From b10506ef7db02489fccbc8bf54396f4a95b588d8 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 4 Sep 2024 19:17:31 -0400 Subject: [PATCH 01/50] Add violin plots by type --- .../cde-visualization.component.html | 42 ++- .../cde-visualization.component.scss | 13 + .../cde-visualization.component.ts | 5 +- .../components/violin/violin.component.html | 44 +++ .../components/violin/violin.component.scss | 78 +++++ .../lib/components/violin/violin.component.ts | 313 ++++++++++++++++++ .../src/lib/components/violin/violin.vl.json | 90 +++++ 7 files changed, 569 insertions(+), 16 deletions(-) create mode 100644 libs/cde-visualization/src/lib/components/violin/violin.component.html create mode 100644 libs/cde-visualization/src/lib/components/violin/violin.component.scss create mode 100644 libs/cde-visualization/src/lib/components/violin/violin.component.ts create mode 100644 libs/cde-visualization/src/lib/components/violin/violin.vl.json diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html index 6786e3620..a9076b948 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html @@ -20,21 +20,33 @@
- +
+ + + +
+ Violin + info + +
Violin plot
+ + + +
+ + +
+ +
diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.scss b/libs/cde-visualization/src/lib/components/violin/violin.component.scss new file mode 100644 index 000000000..ba53de024 --- /dev/null +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.scss @@ -0,0 +1,78 @@ +@use 'sass:map'; +@use '@angular/material' as mat; +@use '../../../../../../apps/cde-ui/src/styles/constants/palettes' as palettes; + +$blue: mat.m2-define-palette(map.get(palettes.$palettes, 'blue'), 600, 500, 700); +$blue-theme: mat.m2-define-light-theme( + ( + color: ( + primary: $blue, + accent: $blue, + ), + ) +); + +:host { + @include mat.button-color($blue-theme); + display: grid; + grid: + 'violin . download' + 'plot plot plot' 1fr + / auto 1fr auto; + grid-template-rows: 2rem calc(100% - 2rem); + align-items: start; + row-gap: 0.75rem; + overflow: hidden; + padding: 0.75rem 1rem; + border-width: 0px 0px 2px 2px; + border-style: solid; + border-color: map.get(map.get(palettes.$palettes, 'blue'), 600); + $button-text-color: map.get(map.get(palettes.$palettes, 'blue'), 900); + --mdc-filled-button-container-height: 2rem; + + span.violin-label { + grid-area: violin; + font-size: 1rem; + height: 2rem; + display: flex; + align-items: center; + gap: 0.25rem; + } + + .download { + grid-area: download; + } + + .violin { + grid-area: plot; + height: 100%; + overflow-y: scroll; + } + + button { + --mdc-filled-button-label-text-color: #201e3d; + padding: 0.375rem 0.5rem; + margin-left: 0.5rem; + + mat-icon { + margin-left: unset; + margin-right: 0.125rem; + font-size: 1.25rem; + height: 1.25rem; + width: 1.25rem; + } + } +} + +::ng-deep { + #vg-tooltip-element.vg-tooltip { + font-family: 'Metropolis'; + font-weight: 500; + font-size: 0.75rem; + line-height: 1.125rem; + color: #201e3d; + padding: 0.5rem; + max-width: 22.5rem; + box-shadow: 0px 5px 16px 0px #201e3d3d; + } +} diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.ts b/libs/cde-visualization/src/lib/components/violin/violin.component.ts new file mode 100644 index 000000000..2b875a3f1 --- /dev/null +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.ts @@ -0,0 +1,313 @@ +import { OverlayModule } from '@angular/cdk/overlay'; +import { CommonModule, DOCUMENT } from '@angular/common'; +import { + ChangeDetectionStrategy, + Component, + computed, + effect, + ElementRef, + inject, + input, + model, + Renderer2, + signal, + viewChild, +} from '@angular/core'; +import { MatButtonModule } from '@angular/material/button'; +import { MatExpansionModule } from '@angular/material/expansion'; +import { MatIconModule } from '@angular/material/icon'; +import { ScrollingModule } from '@hra-ui/design-system/scrolling'; +import { produce } from 'immer'; +import { ColorPickerDirective, ColorPickerModule } from 'ngx-color-picker'; +import { View } from 'vega'; +import embed, { VisualizationSpec } from 'vega-embed'; + +import { CellTypeEntry } from '../../models/cell-type'; +import { colorEquals, Rgb, rgbToHex } from '../../models/color'; +import { edgeDistance, EdgeEntry, EdgeIndex } from '../../models/edge'; +import { NodeEntry, NodeTargetKey } from '../../models/node'; +import { FileSaverService } from '../../services/file-saver/file-saver.service'; +import { emptyArrayEquals } from '../../shared/empty-array-equals'; +import { TOOLTIP_POSITION_RIGHT_SIDE } from '../../shared/tooltip-position'; +import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-label.component'; +import * as VIOLIN_SPEC from './violin.vl.json'; + +/** Interface for representing the distance entry */ +interface DistanceEntry { + /** Type of the entry */ + type: string; + /** Distance value of the entry */ + distance: number; +} + +/** Interface for modifying the violin specification */ +interface ModifiableViolinSpec { + /** Configuration for the padding */ + config: { + padding: { + top: number; + right: number; + bottom: number; + left: number; + }; + }; + /** Width of the violin */ + width: string | number; + /** Height of the violin */ + height: string | number; + /** Data values for the violin */ + data: { + values?: unknown[]; + }; + /** Encoding configuration for the violin */ + encoding: { + color: { + legend: unknown; + scale: { + range: unknown[]; + }; + }; + }; +} + +/** Fonts used in the violin */ +const VIOLIN_FONTS = ['12px Metropolis', '14px Metropolis']; + +/** Label for all cell types */ +const ALL_CELLS_TYPE = 'All Cells'; + +/** Width of the exported image */ +const EXPORT_IMAGE_WIDTH = 1000; + +/** Height of the exported image */ +const EXPORT_IMAGE_HEIGHT = 500; + +/** Padding for the exported image */ +const EXPORT_IMAGE_PADDING = 16; + +/** Configuration for the legend in the exported image */ +const EXPORT_IMAGE_LEGEND_CONFIG = { + title: null, + symbolType: 'circle', + symbolStrokeWidth: 10, + labelFontSize: 14, + titleFontSize: 14, + titleLineHeight: 21, + titleColor: '#201E3D', + titleFontWeight: 500, + labelFontWeight: 500, + labelColor: '#4B4B5E', +}; + +/** Length of the dynamic color range */ +const DYNAMIC_COLOR_RANGE_LENGTH = 2000; + +/** Dynamic color range for the violin */ +const DYNAMIC_COLOR_RANGE = Array(DYNAMIC_COLOR_RANGE_LENGTH) + .fill(0) + .map((_value, index) => ({ expr: `colors[${index}] || '#000'` })); + +/** + * Violin Component + */ +@Component({ + selector: 'cde-violin', + standalone: true, + imports: [ + CommonModule, + MatIconModule, + MatButtonModule, + MatExpansionModule, + ColorPickerModule, + ColorPickerLabelComponent, + OverlayModule, + ScrollingModule, + ], + templateUrl: './violin.component.html', + styleUrl: './violin.component.scss', + changeDetection: ChangeDetectionStrategy.OnPush, +}) +export class ViolinComponent { + /** List of nodes used in the violin */ + readonly nodes = input.required(); + + /** Key used to target specific node properties */ + readonly nodeTargetKey = input.required(); + + /** List of edges connecting nodes */ + readonly edges = input.required(); + + /** Currently selected cell type */ + readonly selectedCellType = input.required(); + + /** List of all cell types */ + readonly cellTypes = model.required(); + + /** List of selected cell types */ + readonly cellTypesSelection = input.required(); + + /** Tooltip position configuration */ + readonly tooltipPosition = TOOLTIP_POSITION_RIGHT_SIDE; + + /** State indicating whether the info panel is open */ + infoOpen = false; + + protected readonly colorPicker = signal(null); + + /** State indicating whether overflow is visible */ + protected readonly overflowVisible = computed(() => !!this.colorPicker()); + + /** List of filtered cell types based on selection */ + protected readonly filteredCellTypes = computed( + () => { + const selection = new Set(this.cellTypesSelection()); + selection.delete(this.selectedCellType()); + const filtered = this.cellTypes().filter(({ name }) => selection.has(name)); + return filtered.sort((a, b) => b.count - a.count); + }, + { equal: emptyArrayEquals }, + ); + + /** Label for the total cell type */ + protected readonly totalCellTypeLabel = ALL_CELLS_TYPE; + + /** Color for the total cell type */ + protected readonly totalCellTypeColor = signal([0, 0, 0], { equal: colorEquals }); + + /** Computed distances between nodes */ + private readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); + + /** Data for the violin visualization */ + private readonly data = computed(() => this.computeData(), { equal: emptyArrayEquals }); + + /** Colors for the violin visualization */ + private readonly colors = computed(() => this.computeColors(), { equal: emptyArrayEquals }); + + /** Reference to the document object */ + private readonly document = inject(DOCUMENT); + + /** Reference to the renderer for DOM manipulation */ + private readonly renderer = inject(Renderer2); + + /** Service for saving files */ + private readonly fileSaver = inject(FileSaverService); + + /** Element reference for the violin container */ + private readonly violinEl = viewChild.required('violin'); + + /** Vega view instance for the violin */ + private readonly view = signal(undefined); + + /** Effect for updating view data */ + protected readonly viewDataRef = effect(() => this.view()?.data('data', this.data()).run()); + + /** Effect for updating view colors */ + protected readonly viewColorsRef = effect(() => { + this.view()?.signal('colors', this.colors()).run(); + this.view()?.resize(); + }); + + /** Effect for creating the Vega view */ + protected readonly viewCreateRef = effect( + async (onCleanup) => { + const el = this.violinEl().nativeElement; + await this.ensureFontsLoaded(); + + const spec = produce(VIOLIN_SPEC, (draft) => { + draft.encoding.color.scale.range = DYNAMIC_COLOR_RANGE; + }); + const { finalize, view } = await embed(el, spec as VisualizationSpec, { + actions: false, + }); + + onCleanup(finalize); + this.view.set(view); + }, + { allowSignalWrites: true }, + ); + + /** Download the violin as an image in the specified format */ + async download(format: string): Promise { + const spec = produce(VIOLIN_SPEC as ModifiableViolinSpec, (draft) => { + draft.width = EXPORT_IMAGE_WIDTH; + draft.height = EXPORT_IMAGE_HEIGHT; + draft.config.padding.bottom = EXPORT_IMAGE_PADDING; + draft.config.padding.top = EXPORT_IMAGE_PADDING; + draft.config.padding.right = EXPORT_IMAGE_PADDING; + draft.config.padding.left = EXPORT_IMAGE_PADDING; + draft.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; + draft.data.values = this.data(); + draft.encoding.color.scale.range = this.colors(); + }); + + const el = this.renderer.createElement('div'); + const { view, finalize } = await embed(el, spec as VisualizationSpec, { + actions: false, + }); + + const url = await view.toImageURL(format); + this.fileSaver.save(url, `cde-violin.${format}`); + finalize(); + } + + /** Update the color of a specific cell type entry */ + updateColor(entry: CellTypeEntry, color: Rgb): void { + const entries = this.cellTypes(); + const index = entries.indexOf(entry); + const copy = [...entries]; + + copy[index] = { ...copy[index], color }; + this.cellTypes.set(copy); + } + + /** Reset the color of the total cell type */ + resetAllCellsColor(): void { + this.totalCellTypeColor.set([0, 0, 0]); + } + + /** Ensure required fonts are loaded for the violin */ + private async ensureFontsLoaded(): Promise { + const loadPromises = VIOLIN_FONTS.map((font) => this.document.fonts.load(font)); + await Promise.all(loadPromises); + } + + /** Compute distances between nodes based on edges */ + private computeDistances(): DistanceEntry[] { + const nodes = this.nodes(); + const edges = this.edges(); + if (nodes.length === 0 || edges.length === 0) { + return []; + } + + const nodeTargetKey = this.nodeTargetKey(); + const selectedCellType = this.selectedCellType(); + const distances: DistanceEntry[] = []; + for (const edge of edges) { + const sourceNode = nodes[edge[EdgeIndex.SourceNode]]; + const type = sourceNode[nodeTargetKey]; + if (type !== selectedCellType) { + distances.push({ type, distance: edgeDistance(edge) }); + } + } + + return distances; + } + + /** Compute data for the violin visualization */ + private computeData(): DistanceEntry[] { + const selection = new Set(this.cellTypesSelection()); + if (selection.size === 0) { + return []; + } + + return this.distances().filter(({ type }) => selection.has(type)); + } + + /** Compute colors for the violin visualization */ + private computeColors(): string[] { + const totalCellType = { name: this.totalCellTypeLabel, color: this.totalCellTypeColor() }; + return [totalCellType, ...this.filteredCellTypes()] + .sort((a, b) => (a.name < b.name ? -1 : a.name === b.name ? 0 : 1)) + .map(({ color }) => rgbToHex(color)); + } +} diff --git a/libs/cde-visualization/src/lib/components/violin/violin.vl.json b/libs/cde-visualization/src/lib/components/violin/violin.vl.json new file mode 100644 index 000000000..507e2d7e8 --- /dev/null +++ b/libs/cde-visualization/src/lib/components/violin/violin.vl.json @@ -0,0 +1,90 @@ +{ + "$schema": "https://vega.github.io/schema/vega-lite/v5.json", + "width": 400, + "height": 120, + "spacing": 0, + "config": { + "font": "Metropolis", + "padding": { + "top": 4, + "right": 16, + "bottom": 4, + "left": 4 + }, + "axis": { + "labelFontSize": 12, + "titleFontSize": 14, + "titleFontWeight": 500, + "labelFontWeight": 500, + "titleLineHeight": 21, + "labelLineHeight": 18, + "titleColor": "#201E3D", + "labelColor": "#4B4B5E", + "labelAngle": -45, + "ticks": false, + "domain": false, + "labelPadding": 8 + } + }, + "data": { + "name": "data" + }, + "params": [ + { + "name": "colors", + "value": [] + } + ], + "transform": [ + { + "calculate": "[datum.type, 'All Cells']", + "as": "type" + }, + { + "flatten": ["type"] + }, + { + "density": "distance", + "bandwidth": 0, + "groupby": ["type"] + } + ], + "mark": "area", + "encoding": { + "x": { + "field": "value", + "type": "quantitative", + "title": "Distance (µm)", + "axis": { + "labelAngle": 0 + } + }, + "y": { + "field": "density", + "type": "quantitative", + "stack": "center", + "impute": null, + "title": null, + "axis": null + }, + "row": { + "field": "type", + "title": "Cell Types" + }, + "color": { + "field": "type", + "legend": null, + "scale": { + "range": [ + { + "expr": "'Replaced/repeated in javascript' || color[0] || '#000'" + } + ] + } + }, + "tooltip": { + "field": "type", + "type": "nominal" + } + } +} From 2735824baecef67cf6036991bb44db99b59d6eaa Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 6 Sep 2024 21:45:44 -0400 Subject: [PATCH 02/50] Improvements to violin plot --- .../cde-visualization.component.scss | 4 +- .../components/violin/violin.component.html | 4 +- .../components/violin/violin.component.scss | 4 +- .../lib/components/violin/violin.component.ts | 84 ++++----- .../src/lib/components/violin/violin.vl.json | 177 ++++++++++++------ 5 files changed, 170 insertions(+), 103 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss index f3665c566..8a8000807 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss @@ -83,12 +83,12 @@ border-width: 0 0 2px 0; border-style: solid; height: 100%; - width: 60%; + width: calc(100% - 488px); } cde-violin { height: 100%; - width: 40%; + width: 488px; } } } diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.html b/libs/cde-visualization/src/lib/components/violin/violin.component.html index fbfaaae98..9e7500b0a 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.html +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.html @@ -41,4 +41,6 @@
