||
data-testclass="handleDeleteValue"
|
||||
data-testid={`handleDeleteValue-${metadataField}`}
|
||||
onClick={this.handleDeleteValue}
|
||||
text={`Delete this label, and reassign all cells to type '${globals.unassignedCategoryLabel}'`}
|
||||
/>
|
||||
) : null}
|
||||
</Menu>
|
||||
}
|
||||
>
|
||||
<Button
|
||||
style={{
|
||||
marginLeft: 0,
|
||||
position: "relative",
|
||||
top: -1,
|
||||
minHeight: 16
|
||||
}}
|
||||
data-testclass="seeActions"
|
||||
data-testid={`seeActions-${metadataField}`}
|
||||
icon="more"
|
||||
small
|
||||
minimal
|
||||
/>
|
||||
</Popover>
|
||||
</span>
|
||||
) : null}
|
||||
</span>
|
||||
</div>
|
||||
</div>
|
||||
);
|
||||
}
|
||||
|
||||
@@ -31,7 +31,6 @@ const Annotations = (
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "configuration load complete": {
|
||||
const DefaultDataCollectionName = null;
|
||||
const dataCollectionName =
|
||||
action.config.parameters?.["annotations-data-collection-name"] ?? null;
|
||||
const dataCollectionNameIsReadOnly =
|
||||
|
||||
@@ -165,9 +165,16 @@ const CrossfilterReducerBase = (
|
||||
return state.delDimension(obsAnnoDimensionName(action.metadataField));
|
||||
}
|
||||
|
||||
case "annotation: add new label to category":
|
||||
case "annotation: label current cell selection":
|
||||
case "annotation: label edited":
|
||||
case "annotation: delete label": {
|
||||
if (
|
||||
action.type === "annotation: add new label to category" &&
|
||||
!action.assignSelectedCells
|
||||
)
|
||||
return state;
|
||||
|
||||
/* we need to reindex the dimension. For now, just drop it and add another */
|
||||
const name = action.metadataField;
|
||||
const dimName = obsAnnoDimensionName(name);
|
||||
|
||||
@@ -18,6 +18,7 @@ import controls from "./controls";
|
||||
import resetCache from "./resetCache";
|
||||
import annotations from "./annotations";
|
||||
import autosave from "./autosave";
|
||||
import ontology from "./ontology";
|
||||
import centroidLabels from "./centroidLabels";
|
||||
import pointDialation from "./pointDilation";
|
||||
|
||||
@@ -28,6 +29,7 @@ const Reducer = undoable(
|
||||
["config", config],
|
||||
["universe", universe],
|
||||
["world", world],
|
||||
["ontology", ontology],
|
||||
["annotations", annotations],
|
||||
["layoutChoice", layoutChoice],
|
||||
["categoricalSelection", categoricalSelection],
|
||||
@@ -45,15 +47,15 @@ const Reducer = undoable(
|
||||
]),
|
||||
[
|
||||
"universe",
|
||||
"categoricalSelection",
|
||||
"world",
|
||||
"categoricalSelection",
|
||||
"continuousSelection",
|
||||
"graphSelection",
|
||||
"crossfilter",
|
||||
"layoutChoice",
|
||||
"colors",
|
||||
"controls",
|
||||
"differential",
|
||||
"colors",
|
||||
"layoutChoice",
|
||||
"centroidLabels",
|
||||
"annotations"
|
||||
],
|
||||
|
||||
@@ -0,0 +1,29 @@
|
||||
// jshint esversion: 6
|
||||
const Ontology = (
|
||||
state = {
|
||||
enabled: false, // are ontology terms enabled?
|
||||
terms: null, // an array of term names, eg, ['cell', 'lung cell', ...]
|
||||
termSet: null, // a Set object containing all terms, for fast lookup
|
||||
loading: true
|
||||
},
|
||||
action
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "configuration load complete":
|
||||
const enabled =
|
||||
action.config?.parameters?.annotations_cell_ontology_enabled ?? false;
|
||||
const terms = action.config?.parameters?.annotations_cell_ontology_terms;
|
||||
const termSet = new Set(terms);
|
||||
return {
|
||||
...state,
|
||||
loading: false,
|
||||
enabled,
|
||||
terms,
|
||||
termSet
|
||||
};
|
||||
default:
|
||||
return state;
|
||||
}
|
||||
};
|
||||
|
||||
export default Ontology;
|
||||
@@ -136,13 +136,27 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
|
||||
"user annotations require a non-zero length string name"
|
||||
);
|
||||
|
||||
/* add the new label to the annotation */
|
||||
/* add the new label to the annotation schema */
|
||||
const schema = AnnotationsHelpers.addObsAnnoCategory(
|
||||
state.schema,
|
||||
annotationName,
|
||||
newLabelName
|
||||
);
|
||||
return { ...state, schema };
|
||||
|
||||
/* if so requested, label the current selection */
|
||||
const { world, crossfilter } = prevSharedState;
|
||||
const { metadataField, newLabelText } = action;
|
||||
const obsAnnotations = !action.assignSelectedCells
|
||||
? state.obsAnnotations
|
||||
: setLabelOnCurrentSelection(
|
||||
state,
|
||||
world,
|
||||
crossfilter,
|
||||
metadataField,
|
||||
newLabelText
|
||||
);
|
||||
|
||||
return { ...state, schema, obsAnnotations };
|
||||
}
|
||||
|
||||
case "annotation: label edited": {
|
||||
@@ -208,23 +222,11 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
|
||||
case "annotation: label current cell selection": {
|
||||
const { metadataField, label } = action;
|
||||
const { world, crossfilter } = prevSharedState;
|
||||
|
||||
/*
|
||||
selection state is relative to world. We need to convert it
|
||||
to a mask for Universe before applying it.