-
+ +
+ diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.scss b/libs/cde-visualization/src/lib/components/violin/violin.component.scss index ba53de024..dab5c4020 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.scss +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.scss @@ -23,7 +23,7 @@ $blue-theme: mat.m2-define-light-theme( align-items: start; row-gap: 0.75rem; overflow: hidden; - padding: 0.75rem 1rem; + padding: 0.75rem 0.5rem; border-width: 0px 0px 2px 2px; border-style: solid; border-color: map.get(map.get(palettes.$palettes, 'blue'), 600); @@ -37,10 +37,12 @@ $blue-theme: mat.m2-define-light-theme( display: flex; align-items: center; gap: 0.25rem; + padding-left: 0.5rem; } .download { grid-area: download; + padding-right: 0.5rem; } .violin { diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.ts b/libs/cde-visualization/src/lib/components/violin/violin.component.ts index 2b875a3f1..99ea66a7f 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.ts +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.ts @@ -18,12 +18,11 @@ import { MatExpansionModule } from '@angular/material/expansion'; import { MatIconModule } from '@angular/material/icon'; import { ScrollingModule } from '@hra-ui/design-system/scrolling'; import { produce } from 'immer'; -import { ColorPickerDirective, ColorPickerModule } from 'ngx-color-picker'; import { View } from 'vega'; import embed, { VisualizationSpec } from 'vega-embed'; import { CellTypeEntry } from '../../models/cell-type'; -import { colorEquals, Rgb, rgbToHex } from '../../models/color'; +import { Rgb, rgbToHex } from '../../models/color'; import { edgeDistance, EdgeEntry, EdgeIndex } from '../../models/edge'; import { NodeEntry, NodeTargetKey } from '../../models/node'; import { FileSaverService } from '../../services/file-saver/file-saver.service'; @@ -51,31 +50,42 @@ interface ModifiableViolinSpec { left: number; }; }; - /** Width of the violin */ - width: string | number; - /** Height of the violin */ - height: string | number; + /** Data values for the violin */ data: { values?: unknown[]; }; /** Encoding configuration for the violin */ - encoding: { - color: { - legend: unknown; - scale: { - range: unknown[]; - }; - }; + spec: { + /** Width of the violin */ + width: string | number; + /** Height of the violin */ + height: string | number; + layer: [ + { + encoding: { + color: { + legend: unknown; + scale: { + range: unknown[]; + }; + }; + }; + }, + { + encoding: { + color: { + value: unknown; + }; + }; + }, + ]; }; } /** Fonts used in the violin */ const VIOLIN_FONTS = ['12px Metropolis', '14px Metropolis']; -/** Label for all cell types */ -const ALL_CELLS_TYPE = 'All Cells'; - /** Width of the exported image */ const EXPORT_IMAGE_WIDTH = 1000; @@ -118,7 +128,6 @@ const DYNAMIC_COLOR_RANGE = Array(DYNAMIC_COLOR_RANGE_LENGTH) MatIconModule, MatButtonModule, MatExpansionModule, - ColorPickerModule, ColorPickerLabelComponent, OverlayModule, ScrollingModule, @@ -152,11 +161,6 @@ export class ViolinComponent { /** State indicating whether the info panel is open */ infoOpen = false; - protected readonly colorPicker = signal(null); - - /** State indicating whether overflow is visible */ - protected readonly overflowVisible = computed(() => !!this.colorPicker()); - /** List of filtered cell types based on selection */ protected readonly filteredCellTypes = computed( () => { @@ -168,12 +172,6 @@ export class ViolinComponent { { equal: emptyArrayEquals }, ); - /** Label for the total cell type */ - protected readonly totalCellTypeLabel = ALL_CELLS_TYPE; - - /** Color for the total cell type */ - protected readonly totalCellTypeColor = signal([0, 0, 0], { equal: colorEquals }); - /** Computed distances between nodes */ private readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); @@ -213,10 +211,12 @@ export class ViolinComponent { const el = this.violinEl().nativeElement; await this.ensureFontsLoaded(); - const spec = produce(VIOLIN_SPEC, (draft) => { - draft.encoding.color.scale.range = DYNAMIC_COLOR_RANGE; + const spec = produce(VIOLIN_SPEC as unknown as ModifiableViolinSpec, (draft) => { + if (draft.spec.layer.length === 2) { + draft.spec.layer[0].encoding.color.scale.range = DYNAMIC_COLOR_RANGE; + } }); - const { finalize, view } = await embed(el, spec as VisualizationSpec, { + const { finalize, view } = await embed(el, spec as unknown as VisualizationSpec, { actions: false, }); @@ -228,20 +228,22 @@ export class ViolinComponent { /** Download the violin as an image in the specified format */ async download(format: string): Promise { - const spec = produce(VIOLIN_SPEC as ModifiableViolinSpec, (draft) => { - draft.width = EXPORT_IMAGE_WIDTH; - draft.height = EXPORT_IMAGE_HEIGHT; + const spec = produce(VIOLIN_SPEC as unknown as ModifiableViolinSpec, (draft) => { + draft.spec.width = EXPORT_IMAGE_WIDTH; + draft.spec.height = EXPORT_IMAGE_HEIGHT; draft.config.padding.bottom = EXPORT_IMAGE_PADDING; draft.config.padding.top = EXPORT_IMAGE_PADDING; draft.config.padding.right = EXPORT_IMAGE_PADDING; draft.config.padding.left = EXPORT_IMAGE_PADDING; - draft.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; + draft.spec.layer[0].encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; draft.data.values = this.data(); - draft.encoding.color.scale.range = this.colors(); + draft.spec.layer[0].encoding.color.scale.range = this.colors(); }); + console.log(spec); + const el = this.renderer.createElement('div'); - const { view, finalize } = await embed(el, spec as VisualizationSpec, { + const { view, finalize } = await embed(el, spec as unknown as VisualizationSpec, { actions: false, }); @@ -260,11 +262,6 @@ export class ViolinComponent { this.cellTypes.set(copy); } - /** Reset the color of the total cell type */ - resetAllCellsColor(): void { - this.totalCellTypeColor.set([0, 0, 0]); - } - /** Ensure required fonts are loaded for the violin */ private async ensureFontsLoaded(): Promise { const loadPromises = VIOLIN_FONTS.map((font) => this.document.fonts.load(font)); @@ -305,8 +302,7 @@ export class ViolinComponent { /** Compute colors for the violin visualization */ private computeColors(): string[] { - const totalCellType = { name: this.totalCellTypeLabel, color: this.totalCellTypeColor() }; - return [totalCellType, ...this.filteredCellTypes()] + return this.filteredCellTypes() .sort((a, b) => (a.name < b.name ? -1 : a.name === b.name ? 0 : 1)) .map(({ color }) => rgbToHex(color)); } diff --git a/libs/cde-visualization/src/lib/components/violin/violin.vl.json b/libs/cde-visualization/src/lib/components/violin/violin.vl.json index 507e2d7e8..74c1801aa 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.vl.json +++ b/libs/cde-visualization/src/lib/components/violin/violin.vl.json @@ -1,19 +1,20 @@ { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "width": 400, - "height": 120, - "spacing": 0, + "spacing": -2, "config": { "font": "Metropolis", "padding": { - "top": 4, - "right": 16, - "bottom": 4, - "left": 4 + "top": 0, + "right": 0, + "bottom": 0, + "left": 0 + }, + "view": { + "stroke": "transparent" }, "axis": { "labelFontSize": 12, - "titleFontSize": 14, + "titleFontSize": 12, "titleFontWeight": 500, "labelFontWeight": 500, "titleLineHeight": 21, @@ -22,8 +23,16 @@ "labelColor": "#4B4B5E", "labelAngle": -45, "ticks": false, - "domain": false, "labelPadding": 8 + }, + "legend": { + "titleFontSize": 14, + "titleLineHeight": 21, + "titleColor": "#201E3D", + "titleFontWeight": 500, + "labelFontSize": 14, + "labelFontWeight": 500, + "labelColor": "#4B4B5E" } }, "data": { @@ -35,56 +44,114 @@ "value": [] } ], - "transform": [ - { - "calculate": "[datum.type, 'All Cells']", - "as": "type" - }, - { - "flatten": ["type"] - }, - { - "density": "distance", - "bandwidth": 0, - "groupby": ["type"] - } - ], - "mark": "area", - "encoding": { - "x": { - "field": "value", - "type": "quantitative", - "title": "Distance (µm)", - "axis": { - "labelAngle": 0 - } - }, - "y": { - "field": "density", - "type": "quantitative", - "stack": "center", - "impute": null, - "title": null, - "axis": null - }, + "facet": { "row": { "field": "type", - "title": "Cell Types" - }, - "color": { - "field": "type", - "legend": null, - "scale": { - "range": [ + "title": "Cell Types", + "header": { + "labelAngle": 0, + "labelPadding": 4, + "labelAlign": "left", + "labelLimit": 65, + "labelBaseline": "middle", + "titlePadding": 8, + "labelFontSize": 12, + "titleFontSize": 12, + "titleFontWeight": 500, + "labelFontWeight": 500 + } + } + }, + "resolve": { + "scale": { + "y": "independent" + } + }, + "spec": { + "height": 80, + "width": 350, + "layer": [ + { + "mark": { + "type": "area", + "stroke": "black", + "strokeWidth": 0.5 + }, + "transform": [ { - "expr": "'Replaced/repeated in javascript' || color[0] || '#000'" + "density": "distance", + "bandwidth": 0, + "groupby": ["type"] + } + ], + "encoding": { + "x": { + "field": "value", + "type": "quantitative", + "title": "Distance (µm)", + "scale": { + "domainMin": -50 + }, + "axis": { + "labelFlush": false, + "grid": true, + "labelAngle": 0, + "labelOverlap": true, + "labelSeparation": 4 + } + }, + "y": { + "field": "density", + "type": "quantitative", + "stack": "center", + "impute": null, + "title": null, + "axis": { + "labels": false, + "grid": false + }, + "scale": { + "nice": false, + "padding": 12 + } + }, + "color": { + "field": "type", + "legend": null, + "scale": { + "range": [ + { + "expr": "'Replaced/repeated in javascript' || 'color[0] || '#000'" + } + ] + } + }, + "tooltip": { + "field": "type", + "type": "nominal" + } + } + }, + { + "mark": { + "type": "boxplot", + "extent": "min-max", + "size": 4 + }, + "encoding": { + "x": { + "field": "distance", + "type": "quantitative", + "title": "Distance (µm)", + "scale": { + "domainMin": -50 + } + }, + "color": { + "value": "black" } - ] + } } - }, - "tooltip": { - "field": "type", - "type": "nominal" - } + ] } } From 39e1c5bb7f8d7e143a95f8358adcf49fb676b8dd Mon Sep 17 00:00:00 2001 From: edlu77 Date: Mon, 9 Sep 2024 17:33:27 -0400 Subject: [PATCH 03/50] Update violin plot upload settings --- .../components/histogram/histogram.vl.json | 9 --- .../lib/components/violin/violin.component.ts | 55 +++++++++---------- .../src/lib/components/violin/violin.vl.json | 11 +--- 3 files changed, 28 insertions(+), 47 deletions(-) diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.vl.json b/libs/cde-visualization/src/lib/components/histogram/histogram.vl.json index 1cfba9d02..f491e15ad 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.vl.json +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.vl.json @@ -23,15 +23,6 @@ "ticks": false, "domain": false, "labelPadding": 8 - }, - "legend": { - "titleFontSize": 14, - "titleLineHeight": 21, - "titleColor": "#201E3D", - "titleFontWeight": 500, - "labelFontSize": 14, - "labelFontWeight": 500, - "labelColor": "#4B4B5E" } }, "data": { diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.ts b/libs/cde-visualization/src/lib/components/violin/violin.component.ts index 99ea66a7f..7d92e9fc9 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.ts +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.ts @@ -61,25 +61,17 @@ interface ModifiableViolinSpec { width: string | number; /** Height of the violin */ height: string | number; - layer: [ - { - encoding: { - color: { - legend: unknown; - scale: { - range: unknown[]; - }; + layer: { + encoding: { + color: { + legend?: unknown; + scale: { + range: unknown[]; }; + value?: string; }; - }, - { - encoding: { - color: { - value: unknown; - }; - }; - }, - ]; + }; + }[]; }; } @@ -90,7 +82,7 @@ const VIOLIN_FONTS = ['12px Metropolis', '14px Metropolis']; const EXPORT_IMAGE_WIDTH = 1000; /** Height of the exported image */ -const EXPORT_IMAGE_HEIGHT = 500; +const EXPORT_IMAGE_HEIGHT = 100; /** Padding for the exported image */ const EXPORT_IMAGE_PADDING = 16; @@ -107,6 +99,8 @@ const EXPORT_IMAGE_LEGEND_CONFIG = { titleFontWeight: 500, labelFontWeight: 500, labelColor: '#4B4B5E', + symbolStrokeColor: 'type', + symbolSize: 400, }; /** Length of the dynamic color range */ @@ -211,12 +205,15 @@ export class ViolinComponent { const el = this.violinEl().nativeElement; await this.ensureFontsLoaded(); - const spec = produce(VIOLIN_SPEC as unknown as ModifiableViolinSpec, (draft) => { - if (draft.spec.layer.length === 2) { - draft.spec.layer[0].encoding.color.scale.range = DYNAMIC_COLOR_RANGE; + const spec = produce(VIOLIN_SPEC, (draft) => { + for (const layer of draft.spec.layer) { + if (layer.encoding.color.legend === null) { + layer.encoding.color.scale = { range: DYNAMIC_COLOR_RANGE }; + } } }); - const { finalize, view } = await embed(el, spec as unknown as VisualizationSpec, { + + const { finalize, view } = await embed(el, spec as VisualizationSpec, { actions: false, }); @@ -228,22 +225,24 @@ export class ViolinComponent { /** Download the violin as an image in the specified format */ async download(format: string): Promise { - const spec = produce(VIOLIN_SPEC as unknown as ModifiableViolinSpec, (draft) => { + const spec = produce(VIOLIN_SPEC as ModifiableViolinSpec, (draft) => { draft.spec.width = EXPORT_IMAGE_WIDTH; + for (const layer of draft.spec.layer) { + if (layer.encoding.color.legend === null) { + layer.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; + layer.encoding.color.scale = { range: this.colors() }; + } + } draft.spec.height = EXPORT_IMAGE_HEIGHT; draft.config.padding.bottom = EXPORT_IMAGE_PADDING; draft.config.padding.top = EXPORT_IMAGE_PADDING; draft.config.padding.right = EXPORT_IMAGE_PADDING; draft.config.padding.left = EXPORT_IMAGE_PADDING; - draft.spec.layer[0].encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; draft.data.values = this.data(); - draft.spec.layer[0].encoding.color.scale.range = this.colors(); }); - console.log(spec); - const el = this.renderer.createElement('div'); - const { view, finalize } = await embed(el, spec as unknown as VisualizationSpec, { + const { view, finalize } = await embed(el, spec as VisualizationSpec, { actions: false, }); diff --git a/libs/cde-visualization/src/lib/components/violin/violin.vl.json b/libs/cde-visualization/src/lib/components/violin/violin.vl.json index 74c1801aa..446fd7f8a 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.vl.json +++ b/libs/cde-visualization/src/lib/components/violin/violin.vl.json @@ -24,15 +24,6 @@ "labelAngle": -45, "ticks": false, "labelPadding": 8 - }, - "legend": { - "titleFontSize": 14, - "titleLineHeight": 21, - "titleColor": "#201E3D", - "titleFontWeight": 500, - "labelFontSize": 14, - "labelFontWeight": 500, - "labelColor": "#4B4B5E" } }, "data": { @@ -121,7 +112,7 @@ "scale": { "range": [ { - "expr": "'Replaced/repeated in javascript' || 'color[0] || '#000'" + "expr": "'Replaced/repeated in javascript' || color[0] || '#000'" } ] } From 6c0358814e861ab4182b48e666bd96fc69aedd68 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 13 Sep 2024 14:03:23 -0400 Subject: [PATCH 04/50] Improvements --- .../components/violin/violin.component.html | 2 +- .../lib/components/violin/violin.component.ts | 2 +- .../src/lib/components/violin/violin.vl.json | 24 ++++++++++--------- 3 files changed, 15 insertions(+), 13 deletions(-) diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.html b/libs/cde-visualization/src/lib/components/violin/violin.component.html index 9e7500b0a..d9b13f4cb 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.html +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.html @@ -1,5 +1,5 @@ - Violin + Violin Graph Date: Fri, 13 Sep 2024 18:45:48 -0400 Subject: [PATCH 05/50] Refactor visualizations --- .../cde-visualization.component.html | 20 ++- .../cde-visualization.component.ts | 81 ++++++++++- .../histogram/histogram.component.html | 2 +- .../histogram/histogram.component.ts | 137 ++++-------------- .../lib/components/violin/violin.component.ts | 108 +------------- 5 files changed, 128 insertions(+), 220 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html index a9076b948..855703824 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html @@ -38,23 +38,21 @@ > diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts index 2b38912ec..582c48470 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts @@ -20,7 +20,7 @@ import { NodeDistVisualizationComponent } from '../components/node-dist-visualiz import { ViolinComponent } from '../components/violin/violin.component'; import { VisualizationHeaderComponent } from '../components/visualization-header/visualization-header.component'; import { CellTypeEntry } from '../models/cell-type'; -import { rgbToHex } from '../models/color'; +import { Rgb, rgbToHex } from '../models/color'; import { ColorMapColorKey, ColorMapEntry, @@ -29,7 +29,7 @@ import { DEFAULT_COLOR_MAP_KEY, DEFAULT_COLOR_MAP_VALUE_KEY, } from '../models/color-map'; -import { DEFAULT_MAX_EDGE_DISTANCE, EdgeEntry } from '../models/edge'; +import { DEFAULT_MAX_EDGE_DISTANCE, edgeDistance, EdgeEntry, EdgeIndex } from '../models/edge'; import { Metadata } from '../models/metadata'; import { DEFAULT_NODE_TARGET_KEY, NodeEntry, NodeTargetKey, selectNodeTargetValue } from '../models/node'; import { ColorMapFileLoaderService } from '../services/data/color-map-loader.service'; @@ -42,6 +42,14 @@ import { createColorGenerator } from '../shared/color-generator'; import { emptyArrayEquals } from '../shared/empty-array-equals'; import { mergeObjects } from '../shared/merge'; +/** Interface for representing the distance entry */ +export interface DistanceEntry { + /** Type of the entry */ + type: string; + /** Distance value of the entry */ + distance: number; +} + /** * CDE Visualization Root Component */ @@ -244,6 +252,26 @@ export class CdeVisualizationComponent { /** View container. Do NOT change the name. It is used by ngx-color-picker! */ readonly vcRef = inject(ViewContainerRef); + /** List of filtered cell types based on selection */ + protected readonly filteredCellTypes = computed( + () => { + const selection = new Set(this.cellTypesSelection()); + selection.delete(this.selectedNodeTargetValue()); + const filtered = this.cellTypes().filter(({ name }) => selection.has(name)); + return filtered.sort((a, b) => b.count - a.count); + }, + { equal: emptyArrayEquals }, + ); + + /** Computed distances between nodes */ + readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); + + /** Data for the histogram visualization */ + readonly data = computed(() => this.computeData(), { equal: emptyArrayEquals }); + + /** Colors for the histogram visualization */ + readonly colors = computed(() => this.computeColors(), { equal: emptyArrayEquals }); + /** Setup component */ constructor() { // Workaround for getting ngx-color-picker to attach to the root view @@ -284,4 +312,53 @@ export class CdeVisualizationComponent { this.fileSaver.saveCsv(data, 'color-map.csv'); } } + + /** Compute distances between nodes based on edges */ + computeDistances(): DistanceEntry[] { + const nodes = this.loadedNodes(); + const edges = this.loadedEdges(); + if (nodes.length === 0 || edges.length === 0) { + return []; + } + + const nodeTypeKey = this.nodeTypeKey(); + const selectedCellType = this.selectedNodeTargetValue(); + const distances: DistanceEntry[] = []; + for (const edge of edges) { + const sourceNode = nodes[edge[EdgeIndex.SourceNode]]; + const type = sourceNode[nodeTypeKey]; + if (type !== selectedCellType) { + distances.push({ type, distance: edgeDistance(edge) }); + } + } + + return distances; + } + + /** Compute data for the violin visualization */ + computeData(): DistanceEntry[] { + const selection = new Set(this.cellTypesSelection()); + if (selection.size === 0) { + return []; + } + + return this.computeDistances().filter(({ type }) => selection.has(type)); + } + + /** Compute colors for the violin visualization */ + computeColors(): string[] { + return this.filteredCellTypes() + .sort((a, b) => (a.name < b.name ? -1 : a.name === b.name ? 0 : 1)) + .map(({ color }) => rgbToHex(color)); + } + + /** Update the color of a specific cell type entry */ + updateColor(entry: CellTypeEntry, color: Rgb): void { + const entries = this.cellTypes(); + const index = entries.indexOf(entry); + const copy = [...entries]; + + copy[index] = { ...copy[index], color }; + this.cellTypes.set(copy); + } } diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.html b/libs/cde-visualization/src/lib/components/histogram/histogram.component.html index 7a203bd1b..7529e405c 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.html +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.html @@ -64,7 +64,7 @@ [color]="type.color" [isAnchor]="type.name === selectedCellType()" (colorPickerOpen)="colorPicker.set($event)" - (colorChange)="updateColor(type, $event)" + (colorChange)="updateColor.emit({ type, color: $event })" > } diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts b/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts index 1310091bf..484ced4c0 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts @@ -3,13 +3,13 @@ import { CommonModule, DOCUMENT } from '@angular/common'; import { ChangeDetectionStrategy, Component, - ElementRef, - Renderer2, computed, effect, + ElementRef, inject, input, - model, + output, + Renderer2, signal, viewChild, } from '@angular/core'; @@ -20,28 +20,23 @@ import { MatExpansionPanelDefaultOptions, } from '@angular/material/expansion'; import { MatIconModule } from '@angular/material/icon'; +import { ScrollingModule } from '@hra-ui/design-system/scrolling'; import { produce } from 'immer'; import { ColorPickerDirective, ColorPickerModule } from 'ngx-color-picker'; import { View } from 'vega'; import embed, { VisualizationSpec } from 'vega-embed'; + +import { DistanceEntry } from '../../cde-visualization/cde-visualization.component'; import { CellTypeEntry } from '../../models/cell-type'; -import { Rgb, colorEquals, rgbToHex } from '../../models/color'; -import { EdgeEntry, EdgeIndex, edgeDistance } from '../../models/edge'; -import { NodeEntry, NodeTargetKey } from '../../models/node'; +import { colorEquals, Rgb } from '../../models/color'; import { FileSaverService } from '../../services/file-saver/file-saver.service'; -import { emptyArrayEquals } from '../../shared/empty-array-equals'; - -import { ScrollingModule } from '@hra-ui/design-system/scrolling'; import { TOOLTIP_POSITION_RIGHT_SIDE } from '../../shared/tooltip-position'; import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-label.component'; import * as HISTOGRAM_SPEC from './histogram.vl.json'; -/** Interface for representing the distance entry */ -interface DistanceEntry { - /** Type of the entry */ - type: string; - /** Distance value of the entry */ - distance: number; +interface UpdateColorData { + type: CellTypeEntry; + color: Rgb; } /** Interface for modifying the histogram specification */ @@ -142,23 +137,21 @@ const DYNAMIC_COLOR_RANGE = Array(DYNAMIC_COLOR_RANGE_LENGTH) changeDetection: ChangeDetectionStrategy.OnPush, }) export class HistogramComponent { - /** List of nodes used in the histogram */ - readonly nodes = input.required(); + /** Computed distances between nodes */ + readonly computedDistances = input.required(); - /** Key used to target specific node properties */ - readonly nodeTargetKey = input.required(); + /** Data for the violin visualization */ + readonly computedData = input.required(); - /** List of edges connecting nodes */ - readonly edges = input.required(); + /** Colors for the violin visualization */ + readonly computedColors = input.required(); - /** Currently selected cell type */ - readonly selectedCellType = input.required(); + readonly cellTypes = input.required(); - /** List of all cell types */ - readonly cellTypes = model.required(); + readonly filteredCellTypes = input.required(); - /** List of selected cell types */ - readonly cellTypesSelection = input.required(); + /** Currently selected cell type */ + readonly selectedCellType = input.required(); /** Tooltip position configuration */ readonly tooltipPosition = TOOLTIP_POSITION_RIGHT_SIDE; @@ -171,32 +164,9 @@ export class HistogramComponent { /** State indicating whether overflow is visible */ protected readonly overflowVisible = computed(() => !!this.colorPicker()); - /** List of filtered cell types based on selection */ - protected readonly filteredCellTypes = computed( - () => { - const selection = new Set(this.cellTypesSelection()); - selection.delete(this.selectedCellType()); - const filtered = this.cellTypes().filter(({ name }) => selection.has(name)); - return filtered.sort((a, b) => b.count - a.count); - }, - { equal: emptyArrayEquals }, - ); - /** Label for the total cell type */ protected readonly totalCellTypeLabel = ALL_CELLS_TYPE; - /** Color for the total cell type */ - protected readonly totalCellTypeColor = signal([0, 0, 0], { equal: colorEquals }); - - /** Computed distances between nodes */ - private readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); - - /** Data for the histogram visualization */ - private readonly data = computed(() => this.computeData(), { equal: emptyArrayEquals }); - - /** Colors for the histogram visualization */ - private readonly colors = computed(() => this.computeColors(), { equal: emptyArrayEquals }); - /** Reference to the document object */ private readonly document = inject(DOCUMENT); @@ -212,11 +182,13 @@ export class HistogramComponent { /** Vega view instance for the histogram */ private readonly view = signal(undefined); + readonly updateColor = output(); + /** Effect for updating view data */ - protected readonly viewDataRef = effect(() => this.view()?.data('data', this.data()).run()); + protected readonly viewDataRef = effect(() => this.view()?.data('data', this.computedData()).run()); /** Effect for updating view colors */ - protected readonly viewColorsRef = effect(() => this.view()?.signal('colors', this.colors()).run()); + protected readonly viewColorsRef = effect(() => this.view()?.signal('colors', this.computedColors()).run()); /** Effect for creating the Vega view */ protected readonly viewCreateRef = effect( @@ -247,8 +219,8 @@ export class HistogramComponent { draft.config.padding.right = EXPORT_IMAGE_PADDING; draft.config.padding.left = EXPORT_IMAGE_PADDING; draft.