|
||||
*/
|
||||
const worldMask = crossfilter.allSelectedMask();
|
||||
const mask = World.worldEqUniverse(world, state)
|
||||
? worldMask
|
||||
: AnnotationsHelpers.worldToUniverseMask(
|
||||
worldMask,
|
||||
world.obsAnnotations,
|
||||
state.nObs
|
||||
);
|
||||
const obsAnnotations = AnnotationsHelpers.setLabelByMask(
|
||||
state.obsAnnotations,
|
||||
const obsAnnotations = setLabelOnCurrentSelection(
|
||||
state,
|
||||
world,
|
||||
crossfilter,
|
||||
metadataField,
|
||||
mask,
|
||||
label
|
||||
);
|
||||
return { ...state, obsAnnotations };
|
||||
@@ -236,4 +238,39 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
|
||||
}
|
||||
};
|
||||
|
||||
function setLabelOnCurrentSelection(
|
||||
universe,
|
||||
world,
|
||||
crossfilter,
|
||||
metadataField,
|
||||
label
|
||||
) {
|
||||
/*
|
||||
Set category `metadataField` to value `label` for anything currently selected.
|
||||
Used by several action type reducers.
|
||||
|
||||
Returns the new obsAnnotations dataframe.
|
||||
*/
|
||||
|
||||
/*
|
||||
selection state is relative to world. We need to convert it
|
||||
to a mask for Universe before applying it.
|
||||
*/
|
||||
const worldMask = crossfilter.allSelectedMask();
|
||||
const mask = World.worldEqUniverse(world, universe)
|
||||
? worldMask
|
||||
: AnnotationsHelpers.worldToUniverseMask(
|
||||
worldMask,
|
||||
world.obsAnnotations,
|
||||
universe.nObs
|
||||
);
|
||||
const obsAnnotations = AnnotationsHelpers.setLabelByMask(
|
||||
universe.obsAnnotations,
|
||||
metadataField,
|
||||
mask,
|
||||
label
|
||||
);
|
||||
return obsAnnotations;
|
||||
}
|
||||
|
||||
export default Universe;
|
||||
|
||||
@@ -196,6 +196,21 @@ const WorldReducer = (
|
||||
case "annotation: add new label to category": {
|
||||
/* add a new label to the schema - schema updated by universe reducer, we just need to note it */
|
||||
const { schema } = nextSharedState.universe;
|
||||
const { metadataField, newLabelText } = action;
|
||||
const { crossfilter } = prevSharedState;
|
||||
|
||||
if (action.assignSelectedCells) {
|
||||
return {
|
||||
...state,
|
||||
schema,
|
||||
...setLabelOnCurrentSelection(
|
||||
state,
|
||||
crossfilter,
|
||||
metadataField,
|
||||
newLabelText
|
||||
)
|
||||
};
|
||||
}
|
||||
return { ...state, schema };
|
||||
}
|
||||
|
||||
@@ -246,21 +261,10 @@ const WorldReducer = (
|
||||
case "annotation: label current cell selection": {
|
||||
const { metadataField, label } = action;
|
||||
const { crossfilter } = prevSharedState;
|
||||
const mask = crossfilter.allSelectedMask();
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: AnnotationsHelpers.setLabelByMask(
|
||||
state.unclipped.obsAnnotations,
|
||||
metadataField,
|
||||
mask,
|
||||
label
|
||||
)
|
||||
return {
|
||||
...state,
|
||||
...setLabelOnCurrentSelection(state, crossfilter, metadataField, label)
|
||||
};
|
||||
const obsAnnotations = state.obsAnnotations.replaceColData(
|
||||
metadataField,
|
||||
unclipped.obsAnnotations.col(metadataField).asArray()
|
||||
);
|
||||
return { ...state, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
default: {
|
||||
@@ -269,4 +273,27 @@ const WorldReducer = (
|
||||
}
|
||||
};
|
||||
|
||||
function setLabelOnCurrentSelection(world, crossfilter, metadataField, label) {
|
||||
/*
|
||||
Set category `metadataField` to value `label` for anything currently selected.
|
||||
Used by several action type reducers.
|
||||
*/
|
||||
const mask = crossfilter.allSelectedMask();
|
||||
const unclipped = {
|
||||
...world.unclipped,
|
||||
obsAnnotations: AnnotationsHelpers.setLabelByMask(
|
||||
world.unclipped.obsAnnotations,
|
||||
metadataField,
|
||||
mask,
|
||||
label
|
||||
)
|
||||
};
|
||||
const obsAnnotations = world.obsAnnotations.replaceColData(
|
||||
metadataField,
|
||||
unclipped.obsAnnotations.col(metadataField).asArray()
|
||||
);
|
||||
|
||||
return { obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
export default WorldReducer;
|
||||
|
||||
@@ -183,7 +183,7 @@ export function createWritableAnnotationDimensions(world, crossfilter) {
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
const legalCharacters = /^(\w|[ .])+$/;
|
||||
const legalCharacters = /^(\w|[ .()-])+$/;
|
||||
export function annotationNameIsErroneous(name) {
|
||||
/*
|
||||
Validate the name - return:
|
||||
@@ -193,10 +193,9 @@ export function annotationNameIsErroneous(name) {
|
||||
Tests:
|
||||
0. must be string, non-null
|
||||
1. no leading or trailing spaces
|
||||
2. only accept alpha, numeric, underscore, period and space
|
||||
2. only accept alpha, numeric, underscore, period, parens, hyphen and space
|
||||
3. no runs of multiple spaces
|
||||
*/
|
||||
|
||||
if (name === "") {
|
||||
return "empty-string";
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user