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; - draft.data.values = this.data(); - draft.encoding.color.scale.range = this.colors(); + draft.data.values = this.computedData(); + draft.encoding.color.scale.range = this.computedColors(); }); const el = this.renderer.createElement('div'); @@ -261,64 +233,17 @@ export class HistogramComponent { finalize(); } - /** Update the color of a specific cell type entry */ - updateColor(entry: CellTypeEntry, color: Rgb): void { - const entries = this.cellTypes(); - const index = entries.indexOf(entry); - const copy = [...entries]; - - copy[index] = { ...copy[index], color }; - this.cellTypes.set(copy); - } - - /** Reset the color of the total cell type */ - resetAllCellsColor(): void { - this.totalCellTypeColor.set([0, 0, 0]); - } - /** Ensure required fonts are loaded for the histogram */ private async ensureFontsLoaded(): Promise { const loadPromises = HISTOGRAM_FONTS.map((font) => this.document.fonts.load(font)); await Promise.all(loadPromises); } - /** Compute distances between nodes based on edges */ - private computeDistances(): DistanceEntry[] { - const nodes = this.nodes(); - const edges = this.edges(); - if (nodes.length === 0 || edges.length === 0) { - return []; - } - - const nodeTargetKey = this.nodeTargetKey(); - const selectedCellType = this.selectedCellType(); - const distances: DistanceEntry[] = []; - for (const edge of edges) { - const sourceNode = nodes[edge[EdgeIndex.SourceNode]]; - const type = sourceNode[nodeTargetKey]; - if (type !== selectedCellType) { - distances.push({ type, distance: edgeDistance(edge) }); - } - } - - return distances; - } - - /** Compute data for the histogram visualization */ - private computeData(): DistanceEntry[] { - const selection = new Set(this.cellTypesSelection()); - if (selection.size === 0) { - return []; - } - - return this.distances().filter(({ type }) => selection.has(type)); - } + /** Color for the total cell type */ + protected readonly totalCellTypeColor = signal([0, 0, 0], { equal: colorEquals }); - /** Compute colors for the histogram visualization */ - private computeColors(): string[] { - const totalCellType = { name: this.totalCellTypeLabel, color: this.totalCellTypeColor() }; - return [totalCellType, ...this.filteredCellTypes()] - .sort((a, b) => (a.name < b.name ? -1 : a.name === b.name ? 0 : 1)) - .map(({ color }) => rgbToHex(color)); + /** Reset the color of the total cell type */ + resetAllCellsColor(): void { + this.totalCellTypeColor.set([0, 0, 0]); } } diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.ts b/libs/cde-visualization/src/lib/components/violin/violin.component.ts index 1f76c554a..0522e0e1d 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.ts +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.ts @@ -3,12 +3,10 @@ import { CommonModule, DOCUMENT } from '@angular/common'; import { ChangeDetectionStrategy, Component, - computed, effect, ElementRef, inject, input, - model, Renderer2, signal, viewChild, @@ -21,24 +19,12 @@ import { produce } from 'immer'; import { View } from 'vega'; import embed, { VisualizationSpec } from 'vega-embed'; -import { CellTypeEntry } from '../../models/cell-type'; -import { Rgb, rgbToHex } from '../../models/color'; -import { edgeDistance, EdgeEntry, EdgeIndex } from '../../models/edge'; -import { NodeEntry, NodeTargetKey } from '../../models/node'; +import { DistanceEntry } from '../../cde-visualization/cde-visualization.component'; import { FileSaverService } from '../../services/file-saver/file-saver.service'; -import { emptyArrayEquals } from '../../shared/empty-array-equals'; import { TOOLTIP_POSITION_RIGHT_SIDE } from '../../shared/tooltip-position'; import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-label.component'; import * as VIOLIN_SPEC from './violin.vl.json'; -/** Interface for representing the distance entry */ -interface DistanceEntry { - /** Type of the entry */ - type: string; - /** Distance value of the entry */ - distance: number; -} - /** Interface for modifying the violin specification */ interface ModifiableViolinSpec { /** Configuration for the padding */ @@ -131,49 +117,20 @@ const DYNAMIC_COLOR_RANGE = Array(DYNAMIC_COLOR_RANGE_LENGTH) changeDetection: ChangeDetectionStrategy.OnPush, }) export class ViolinComponent { - /** List of nodes used in the violin */ - readonly nodes = input.required(); - - /** Key used to target specific node properties */ - readonly nodeTargetKey = input.required(); - - /** List of edges connecting nodes */ - readonly edges = input.required(); - - /** Currently selected cell type */ - readonly selectedCellType = input.required(); - - /** List of all cell types */ - readonly cellTypes = model.required(); - - /** List of selected cell types */ - readonly cellTypesSelection = input.required(); - /** Tooltip position configuration */ readonly tooltipPosition = TOOLTIP_POSITION_RIGHT_SIDE; /** State indicating whether the info panel is open */ infoOpen = false; - /** List of filtered cell types based on selection */ - protected readonly filteredCellTypes = computed( - () => { - const selection = new Set(this.cellTypesSelection()); - selection.delete(this.selectedCellType()); - const filtered = this.cellTypes().filter(({ name }) => selection.has(name)); - return filtered.sort((a, b) => b.count - a.count); - }, - { equal: emptyArrayEquals }, - ); - /** Computed distances between nodes */ - private readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); + readonly computedDistances = input.required(); /** Data for the violin visualization */ - private readonly data = computed(() => this.computeData(), { equal: emptyArrayEquals }); + readonly computedData = input.required(); /** Colors for the violin visualization */ - private readonly colors = computed(() => this.computeColors(), { equal: emptyArrayEquals }); + readonly computedColors = input.required(); /** Reference to the document object */ private readonly document = inject(DOCUMENT); @@ -191,11 +148,11 @@ export class ViolinComponent { private readonly view = signal(undefined); /** Effect for updating view data */ - protected readonly viewDataRef = effect(() => this.view()?.data('data', this.data()).run()); + protected readonly viewDataRef = effect(() => this.view()?.data('data', this.computedData()).run()); /** Effect for updating view colors */ protected readonly viewColorsRef = effect(() => { - this.view()?.signal('colors', this.colors()).run(); + this.view()?.signal('colors', this.computedColors()).run(); this.view()?.resize(); }); @@ -230,7 +187,7 @@ export class ViolinComponent { for (const layer of draft.spec.layer) { if (layer.encoding.color.legend === null) { layer.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; - layer.encoding.color.scale = { range: this.colors() }; + layer.encoding.color.scale = { range: this.computedColors() }; } } draft.spec.height = EXPORT_IMAGE_HEIGHT; @@ -238,7 +195,7 @@ export class ViolinComponent { draft.config.padding.top = EXPORT_IMAGE_PADDING; draft.config.padding.right = EXPORT_IMAGE_PADDING; draft.config.padding.left = EXPORT_IMAGE_PADDING; - draft.data.values = this.data(); + draft.data.values = this.computedData(); }); const el = this.renderer.createElement('div'); @@ -251,58 +208,9 @@ export class ViolinComponent { finalize(); } - /** Update the color of a specific cell type entry */ - updateColor(entry: CellTypeEntry, color: Rgb): void { - const entries = this.cellTypes(); - const index = entries.indexOf(entry); - const copy = [...entries]; - - copy[index] = { ...copy[index], color }; - this.cellTypes.set(copy); - } - /** Ensure required fonts are loaded for the violin */ private async ensureFontsLoaded(): Promise { const loadPromises = VIOLIN_FONTS.map((font) => this.document.fonts.load(font)); await Promise.all(loadPromises); } - - /** Compute distances between nodes based on edges */ - private computeDistances(): DistanceEntry[] { - const nodes = this.nodes(); - const edges = this.edges(); - if (nodes.length === 0 || edges.length === 0) { - return []; - } - - const nodeTargetKey = this.nodeTargetKey(); - const selectedCellType = this.selectedCellType(); - const distances: DistanceEntry[] = []; - for (const edge of edges) { - const sourceNode = nodes[edge[EdgeIndex.SourceNode]]; - const type = sourceNode[nodeTargetKey]; - if (type !== selectedCellType) { - distances.push({ type, distance: edgeDistance(edge) }); - } - } - - return distances; - } - - /** Compute data for the violin visualization */ - private computeData(): DistanceEntry[] { - const selection = new Set(this.cellTypesSelection()); - if (selection.size === 0) { - return []; - } - - return this.distances().filter(({ type }) => selection.has(type)); - } - - /** Compute colors for the violin visualization */ - private computeColors(): string[] { - return this.filteredCellTypes() - .sort((a, b) => (a.name < b.name ? -1 : a.name === b.name ? 0 : 1)) - .map(({ color }) => rgbToHex(color)); - } } From d3d6408e5ca3ecb5fe3eb6c61e88b4582dd812e1 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Mon, 16 Sep 2024 13:16:45 -0400 Subject: [PATCH 06/50] Testing --- .../cde-visualization.component.html | 9 +-- .../histogram/histogram.component.spec.ts | 76 ++++++------------- .../histogram/histogram.component.ts | 5 -- .../lib/components/violin/violin.component.ts | 3 - 4 files changed, 25 insertions(+), 68 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html index 855703824..2acdea8f8 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html @@ -37,20 +37,13 @@ #visualization > - + { } const sampleNodes = [createNodeEntry('a', 0, 0), createNodeEntry('b', 0, 2), createNodeEntry('c', 0, 4)]; - const sampleEdges: EdgeEntry[] = [ - [0, 0, 0, 3, 4, 5, 6], - [1, 0, 2, 3, 4, 5, 6], - [2, 0, 4, 3, 4, 5, 6], - ]; - const sampleCellTypes: CellTypeEntry[] = [ - { name: 'a', count: 2, color: [0, 0, 0] }, - { name: 'b', count: 4, color: [0, 1, 2] }, - { name: 'c', count: 6, color: [0, 1, 3] }, + const sampleData = [ + { + type: 'A', + distance: 5, + }, + { + type: 'B', + distance: 7, + }, ]; - const sampleCellTypesSelection: string[] = [sampleCellTypes[0].name, sampleCellTypes[1].name]; const embedResult = mockDeep(); @@ -61,12 +59,10 @@ describe('HistogramComponent', () => { it('should render the histogram using vega', async () => { const { fixture } = await setup({ componentInputs: { - nodes: sampleNodes, - nodeTargetKey, - edges: sampleEdges, + computedData: sampleData, + computedColors: [], + filteredCellTypes: [], selectedCellType: sampleNodes[0][nodeTargetKey], - cellTypes: sampleCellTypes, - cellTypesSelection: sampleCellTypesSelection, }, }); await fixture.whenStable(); @@ -75,15 +71,13 @@ describe('HistogramComponent', () => { expect(embed).toHaveBeenCalledWith(container, expect.anything(), expect.anything()); }); - it('should set empty data when nodes or edges are empty', async () => { + it('should set empty data when input data is empty', async () => { const { fixture } = await setup({ componentInputs: { - nodes: [], - nodeTargetKey, - edges: [], + computedData: [], + computedColors: [], + filteredCellTypes: [], selectedCellType: sampleNodes[0][nodeTargetKey], - cellTypes: sampleCellTypes, - cellTypesSelection: sampleCellTypesSelection, }, }); await fixture.whenStable(); @@ -94,12 +88,10 @@ describe('HistogramComponent', () => { it('should download in the specified format', async () => { await setup({ componentInputs: { - nodes: [], - nodeTargetKey, - edges: [], + computedData: [], + computedColors: [], + filteredCellTypes: [], selectedCellType: '', - cellTypes: [], - cellTypesSelection: [], }, }); @@ -115,35 +107,15 @@ describe('HistogramComponent', () => { expect(fileSaveSpy).toHaveBeenCalledWith(imageUrl, 'cde-histogram.svg'); }); - it('should updateColor', async () => { - const { - fixture: { componentInstance: instance }, - } = await setup({ - componentInputs: { - nodes: [], - nodeTargetKey: 'key', - edges: [], - selectedCellType: 'type', - cellTypes: sampleCellTypes, - cellTypesSelection: sampleCellTypesSelection, - }, - }); - - instance.updateColor(sampleCellTypes[0], [255, 255, 255]); - expect(instance.cellTypes()[0].color).toEqual([255, 255, 255]); - }); - it('should reset all cell colors', async () => { const { fixture: { componentInstance: instance }, } = await setup({ componentInputs: { - nodes: [], - nodeTargetKey, - edges: [], + computedData: [], + computedColors: [], + filteredCellTypes: [], selectedCellType: '', - cellTypes: [], - cellTypesSelection: [], }, }); diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts b/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts index 484ced4c0..4e61c0209 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts @@ -137,17 +137,12 @@ const DYNAMIC_COLOR_RANGE = Array(DYNAMIC_COLOR_RANGE_LENGTH) changeDetection: ChangeDetectionStrategy.OnPush, }) export class HistogramComponent { - /** Computed distances between nodes */ - readonly computedDistances = input.required(); - /** Data for the violin visualization */ readonly computedData = input.required(); /** Colors for the violin visualization */ readonly computedColors = input.required(); - readonly cellTypes = input.required(); - readonly filteredCellTypes = input.required(); /** Currently selected cell type */ diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.ts b/libs/cde-visualization/src/lib/components/violin/violin.component.ts index 0522e0e1d..1447c232a 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.ts +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.ts @@ -123,9 +123,6 @@ export class ViolinComponent { /** State indicating whether the info panel is open */ infoOpen = false; - /** Computed distances between nodes */ - readonly computedDistances = input.required(); - /** Data for the violin visualization */ readonly computedData = input.required(); From 8c553e4f648508db26212f6a5593a528fcd28bdb Mon Sep 17 00:00:00 2001 From: edlu77 Date: Mon, 16 Sep 2024 19:10:54 -0400 Subject: [PATCH 07/50] Upload Data module updates --- .../file-upload/file-upload.component.html | 12 ---- .../create-visualization-page.component.html | 39 +++++++++++-- .../create-visualization-page.component.scss | 57 ++++++++++++------- .../create-visualization-page.component.ts | 2 + 4 files changed, 72 insertions(+), 38 deletions(-) diff --git a/apps/cde-ui/src/app/components/file-upload/file-upload.component.html b/apps/cde-ui/src/app/components/file-upload/file-upload.component.html index 81ba5ca4c..0f6edd9b2 100644 --- a/apps/cde-ui/src/app/components/file-upload/file-upload.component.html +++ b/apps/cde-ui/src/app/components/file-upload/file-upload.component.html @@ -38,15 +38,3 @@

#fileInput /> } - - Use Template - arrow_right_alt - diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index 57e7e99ec..36fbcc683 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -13,8 +13,7 @@

Create a Cell Distance Visualization

1 - Format and Upload Data -
+ Upload Data coordinates should be in micrometers. Damage and proliferation markers can be included.

+
+ + Use Template + arrow_right_alt +

- Required Columns: + + + + + + + + + + + + + + + + + + + + +
Required ColumnsOptional ColumnsSupported Format
• X• Z• CSV
• Y• Cell Ontology ID
• Cell Type
(): T | null { MatIconModule, MatInputModule, MatSelectModule, + MatTableModule, FileUploadComponent, FooterComponent, From 4133446dfbf592d5e0fea1beaf4b0d6a1cef02f2 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Tue, 17 Sep 2024 17:29:00 -0400 Subject: [PATCH 08/50] Upload Data style updates --- .../file-upload/file-upload.component.html | 18 ++--- .../file-upload/file-upload.component.scss | 76 +++++++++++++------ .../create-visualization-page.component.html | 8 +- .../create-visualization-page.component.scss | 20 +++-- ...te-visualization-page.component.theme.scss | 16 ++-- .../create-visualization-page.component.ts | 2 +- apps/cde-ui/src/styles/constants/_colors.scss | 2 +- 7 files changed, 82 insertions(+), 60 deletions(-) diff --git a/apps/cde-ui/src/app/components/file-upload/file-upload.component.html b/apps/cde-ui/src/app/components/file-upload/file-upload.component.html index 0f6edd9b2..d8226f2b2 100644 --- a/apps/cde-ui/src/app/components/file-upload/file-upload.component.html +++ b/apps/cde-ui/src/app/components/file-upload/file-upload.component.html @@ -7,27 +7,23 @@

@if (!file && errorMessage()) {
- {{ errorMessage() }} - {{ errorActionMessage() }} + error +
+ {{ errorActionMessage() }} + {{ errorMessage() }} +
} @if (file && !errorMessage()) {
- File loaded: {{ file ? file.name : '' }}
- + delete
} @else { - + target="_blank" rel="noopener noreferrer" > - Use Template - arrow_right_alt + download + Template

- diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index 9d1bdbec6..3425e2e31 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -77,7 +77,7 @@ grid: 'header header' 'table table' - 'upload-csv upload-csv' / 1fr; + 'upload-csv .' / auto 1fr; grid-template-rows: auto auto auto; row-gap: 2rem; @@ -91,10 +91,18 @@ } .use-template { - --mdc-text-button-label-text-size: 1rem; - --mat-text-button-with-icon-horizontal-padding: 0rem; + --mdc-text-button-label-text-size: 14px; + --mat-text-button-with-icon-horizontal-padding: 1rem; --mdc-text-button-label-text-tracking: 0.02em; - --mat-text-button-icon-spacing: 0.25rem; + --mat-text-button-icon-offset: 0.75rem; + --mdc-text-button-container-height: 2.5rem; + + mat-icon { + font-size: 1.5rem; + height: 1.5rem; + width: 1.5rem; + margin-left: 0; + } } th, @@ -116,10 +124,6 @@ .upload-csv { grid-area: upload-csv; - - ::ng-deep .error { - margin-bottom: 3rem; - } } } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index ab9ddf437..381fac8a3 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -4,6 +4,7 @@ @use '../../../styles/breakpoints' as breakpoints; $gray-palette: map.get(palettes.$palettes, 'gray'); +$blue-palette: map.get(palettes.$palettes, 'blue'); @mixin color($theme) { cde-create-visualization-page { @@ -30,24 +31,19 @@ $gray-palette: map.get(palettes.$palettes, 'gray'); .header { .step-number { - background-color: map.get($gray-palette, 700); + background-color: map.get($blue-palette, 800); color: white; } - mat-icon { - color: mat.get-theme-color($theme, accent, darker); + .use-template { + color: mat.get-theme-color($theme, primary, 700); } } } .data-upload { - .required-columns, - .optional-columns { - color: mat.get-theme-color($theme, accent, 800); - } - - .use-template { - color: mat.get-theme-color($theme, primary, 700); + td { + color: map.get($gray-palette, 700); } } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index ab57ed206..625de1cb9 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -389,7 +389,7 @@ export class CreateVisualizationPageComponent { case 'type-error': return `Please upload a ${fileDescription} CSV file.`; default: - return 'Please upload a CSV file with the required columns.'; + return 'Please upload a file with the required columns.'; } } } diff --git a/apps/cde-ui/src/styles/constants/_colors.scss b/apps/cde-ui/src/styles/constants/_colors.scss index a8d755629..74a6dbe69 100644 --- a/apps/cde-ui/src/styles/constants/_colors.scss +++ b/apps/cde-ui/src/styles/constants/_colors.scss @@ -10,7 +10,7 @@ $colors: ( 'blue-4': #d5dbe3, 'blue-5': #eff2f5, 'gray-1': #464954, - 'gray-2': #51535d, + 'gray-2': #4c4c58, 'gray-3': #fcfcfc, 'white': #ffffff, 'black': #000000, From d9ccc53af63a57943df29a0bbd357a205f11d852 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 18 Sep 2024 20:04:11 -0400 Subject: [PATCH 09/50] Add column header checking --- .../file-upload/file-upload.component.html | 2 +- .../file-upload/file-upload.component.ts | 3 - .../create-visualization-page.component.html | 117 ++++++++++++++++-- .../create-visualization-page.component.scss | 76 ++++++++---- .../create-visualization-page.component.ts | 98 +++++++++++++-- 5 files changed, 253 insertions(+), 43 deletions(-) diff --git a/apps/cde-ui/src/app/components/file-upload/file-upload.component.html b/apps/cde-ui/src/app/components/file-upload/file-upload.component.html index d8226f2b2..45f0b5def 100644 --- a/apps/cde-ui/src/app/components/file-upload/file-upload.component.html +++ b/apps/cde-ui/src/app/components/file-upload/file-upload.component.html @@ -9,8 +9,8 @@

error
- {{ errorActionMessage() }} {{ errorMessage() }} + {{ errorActionMessage() }}
} diff --git a/apps/cde-ui/src/app/components/file-upload/file-upload.component.ts b/apps/cde-ui/src/app/components/file-upload/file-upload.component.ts index fbcdcf4c5..362e25f17 100644 --- a/apps/cde-ui/src/app/components/file-upload/file-upload.component.ts +++ b/apps/cde-ui/src/app/components/file-upload/file-upload.component.ts @@ -43,9 +43,6 @@ export class FileUploadComponent { /** Notification for action required */ readonly actionNotification = input(); - /** Url for template data */ - readonly templateUrl = input(); - /** Upload error message */ readonly errorMessage = input(); /** Upload error action message */ diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index 293de5b0e..609f50e5e 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -34,8 +34,8 @@

[cdkConnectedOverlayPush]="true" >

- Format single-cell spatial feature tables into the Cell Type Table template to upload and explore data. Cell - coordinates should be in micrometers. Damage and proliferation markers can be included. + Use the template to format single-cell spatial feature tables for exploration. The cell type column can + include damage and proliferation markers.

@@ -47,7 +47,6 @@

target="_blank" rel="noopener noreferrer" > - download Template

@@ -83,13 +82,12 @@

(loadErrored)="nodesLoadError = $event" [errorMessage]="nodesErrorMessage" [errorActionMessage]="nodesErrorActionMessage" - templateUrl="https://docs.google.com/spreadsheets/d/1EUf7CUZb0NprgxBeX3nS3GXyUM89edIRH6NSeUsR3nY/edit?gid=47698780#gid=47698780" #nodesFileUpload > -
+ + +
+

+ 2 + Organize Data +
+ + info + + + +

Verify column headers and edit as needed. Select optional column headers.

+ +

+ + + +
+ Required: Verify column headers + + + X Axis + + @for (option of dataHeaders; track option) { + {{ option }} + } + + + + + Y Axis + + @for (option of dataHeaders; track option) { + {{ option }} + } + + + + + Cell Type + + @for (option of dataHeaders; track option) { + {{ option }} + } + + +
+ + @if (columnErrorActionMessage) { +
+ error +
+ {{ columnErrorActionMessage }} +
+
+ } + +
+ Optional: Add column headers + + + Z Axis + + @for (option of dataHeaders; track option) { + {{ option }} + } + + + + + Cell Ontology ID + + @for (option of dataHeaders; track option) { + {{ option }} + } + + +
@@ -206,10 +309,10 @@

- +

diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index 3425e2e31..f4603ae5c 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -66,6 +66,10 @@ font-size: 1rem; } + .card-title { + margin-right: 0.75rem; + } + .info { margin: 0.25rem; } @@ -96,13 +100,6 @@ --mdc-text-button-label-text-tracking: 0.02em; --mat-text-button-icon-offset: 0.75rem; --mdc-text-button-container-height: 2.5rem; - - mat-icon { - font-size: 1.5rem; - height: 1.5rem; - width: 1.5rem; - margin-left: 0; - } } th, @@ -118,35 +115,70 @@ padding-left: 1.5rem; } - span { - margin-right: 0.75rem; - } - .upload-csv { grid-area: upload-csv; } } - .anchor-selection { - .header { - margin-bottom: 0.5rem; + // .anchor-selection { + // .header { + // margin-bottom: 0.5rem; + // } + + // .select-form { + // width: calc(100% - 6rem); + // margin: 1.5rem 3rem; + // } + // } + + .organize-data { + .required-headers, + .optional-headers { + display: grid; + } + + .required-headers { + grid: 'subheader subheader'; + } + .optional-headers { + grid: 'subheader subheader'; } - .select-form { - width: calc(100% - 6rem); - margin: 1.5rem 3rem; + .subheader { + grid-area: subheader; + } + + .error { + display: flex; + align-items: center; + gap: 0.5rem; + margin-bottom: 2rem; + background-color: rgb(from #ffdcc4 r g b / 0.8); + padding: 0.5rem 0.75rem; + border-radius: 0.25rem; + + .alert { + color: #bc4f00; + } + + .error-messages { + display: flex; + flex-direction: column; + color: #2f1400; + } + } + + mat-form-field { + margin: 1.5rem 0; + max-width: 17.5rem; } } .metadata { display: grid; - grid: 'header'; gap: 0.5rem; column-gap: 2.5rem; - - @include breakpoints.breakpoint('medium', 'large', 'x-large', 'xx-large', 'xxx-large') { - grid: 'header header'; - } + grid: 'header header'; .header { grid-area: header; diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index 625de1cb9..d5644bd71 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -98,7 +98,32 @@ export class CreateVisualizationPageComponent { /** Component form controller */ readonly visualizationForm = this.fbnn.group({ + // nodeTargetValue: [DEFAULT_NODE_TARGET_VALUE], + // metadata: this.fb.group({ + // title: [optionalValue()], + // technology: [optionalValue()], + // organ: [optionalValue()], + // sex: [optionalValue()], + // age: [optionalValue(), [Validators.min(0), Validators.max(120), validateInteger()]], + // thickness: [optionalValue(), Validators.min(0)], + // pixelSize: [optionalValue(), Validators.min(0)], + // }), + // colorMapType: ['default'], nodeTargetValue: [DEFAULT_NODE_TARGET_VALUE], + headers: this.fb.group({ + xAxis: [optionalValue()], + yAxis: [optionalValue()], + cellType: [optionalValue()], + zAxis: [optionalValue()], + ontologyId: [optionalValue()], + }), + parameters: this.fb.group({ + anchorCellType: [optionalValue()], + distanceThreshold: [optionalValue()], + pixelSizeX: [optionalValue(), Validators.min(0)], + pixelSizeY: [optionalValue(), Validators.min(0)], + pixelSizeZ: [optionalValue(), Validators.min(0)], + }), metadata: this.fb.group({ title: [optionalValue()], technology: [optionalValue()], @@ -106,7 +131,6 @@ export class CreateVisualizationPageComponent { sex: [optionalValue()], age: [optionalValue(), [Validators.min(0), Validators.max(120), validateInteger()]], thickness: [optionalValue(), Validators.min(0)], - pixelSize: [optionalValue(), Validators.min(0)], }), colorMapType: ['default'], }); @@ -145,8 +169,8 @@ export class CreateVisualizationPageComponent { /** Whether to show upload info tooltip */ uploadInfoOpen = false; - /** Whether to show anchor info tooltip */ - anchorInfoOpen = false; + /** Whether to show organize data tooltip */ + organizeDataOpen = false; /** Whether to show metadata info tooltip */ metadataInfoOpen = false; /** Whether to show color map info tooltip */ @@ -157,6 +181,8 @@ export class CreateVisualizationPageComponent { /** Cell types included in uploaded data */ cellTypes = [DEFAULT_NODE_TARGET_VALUE]; + dataHeaders: string[] = []; + /** Node CSV load error */ nodesLoadError?: ExtendedFileLoadError; /** Color map CSV load error */ @@ -181,6 +207,20 @@ export class CreateVisualizationPageComponent { return this.getErrorActionMessage(this.customColorMapLoadError, 'color map'); } + get columnErrorActionMessage(): string | undefined { + const { xAxis, yAxis, cellType } = this.visualizationForm.controls['headers'].value; + const xError = xAxis ? undefined : 'X Axis'; + const yError = yAxis ? undefined : 'Y Axis'; + const ctError = cellType ? undefined : 'Cell Type'; + const errorColumns = [xError, yError, ctError].filter((e) => !!e); + + const columnErrorMessage = + errorColumns.length > 0 + ? `Please select the required column headers: ${[xError, yError, ctError].filter((e) => !!e).join(', ')}` + : undefined; + return columnErrorMessage; + } + /** Current nodes */ private nodes?: NodeEntry[]; /** Current color map */ @@ -191,11 +231,13 @@ export class CreateVisualizationPageComponent { * @param nodes Nodes to set */ setNodes(nodes: NodeEntry[]): void { - this.nodesLoadError = this.checkRequiredKeys(nodes, ['Cell Type', 'x', 'y']); - if (this.nodesLoadError) { - this.nodesFileUpload().reset(); - return; - } + // this.nodesLoadError = this.checkRequiredKeys(nodes, ['Cell Type', 'x', 'y']); + // if (this.nodesLoadError) { + // this.nodesFileUpload().reset(); + // return; + // } + + this.setHeaders(nodes); const uniqueCellTypes = new Set(nodes.map((node) => node[DEFAULT_NODE_TARGET_KEY])); this.nodes = nodes; @@ -209,6 +251,42 @@ export class CreateVisualizationPageComponent { }); } + setHeaders(nodes: NodeEntry[]): void { + this.dataHeaders = Object.keys(nodes[0]); + this.visualizationForm.controls['headers'].setValue({ + xAxis: this.preSelectedHeader(this.dataHeaders, 'x'), + yAxis: this.preSelectedHeader(this.dataHeaders, 'y'), + cellType: this.preSelectedHeader(this.dataHeaders, 'cellType'), + zAxis: this.preSelectedHeader(this.dataHeaders, 'z'), + ontologyId: this.preSelectedHeader(this.dataHeaders, 'ontologyId'), + }); + } + + preSelectedHeader(headers: string[], field: string): string | null { + const acceptableCellTypeHeaders = ['celltype', 'cell type', 'cell_type']; + const acceptableOntologyHeaders = [ + 'ontologyid', + 'cellontologyid', + 'ontology id', + 'cell ontology id', + 'ontology_id', + 'cell_ontology_id', + ]; + if (field === 'x') { + return headers.find((h) => h.toLowerCase() === 'x') || null; + } else if (field === 'y') { + return headers.find((h) => h.toLowerCase() === 'y') || null; + } else if (field === 'z') { + return headers.find((h) => h.toLowerCase() === 'z') || null; + } else if (field === 'cellType') { + return headers.find((h) => acceptableCellTypeHeaders.includes(h.toLowerCase())) || null; + } else if (field === 'ontologyId') { + return headers.find((h) => acceptableOntologyHeaders.includes(h.toLowerCase())) || null; + } else { + return null; + } + } + /** * Clears all nodes and node load errors */ @@ -333,8 +411,8 @@ export class CreateVisualizationPageComponent { */ private formatErrorMessage(error: ExtendedFileLoadError): string { switch (error.type) { - case 'missing-key-error': - return `Required columns missing: ${error.keys.join(', ')}`; + // case 'missing-key-error': + // return `Required columns missing: ${error.keys.join(', ')}`; case 'type-error': return `Invalid file type: ${error.received}, expected csv`; From ea6ab7f87d4e341bb683111b761e73020dff543e Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 20 Sep 2024 05:32:13 -0400 Subject: [PATCH 10/50] Add configure parameters card + styling updates --- .../create-visualization-page.component.html | 159 ++++++++++-------- .../create-visualization-page.component.scss | 56 +++--- ...te-visualization-page.component.theme.scss | 6 +- .../create-visualization-page.component.ts | 33 ++-- 4 files changed, 137 insertions(+), 117 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index 609f50e5e..8936237d4 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -87,67 +87,16 @@

- -

2 Organize Data -
info @@ -157,7 +106,7 @@

[cdkConnectedOverlayPanelClass]="['info-tooltip-panel', 'organize-data-tooltip']" [cdkConnectedOverlayOrigin]="organizeDataTrigger" [cdkConnectedOverlayPositions]="tooltipPosition" - [cdkConnectedOverlayOpen]="organizeDataOpen" + [cdkConnectedOverlayOpen]="organizeDataInfoOpen" [cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > @@ -165,20 +114,6 @@

- -
Required: Verify column headers @@ -242,9 +177,89 @@

-
+

3 +
Configure Parameters
+ + info + + +

Anchor Cell Type

+

+ The anchor cell type represents the cell type to which the nearest cell distance distributions should be + computed and visualized. Euclidian distance is used to compute the distance between two cells. +

+

+ “Endothelial” is used as the default anchor cell type. If an “Endothelial” cell label is not present, the + first listed cell type label is used as the anchor cell type. +

+

Distance Threshold (µm)

+

Configure the distance threshold to modify visualizations for analysis.

+

Pixel Size (µm/pixel)

+

+ Pixel size is used as a scaling factor to convert coordinates to micrometers. Use 1 if coordinates are already + in micrometers. +

+ +

+ +
+ + Anchor Cell Type + + @for (type of cellTypes; track type) { + {{ type }} + } + + + + + Distance Threshold + + +
+ +
+ + Pixel size (X) (µm/pixel) + + + + + Pixel size (Y) (µm/pixel) + + + + + Pixel size (Z) (µm/pixel) + + +
+
+ +
+

+ 4
Optional: Add Metadata

- 4 + 5
Optional: Configure Colors

- 5 + 6
Visualize Cell Distance Data
[cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

Inputs on the Create Visualization page cannot be modified after a visualization is generated.

+

Data on the Create Visualization page cannot be modified after a visualization is generated.

diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index f4603ae5c..d71664228 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -135,13 +135,8 @@ .required-headers, .optional-headers { display: grid; - } - - .required-headers { - grid: 'subheader subheader'; - } - .optional-headers { grid: 'subheader subheader'; + column-gap: 1.5rem; } .subheader { @@ -167,28 +162,32 @@ color: #2f1400; } } + } + + .parameters { + .parameters-1 { + display: grid; + grid: '. .'; + column-gap: 1.5rem; + } - mat-form-field { - margin: 1.5rem 0; - max-width: 17.5rem; + .parameters-2 { + display: grid; + grid: '. . .'; + column-gap: 1.5rem; } } .metadata { display: grid; gap: 0.5rem; - column-gap: 2.5rem; + column-gap: 1.5rem; grid: 'header header'; .header { grid-area: header; margin-bottom: 0; } - - mat-form-field { - margin: 1.5rem 0; - max-width: 17.5rem; - } } .color-config { @@ -238,27 +237,28 @@ } ::ng-deep mat-form-field { - --mat-form-field-container-height: 3.625rem; - --mat-form-field-filled-with-label-container-padding-top: 1.5rem; - --mat-form-field-filled-with-label-container-padding-bottom: 0; - box-shadow: 0 0.3125rem 1rem 0 #201e3d3d; - border-radius: 1rem; + margin: 1rem 0; + --mat-form-field-container-height: 3rem; + --mat-form-field-filled-with-label-container-padding-top: 1.25rem; + --mat-form-field-filled-with-label-container-padding-bottom: 0.25rem; + // box-shadow: 0 0.3125rem 1rem 0 #201e3d3d; + // border-radius: 1rem; .mat-mdc-text-field-wrapper { - border-radius: 1rem; - padding: 0 1.5rem; + border-radius: 4px 4px 0 0; + padding: 0 1rem; } .mat-mdc-form-field-subscript-wrapper { display: none; } - .mdc-line-ripple { - &::before, - &::after { - display: none; - } - } + // .mdc-line-ripple { + // &::before, + // &::after { + // display: none; + // } + // } } ::ng-deep .info-tooltip-panel { diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index 381fac8a3..cdbca0d55 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -72,17 +72,13 @@ $blue-palette: map.get(palettes.$palettes, 'blue'); } mat-form-field { - --mdc-filled-text-field-container-color: #{mat.get-theme-color($theme, accent, lighter)}; + --mdc-filled-text-field-container-color: #{map.get($blue-palette, 500)}; --mdc-filled-text-field-focus-label-text-color: #{mat.get-theme-color($theme, primary, darker)}; --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; --mat-select-enabled-arrow-color: #{map.get($gray-palette, 700)}; --mat-select-focused-arrow-color: #{mat.get-theme-color($theme, primary, darker)}; } - .mat-form-field-hide-placeholder { - --mdc-filled-text-field-container-color: white; - } - .select-panel { --mat-option-selected-state-layer-color: #{mat.get-theme-color($theme, accent, lighter)}; --mat-option-label-text-color: #{map.get($gray-palette, 700)}; diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index d5644bd71..5b9a2f5ec 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -109,20 +109,20 @@ export class CreateVisualizationPageComponent { // pixelSize: [optionalValue(), Validators.min(0)], // }), // colorMapType: ['default'], - nodeTargetValue: [DEFAULT_NODE_TARGET_VALUE], headers: this.fb.group({ - xAxis: [optionalValue()], - yAxis: [optionalValue()], - cellType: [optionalValue()], + xAxis: [''], + yAxis: [''], + cellType: [''], zAxis: [optionalValue()], ontologyId: [optionalValue()], }), parameters: this.fb.group({ - anchorCellType: [optionalValue()], - distanceThreshold: [optionalValue()], - pixelSizeX: [optionalValue(), Validators.min(0)], - pixelSizeY: [optionalValue(), Validators.min(0)], - pixelSizeZ: [optionalValue(), Validators.min(0)], + nodeTargetValue: [DEFAULT_NODE_TARGET_VALUE], + // anchorCellType: [optionalValue()], + distanceThreshold: [1000], + pixelSizeX: [1, Validators.min(1)], + pixelSizeY: [1, Validators.min(1)], + pixelSizeZ: [1, Validators.min(1)], }), metadata: this.fb.group({ title: [optionalValue()], @@ -170,11 +170,16 @@ export class CreateVisualizationPageComponent { /** Whether to show upload info tooltip */ uploadInfoOpen = false; /** Whether to show organize data tooltip */ - organizeDataOpen = false; + organizeDataInfoOpen = false; + + parametersInfoOpen = false; + /** Whether to show metadata info tooltip */ metadataInfoOpen = false; + /** Whether to show color map info tooltip */ colorInfoOpen = false; + /** Whether to show visualize info tooltip */ visualizeInfoOpen = false; @@ -246,7 +251,7 @@ export class CreateVisualizationPageComponent { const defaultCellType = uniqueCellTypes.has(DEFAULT_NODE_TARGET_VALUE) ? DEFAULT_NODE_TARGET_VALUE : this.cellTypes[0]; - this.visualizationForm.patchValue({ + this.visualizationForm.controls['parameters'].patchValue({ nodeTargetValue: defaultCellType, }); } @@ -348,7 +353,11 @@ export class CreateVisualizationPageComponent { } const { nodes, customColorMap, visualizationForm } = this; - const { nodeTargetValue, colorMapType, metadata } = visualizationForm.value; + const { colorMapType, metadata } = visualizationForm.value; + + const nodeTargetValue = visualizationForm.value.parameters + ? visualizationForm.value.parameters.nodeTargetValue + : undefined; const colorMap = colorMapType === 'custom' && this.hasValidCustomColorMap() ? customColorMap : undefined; const normalizedMetadata = this.removeNullishValues({ ...metadata, From 35ba554e69551f3859cd9b21489cce5c38c5fa10 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Mon, 23 Sep 2024 12:06:31 -0400 Subject: [PATCH 11/50] Color map selection updates --- .../create-visualization-page.component.html | 47 +++++++++++-------- .../create-visualization-page.component.scss | 34 +++++++++----- ...te-visualization-page.component.theme.scss | 6 +-- .../create-visualization-page.component.ts | 2 +- 4 files changed, 53 insertions(+), 36 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index 8936237d4..dcfd94b77 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -118,7 +118,7 @@

Required: Verify column headers - X Axis + X Axis @for (option of dataHeaders; track option) { {{ option }} @@ -127,7 +127,7 @@

- Y Axis + Y Axis @for (option of dataHeaders; track option) { {{ option }} @@ -136,7 +136,7 @@

- Cell Type + Cell Type @for (option of dataHeaders; track option) { {{ option }} @@ -158,7 +158,7 @@

Optional: Add column headers - Z Axis + Z Axis @for (option of dataHeaders; track option) { {{ option }} @@ -167,7 +167,7 @@

- Cell Ontology ID + Cell Ontology ID @for (option of dataHeaders; track option) { {{ option }} @@ -220,7 +220,7 @@

- Anchor Cell Type + Anchor Cell Type - Distance Threshold + Distance Threshold
- Pixel size (X) (µm/pixel) + Pixel size (X) (µm/pixel) - Pixel size (Y) (µm/pixel) + Pixel size (Y) (µm/pixel) - Pixel size (Z) (µm/pixel) + Pixel size (Z) (µm/pixel)
@@ -288,17 +288,17 @@

- Visualization Title + Visualization Title - Imaging Technology + Imaging Technology - Organ + Organ @for (organ of organs(); track organ) { {{ organ.label | titlecase }} @@ -307,7 +307,7 @@

- Sex + Sex Male Female @@ -315,12 +315,12 @@

- Age + Age - Thickness (µm) + Thickness (µm) @@ -334,7 +334,6 @@

5
Optional: Configure Colors
-
colors may be changed individually while exploring the visualization in the Visualization App.

+
+ + Template +

- + Use Default Colors Upload Color Map @@ -369,7 +379,6 @@

@if (useCustomColorMap) { Date: Mon, 23 Sep 2024 20:14:24 -0400 Subject: [PATCH 12/50] Fix validation of inputs --- ....csv => color_map_missing_column_name.csv} | 0 .../cde-ui/example-data/color_map_working.csv | 10 ++ .../create-visualization-page.component.html | 25 +++-- .../create-visualization-page.component.scss | 42 ++++---- .../create-visualization-page.component.ts | 97 ++++++++++++------- .../services/data/color-map-loader.service.ts | 1 + 6 files changed, 112 insertions(+), 63 deletions(-) rename apps/cde-ui/example-data/{color_map.csv => color_map_missing_column_name.csv} (100%) create mode 100644 apps/cde-ui/example-data/color_map_working.csv diff --git a/apps/cde-ui/example-data/color_map.csv b/apps/cde-ui/example-data/color_map_missing_column_name.csv similarity index 100% rename from apps/cde-ui/example-data/color_map.csv rename to apps/cde-ui/example-data/color_map_missing_column_name.csv diff --git a/apps/cde-ui/example-data/color_map_working.csv b/apps/cde-ui/example-data/color_map_working.csv new file mode 100644 index 000000000..553402009 --- /dev/null +++ b/apps/cde-ui/example-data/color_map_working.csv @@ -0,0 +1,10 @@ +cell_id,Cell Type,HEX +1,T-Killer,"[255, 0, 255]" +2,T-Helper,"[0, 0, 255]" +3,T-Reg,"[0, 255, 0]" +4,CD68,"[255, 215, 0]" +5,Endothelial,"[255, 0, 0]" +6,DDB2,"[0, 153, 76]" +7,P53,"[153, 76, 0]" +8,KI67,"[0, 255, 255]" +9,skin,"[192, 192, 192]" diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index dcfd94b77..c0cf72c5b 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -377,6 +377,19 @@

@if (useCustomColorMap) { +

Required Columns
+ + + + + + + + + + + +
Required ColumnsSupported Format
• Cell Type• CSV
• HEX
(loadCompleted)="setCustomColorMap($event[0])" (loadCancelled)="clearCustomColorMap()" (loadErrored)="customColorMapLoadError = $event" - data-testid="color-map-upload" - #customColorMapFileUpload [errorMessage]="colorErrorMessage" [errorActionMessage]="colorErrorActionMessage" - templateUrl="https://docs.google.com/spreadsheets/d/1sjaGTCs3J9CjrkowxkyJrIfHk64w_nDyYrgprbMbdqE/edit?gid=0#gid=0" + #customColorMapFileUpload + data-testid="color-map-upload" > } @@ -399,7 +411,6 @@

6
Visualize Cell Distance Data
-

- @if (hasValidNodes()) { + @if (hasValidNodes() && hasValidData()) { } @else { - Please format and upload data to explore a visualization. + + error + Please upload a dataset. }
diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index 02fb106e3..69167bdfb 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -80,6 +80,24 @@ flex-grow: 1; } + table { + grid-area: table; + margin: 0.5rem 0; + + th, + td { + font-weight: 500; + padding-left: 1rem; + text-align: left; + min-width: 216px; + height: 1.5rem; + } + + td { + padding-left: 1.5rem; + } + } + .use-template { --mdc-text-button-label-text-size: 14px; --mat-text-button-with-icon-horizontal-padding: 1rem; @@ -97,24 +115,6 @@ grid-template-rows: auto auto auto; row-gap: 2rem; - table { - grid-area: table; - margin: 0.5rem 0; - } - - th, - td { - font-weight: 500; - padding-left: 1rem; - text-align: left; - min-width: 216px; - height: 1.5rem; - } - - td { - padding-left: 1.5rem; - } - .upload-csv { grid-area: upload-csv; } @@ -195,7 +195,10 @@ grid: 'header header' 'toggle toggle' - '. upload-colormap' / 3rem auto; + 'table table' + 'upload-colormap .' / auto 1fr; + grid-template-rows: auto auto auto auto; + row-gap: 2rem; mat-button-toggle-group { grid-area: toggle; @@ -211,7 +214,6 @@ .upload-colormap { grid-area: upload-colormap; - margin-top: 2rem; } } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index 7e5b82ab8..0fdb5bc52 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -96,19 +96,18 @@ export class CreateVisualizationPageComponent { /** Visualization data service */ private readonly dataService = inject(VisualizationDataService); + private readonly acceptableCellTypeHeaders = ['celltype', 'cell type', 'cell_type']; + private readonly acceptableOntologyHeaders = [ + 'ontologyid', + 'cellontologyid', + 'ontology id', + 'cell ontology id', + 'ontology_id', + 'cell_ontology_id', + ]; + /** Component form controller */ readonly visualizationForm = this.fbnn.group({ - // nodeTargetValue: [DEFAULT_NODE_TARGET_VALUE], - // metadata: this.fb.group({ - // title: [optionalValue()], - // technology: [optionalValue()], - // organ: [optionalValue()], - // sex: [optionalValue()], - // age: [optionalValue(), [Validators.min(0), Validators.max(120), validateInteger()]], - // thickness: [optionalValue(), Validators.min(0)], - // pixelSize: [optionalValue(), Validators.min(0)], - // }), - // colorMapType: ['default'], headers: this.fb.group({ xAxis: [''], yAxis: [''], @@ -236,11 +235,12 @@ export class CreateVisualizationPageComponent { * @param nodes Nodes to set */ setNodes(nodes: NodeEntry[]): void { - // this.nodesLoadError = this.checkRequiredKeys(nodes, ['Cell Type', 'x', 'y']); - // if (this.nodesLoadError) { - // this.nodesFileUpload().reset(); - // return; - // } + this.nodesLoadError = this.checkRequiredNodeKeys(nodes); + if (this.nodesLoadError) { + this.nodesFileUpload().reset(); + this.setHeaders([]); + return; + } this.setHeaders(nodes); @@ -257,7 +257,7 @@ export class CreateVisualizationPageComponent { } setHeaders(nodes: NodeEntry[]): void { - this.dataHeaders = Object.keys(nodes[0]); + this.dataHeaders = nodes[0] ? Object.keys(nodes[0]) : []; this.visualizationForm.controls['headers'].setValue({ xAxis: this.preSelectedHeader(this.dataHeaders, 'x'), yAxis: this.preSelectedHeader(this.dataHeaders, 'y'), @@ -268,25 +268,12 @@ export class CreateVisualizationPageComponent { } preSelectedHeader(headers: string[], field: string): string | null { - const acceptableCellTypeHeaders = ['celltype', 'cell type', 'cell_type']; - const acceptableOntologyHeaders = [ - 'ontologyid', - 'cellontologyid', - 'ontology id', - 'cell ontology id', - 'ontology_id', - 'cell_ontology_id', - ]; - if (field === 'x') { - return headers.find((h) => h.toLowerCase() === 'x') || null; - } else if (field === 'y') { - return headers.find((h) => h.toLowerCase() === 'y') || null; - } else if (field === 'z') { - return headers.find((h) => h.toLowerCase() === 'z') || null; + if (field === 'x' || field === 'y' || field === 'z') { + return headers.find((h) => h.toLowerCase() === field) || null; } else if (field === 'cellType') { - return headers.find((h) => acceptableCellTypeHeaders.includes(h.toLowerCase())) || null; + return headers.find((h) => this.acceptableCellTypeHeaders.includes(h.toLowerCase())) || null; } else if (field === 'ontologyId') { - return headers.find((h) => acceptableOntologyHeaders.includes(h.toLowerCase())) || null; + return headers.find((h) => this.acceptableOntologyHeaders.includes(h.toLowerCase())) || null; } else { return null; } @@ -298,6 +285,7 @@ export class CreateVisualizationPageComponent { clearNodes(): void { this.nodes = undefined; this.nodesLoadError = undefined; + this.setHeaders([]); } /** @@ -309,6 +297,22 @@ export class CreateVisualizationPageComponent { return !!(nodes && nodes.length > 0 && DEFAULT_NODE_TARGET_KEY in nodes[0]); } + hasValidData(): boolean { + const { xAxis, yAxis, cellType } = this.visualizationForm.controls['headers'].value; + const { nodeTargetValue, pixelSizeX, pixelSizeY, pixelSizeZ, distanceThreshold } = + this.visualizationForm.controls['parameters'].value; + return ( + !!xAxis && + !!yAxis && + !!cellType && + !!nodeTargetValue && + !!pixelSizeX && + !!pixelSizeY && + !!pixelSizeZ && + !!distanceThreshold + ); + } + /** * Sets custom color map * @param colorMap Color map entries @@ -413,6 +417,25 @@ export class CreateVisualizationPageComponent { return missingKeys.length > 0 ? { type: 'missing-key-error', keys: missingKeys } : undefined; } + private checkRequiredNodeKeys(data: object[]): MissingKeyError | undefined { + const missingKeys = []; + const typeKeyMissing = + Object.keys(data[0]).filter((x) => this.acceptableCellTypeHeaders.includes(x.toLowerCase())).length === 0; + const xKeyMissing = Object.keys(data[0]).filter((k) => k.toLowerCase() === 'x').length === 0; + const yKeyMissing = Object.keys(data[0]).filter((k) => k.toLowerCase() === 'y').length === 0; + + if (typeKeyMissing) { + missingKeys.push('Cell Type'); + } + if (xKeyMissing) { + missingKeys.push('X'); + } + if (yKeyMissing) { + missingKeys.push('Y'); + } + return missingKeys.length > 0 ? { type: 'missing-key-error', keys: missingKeys } : undefined; + } + /** * Formats error message according to the error type * @param error Error @@ -420,8 +443,8 @@ export class CreateVisualizationPageComponent { */ private formatErrorMessage(error: ExtendedFileLoadError): string { switch (error.type) { - // case 'missing-key-error': - // return `Required columns missing: ${error.keys.join(', ')}`; + case 'missing-key-error': + return `Required columns missing: ${error.keys.join(', ')}`; case 'type-error': return `Invalid file type: ${error.received}, expected csv`; @@ -430,7 +453,7 @@ export class CreateVisualizationPageComponent { if (Array.isArray(error.cause)) { return `Invalid file: ${this.formatCsvErrors(error.cause)}`; } else if (error.cause instanceof Error) { - return 'Required columns missing: cell_color'; + return 'Required color format not detected. Please use [R, G, B].'; } return 'Invalid file: too many invalid rows.'; diff --git a/libs/cde-visualization/src/lib/services/data/color-map-loader.service.ts b/libs/cde-visualization/src/lib/services/data/color-map-loader.service.ts index 33703d4ed..4aa4d3259 100644 --- a/libs/cde-visualization/src/lib/services/data/color-map-loader.service.ts +++ b/libs/cde-visualization/src/lib/services/data/color-map-loader.service.ts @@ -35,6 +35,7 @@ export class ColorMapFileLoaderService implements FileLoader Date: Wed, 25 Sep 2024 02:13:30 -0400 Subject: [PATCH 13/50] Move column header errors to step 2; styling improvements --- .../create-visualization-page.component.html | 36 +++++---- .../create-visualization-page.component.scss | 79 ++++++++++++------- ...te-visualization-page.component.theme.scss | 8 +- .../create-visualization-page.component.ts | 16 ++-- 4 files changed, 87 insertions(+), 52 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index c0cf72c5b..15b48b684 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -261,7 +261,6 @@

4
Optional: Add Metadata
-
Thickness (µm) - - -
+

5
Optional: Configure Colors
@@ -381,6 +375,8 @@

Required Columns Supported Format + + • Cell Type @@ -434,16 +430,24 @@

- @if (hasValidNodes() && hasValidData()) { - - } @else { - - error - Please upload a dataset. + @if (!hasValidNodes() || !hasValidData()) { +
+ error + Please upload a dataset. +
} + +
diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index 69167bdfb..7589a5512 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -120,17 +120,6 @@ } } - // .anchor-selection { - // .header { - // margin-bottom: 0.5rem; - // } - - // .select-form { - // width: calc(100% - 6rem); - // margin: 1.5rem 3rem; - // } - // } - .organize-data { .required-headers, .optional-headers { @@ -139,6 +128,10 @@ column-gap: 1.5rem; } + .required-headers { + margin-bottom: 1rem; + } + .subheader { grid-area: subheader; } @@ -192,13 +185,27 @@ .color-config { display: grid; + row-gap: 2rem; grid: 'header header' - 'toggle toggle' - 'table table' - 'upload-colormap .' / auto 1fr; - grid-template-rows: auto auto auto auto; - row-gap: 2rem; + 'toggle toggle' / auto 1fr; + + &.custom { + grid: + 'header header' + 'toggle toggle' + 'table table' + 'upload-colormap .' / auto 1fr; + } + + table { + width: 66%; + + th, + td { + min-width: 0; + } + } mat-button-toggle-group { grid-area: toggle; @@ -208,7 +215,12 @@ mat-button-toggle { width: 50%; - border: none; + border-width: 0; + + &:first-child { + border-right-width: 1px; + border-style: solid; + } } } @@ -218,15 +230,34 @@ } .visualize { - .visualize-notification, + .visualize-notification { + display: flex; + align-items: center; + gap: 0.5rem; + margin: 2rem 0; + background-color: rgb(from #ffdcc4 r g b / 0.8); + padding: 0.5rem 0.75rem; + border-radius: 0.25rem; + + .alert { + color: #bc4f00; + } + + .span { + display: flex; + flex-direction: column; + color: #2f1400; + } + } + .visualize-button { display: flex; - margin-left: 3rem; --mdc-filled-button-label-text-size: 1rem; --mat-filled-button-horizontal-padding: 1.5rem; --mdc-filled-button-label-text-tracking: 0.02em; --mat-filled-button-icon-spacing: 0.75rem; --mat-filled-button-icon-offset: -0.375rem; + margin-top: 2rem; mat-icon { font-size: 1.5rem; @@ -251,9 +282,6 @@ line-height: 18px !important; } - // box-shadow: 0 0.3125rem 1rem 0 #201e3d3d; - // border-radius: 1rem; - .mat-mdc-text-field-wrapper { border-radius: 4px 4px 0 0; padding: 0 1rem; @@ -262,13 +290,6 @@ .mat-mdc-form-field-subscript-wrapper { display: none; } - - // .mdc-line-ripple { - // &::before, - // &::after { - // display: none; - // } - // } } ::ng-deep .info-tooltip-panel { diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index 883775b8c..fb5bf0bee 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -49,13 +49,19 @@ $blue-palette: map.get(palettes.$palettes, 'blue'); .color-config { mat-button-toggle-group { - border-color: map.get($gray-palette, 700); + border-color: map.get($gray-palette, 600); --mat-standard-button-toggle-text-color: #{mat.get-theme-color($theme, accent, darker)}; --mat-standard-button-toggle-selected-state-background-color: rgb( from #{mat.get-theme-color($theme, primary, 600)} r g b / 0.24 ); } + mat-button-toggle { + &:first-child { + border-color: map.get($gray-palette, 600); + } + } + .use-template { color: mat.get-theme-color($theme, primary, 700); } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index 0fdb5bc52..16ca5cc11 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -212,6 +212,9 @@ export class CreateVisualizationPageComponent { } get columnErrorActionMessage(): string | undefined { + if (!this.nodes) { + return undefined; + } const { xAxis, yAxis, cellType } = this.visualizationForm.controls['headers'].value; const xError = xAxis ? undefined : 'X Axis'; const yError = yAxis ? undefined : 'Y Axis'; @@ -235,12 +238,13 @@ export class CreateVisualizationPageComponent { * @param nodes Nodes to set */ setNodes(nodes: NodeEntry[]): void { - this.nodesLoadError = this.checkRequiredNodeKeys(nodes); - if (this.nodesLoadError) { - this.nodesFileUpload().reset(); - this.setHeaders([]); - return; - } + const columnsError = this.checkRequiredNodeKeys(nodes); + console.log(columnsError); + // if (columnsError) { + // this.nodesFileUpload().reset(); + // this.setHeaders([]); + // return; + // } this.setHeaders(nodes); From 9a7c6cbd88dccaa2de1d15f563dcb165abe85512 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 25 Sep 2024 11:09:47 -0400 Subject: [PATCH 14/50] Remove unused code --- .../{color_map_working.csv => color_map.csv} | 0 ...me.csv => color_map_wrong_column_name.csv} | 0 .../example-data/nodes_renamed_columns.csv | 2869 +++++++++++++++++ .../create-visualization-page.component.ts | 30 - 4 files changed, 2869 insertions(+), 30 deletions(-) rename apps/cde-ui/example-data/{color_map_working.csv => color_map.csv} (100%) rename apps/cde-ui/example-data/{color_map_missing_column_name.csv => color_map_wrong_column_name.csv} (100%) create mode 100644 apps/cde-ui/example-data/nodes_renamed_columns.csv diff --git a/apps/cde-ui/example-data/color_map_working.csv b/apps/cde-ui/example-data/color_map.csv similarity index 100% rename from apps/cde-ui/example-data/color_map_working.csv rename to apps/cde-ui/example-data/color_map.csv diff 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nodes Nodes to set */ setNodes(nodes: NodeEntry[]): void { - const columnsError = this.checkRequiredNodeKeys(nodes); - console.log(columnsError); - // if (columnsError) { - // this.nodesFileUpload().reset(); - // this.setHeaders([]); - // return; - // } - this.setHeaders(nodes); const uniqueCellTypes = new Set(nodes.map((node) => node[DEFAULT_NODE_TARGET_KEY])); @@ -421,25 +413,6 @@ export class CreateVisualizationPageComponent { return missingKeys.length > 0 ? { type: 'missing-key-error', keys: missingKeys } : undefined; } - private checkRequiredNodeKeys(data: object[]): MissingKeyError | undefined { - const missingKeys = []; - const typeKeyMissing = - Object.keys(data[0]).filter((x) => this.acceptableCellTypeHeaders.includes(x.toLowerCase())).length === 0; - const xKeyMissing = Object.keys(data[0]).filter((k) => k.toLowerCase() === 'x').length === 0; - const yKeyMissing = Object.keys(data[0]).filter((k) => k.toLowerCase() === 'y').length === 0; - - if (typeKeyMissing) { - missingKeys.push('Cell Type'); - } - if (xKeyMissing) { - missingKeys.push('X'); - } - if (yKeyMissing) { - missingKeys.push('Y'); - } - return missingKeys.length > 0 ? { type: 'missing-key-error', keys: missingKeys } : undefined; - } - /** * Formats error message according to the error type * @param error Error @@ -447,9 +420,6 @@ export class CreateVisualizationPageComponent { */ private formatErrorMessage(error: ExtendedFileLoadError): string { switch (error.type) { - case 'missing-key-error': - return `Required columns missing: ${error.keys.join(', ')}`; - case 'type-error': return `Invalid file type: ${error.received}, expected csv`; From 11bce180991847d945bcc39544f067dfe5ea8657 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 25 Sep 2024 16:17:58 -0400 Subject: [PATCH 15/50] Set headers in submitted data to selected values --- .../create-visualization-page.component.ts | 43 ++++++++++++++----- 1 file changed, 32 insertions(+), 11 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index 51c5d552e..5435e1610 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -20,6 +20,7 @@ import { DEFAULT_NODE_TARGET_KEY, DEFAULT_NODE_TARGET_VALUE, NodeEntry, + NodeTargetKey, TOOLTIP_POSITION_BELOW, } from '@hra-ui/cde-visualization'; import { FooterComponent } from '@hra-ui/design-system/footer'; @@ -368,19 +369,36 @@ export class CreateVisualizationPageComponent { creationTimestamp: Date.now(), }); - this.dataService.setData( - this.removeNullishValues({ - nodes, - nodeTargetKey: DEFAULT_NODE_TARGET_KEY, - nodeTargetValue, + const nullishRemovedData = this.removeNullishValues({ + nodes, + nodeTargetKey: DEFAULT_NODE_TARGET_KEY, + nodeTargetValue, - colorMap, - colorMapKey: DEFAULT_COLOR_MAP_KEY, - colorMapValueKey: DEFAULT_COLOR_MAP_VALUE_KEY, + colorMap, + colorMapKey: DEFAULT_COLOR_MAP_KEY, + colorMapValueKey: DEFAULT_COLOR_MAP_VALUE_KEY, - metadata: normalizedMetadata, - }), - ); + metadata: normalizedMetadata, + }); + const headers = visualizationForm.value.headers; + const xKey = (headers?.xAxis || '') as NodeTargetKey; + const yKey = (headers?.yAxis || '') as NodeTargetKey; + const zKey = (headers?.zAxis || '') as NodeTargetKey; + const ctKey = (headers?.cellType || '') as NodeTargetKey; + + const convertedHeaderNodes = (nullishRemovedData.nodes = nullishRemovedData.nodes + ? nullishRemovedData.nodes.map( + (node) => + ({ + x: node[xKey] as unknown as number, + y: node[yKey] as unknown as number, + z: node[zKey] as unknown as number, + 'Cell Type': node[ctKey], + }) as NodeEntry, + ) + : []); + nullishRemovedData.nodes = convertedHeaderNodes; + this.dataService.setData(nullishRemovedData); this.router.navigate(['/visualize']); } @@ -420,6 +438,9 @@ export class CreateVisualizationPageComponent { */ private formatErrorMessage(error: ExtendedFileLoadError): string { switch (error.type) { + case 'missing-key-error': + return `Required columns missing: ${error.keys.join(', ')}`; + case 'type-error': return `Invalid file type: ${error.received}, expected csv`; From f1bc2cd4e7bdd2e65bd5c0d6b0964c1c1f88e74c Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 25 Sep 2024 21:37:12 -0400 Subject: [PATCH 16/50] Fix cell types check --- .../example-data/nodes_renamed_columns.csv | 2 +- .../nodes_slightly_renamed_columns.csv | 2869 +++++++++++++++++ .../create-visualization-page.component.ts | 15 +- 3 files changed, 2881 insertions(+), 5 deletions(-) create mode 100644 apps/cde-ui/example-data/nodes_slightly_renamed_columns.csv diff --git a/apps/cde-ui/example-data/nodes_renamed_columns.csv b/apps/cde-ui/example-data/nodes_renamed_columns.csv index d8e46e2a3..a10066b28 100644 --- 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parameters: this.fb.group({ nodeTargetValue: [DEFAULT_NODE_TARGET_VALUE], - // anchorCellType: [optionalValue()], distanceThreshold: [1000], pixelSizeX: [1, Validators.min(1)], pixelSizeY: [1, Validators.min(1)], @@ -241,7 +240,8 @@ export class CreateVisualizationPageComponent { setNodes(nodes: NodeEntry[]): void { this.setHeaders(nodes); - const uniqueCellTypes = new Set(nodes.map((node) => node[DEFAULT_NODE_TARGET_KEY])); + const cellTypeHeader = this.visualizationForm.controls['headers'].value.cellType as NodeTargetKey; + const uniqueCellTypes = new Set(nodes.map((node) => node[cellTypeHeader])); this.nodes = nodes; this.cellTypes = Array.from(uniqueCellTypes); @@ -290,8 +290,14 @@ export class CreateVisualizationPageComponent { * @returns boolean */ hasValidNodes(): boolean { + // Set the cell type header value when valid nodes checked + const cellTypeHeader = this.visualizationForm.controls['headers'].value.cellType as NodeTargetKey; + if (cellTypeHeader && this.nodes) { + const uniqueCellTypes = new Set(this.nodes.map((node) => node[cellTypeHeader])); + this.cellTypes = Array.from(uniqueCellTypes); + } const { nodes } = this; - return !!(nodes && nodes.length > 0 && DEFAULT_NODE_TARGET_KEY in nodes[0]); + return !!(nodes && nodes.length > 0 && cellTypeHeader in nodes[0]); } hasValidData(): boolean { @@ -380,6 +386,7 @@ export class CreateVisualizationPageComponent { metadata: normalizedMetadata, }); + const ntKey = nullishRemovedData.nodeTargetKey as string; const headers = visualizationForm.value.headers; const xKey = (headers?.xAxis || '') as NodeTargetKey; const yKey = (headers?.yAxis || '') as NodeTargetKey; @@ -393,7 +400,7 @@ export class CreateVisualizationPageComponent { x: node[xKey] as unknown as number, y: node[yKey] as unknown as number, z: node[zKey] as unknown as number, - 'Cell Type': node[ctKey], + [ntKey]: node[ctKey], }) as NodeEntry, ) : []); From 74dea9247fe497d2f0fcf8526b9f9ef8061f6c90 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Thu, 26 Sep 2024 13:26:45 -0400 Subject: [PATCH 17/50] Fix broken tests --- ...reate-visualization-page.component.spec.ts | 32 +++++++++++-------- .../create-visualization-page.component.ts | 6 ++-- .../src/lib/models/color-map.ts | 4 +-- 3 files changed, 23 insertions(+), 19 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts index cd10579ff..30f54fcc3 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts @@ -38,17 +38,17 @@ const sampleNodes = [ createNodeEntry(nodeTargetKey, 'c', 0, 4), ]; const processedSampleData = { - colorMapKey: 'cell_type', - colorMapValueKey: 'cell_color', + colorMapKey: 'Cell Type', + colorMapValueKey: 'HEX', metadata: { creationTimestamp: 0, } satisfies Metadata, nodeTargetKey: 'Cell Type', nodeTargetValue: 'a', nodes: [ - { 'Cell Type': 'a', x: 0, y: 0 }, - { 'Cell Type': 'b', x: 0, y: 2 }, - { 'Cell Type': 'c', x: 0, y: 4 }, + { 'Cell Type': 'a', x: 0, y: 0, z: undefined }, + { 'Cell Type': 'b', x: 0, y: 2, z: undefined }, + { 'Cell Type': 'c', x: 0, y: 4, z: undefined }, ], }; @@ -82,13 +82,13 @@ const csvNodeDataMissingValues = `Cell Type,x,y a,0 b,1,2`; -const csvColorMap = `cell_id,cell_type,cell_color - 0,cell1,[0,0,0] - 1,cell2,[1,1,1]`; +const csvColorMap = `cell_id,Cell Type,HEX + 0,cell1,"[0,0,0]" + 1,cell2,"[1,1,1]"`; const csvColorMapWrongKeys = `BADKEY,cell_type,cell_color - 0,cell1,[0,0,0] - 1,cell2,[1,1,1]`; + 0,cell1,"[0,0,0]" + 1,cell2,"[1,1,1]"`; describe('CreateVisualizationPageComponent', () => { let instance: CreateVisualizationPageComponent; @@ -110,7 +110,7 @@ describe('CreateVisualizationPageComponent', () => { }); describe('setNodes()', () => { - it('checks for required keys, if missing do not update data', async () => { + it('checks for required keys, if missing tell the user the missing columns', async () => { const nodeDataEl = screen.getAllByTestId(testId)[0]; const data = new File([csvNodeDataWrongKeys], 'blah.csv', { type: 'text/csv' }); const spy = jest.spyOn(instance.visualizationForm, 'patchValue'); @@ -118,7 +118,7 @@ describe('CreateVisualizationPageComponent', () => { fixture.autoDetectChanges(); await new Promise((resolve) => setTimeout(resolve, 50)); expect(spy).toHaveBeenCalledTimes(0); - expect(instance.nodesErrorMessage).toMatch(/Required columns missing/); + expect(instance.columnErrorActionMessage).toMatch(/Please select the required column headers: Cell Type/); }); it('sets nodes', async () => { @@ -134,7 +134,9 @@ describe('CreateVisualizationPageComponent', () => { createNodeEntry(nodeTargetKey, DEFAULT_NODE_TARGET_VALUE, 0, 4), ]; instance.setNodes(sampleNodes2); - expect(instance.visualizationForm.value.nodeTargetValue).toEqual(DEFAULT_NODE_TARGET_VALUE); + expect(instance.visualizationForm.controls['parameters'].value.nodeTargetValue).toEqual( + DEFAULT_NODE_TARGET_VALUE, + ); }); }); @@ -285,7 +287,9 @@ describe('CreateVisualizationPageComponent', () => { type: 'parse-error', cause: new Error(), }; - expect(priedInstance.formatErrorMessage(testError)).toMatch(/Required columns missing/); + expect(priedInstance.formatErrorMessage(testError)).toMatch( + 'Required color format not detected. Please use [R, G, B].', + ); }); it('shows parse errors (cause is some other type)', async () => { diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index 39023e3c0..397ba6ea9 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -253,7 +253,7 @@ export class CreateVisualizationPageComponent { }); } - setHeaders(nodes: NodeEntry[]): void { + private setHeaders(nodes: NodeEntry[]): void { this.dataHeaders = nodes[0] ? Object.keys(nodes[0]) : []; this.visualizationForm.controls['headers'].setValue({ xAxis: this.preSelectedHeader(this.dataHeaders, 'x'), @@ -264,7 +264,7 @@ export class CreateVisualizationPageComponent { }); } - preSelectedHeader(headers: string[], field: string): string | null { + private preSelectedHeader(headers: string[], field: string): string | null { if (field === 'x' || field === 'y' || field === 'z') { return headers.find((h) => h.toLowerCase() === field) || null; } else if (field === 'cellType') { @@ -455,7 +455,7 @@ export class CreateVisualizationPageComponent { if (Array.isArray(error.cause)) { return `Invalid file: ${this.formatCsvErrors(error.cause)}`; } else if (error.cause instanceof Error) { - return 'Required color format not detected. Please use [R, G, B].'; + return `Required color format not detected. Please use [R, G, B].`; } return 'Invalid file: too many invalid rows.'; diff --git a/libs/cde-visualization/src/lib/models/color-map.ts b/libs/cde-visualization/src/lib/models/color-map.ts index 3010d1e8b..cf4214e22 100644 --- a/libs/cde-visualization/src/lib/models/color-map.ts +++ b/libs/cde-visualization/src/lib/models/color-map.ts @@ -17,10 +17,10 @@ export interface ColorMapEntry { } /** Default key for the color map type */ -export const DEFAULT_COLOR_MAP_KEY = 'cell_type' as ColorMapTypeKey; +export const DEFAULT_COLOR_MAP_KEY = 'Cell Type' as ColorMapTypeKey; /** Default key for the color map value */ -export const DEFAULT_COLOR_MAP_VALUE_KEY = 'cell_color' as ColorMapColorKey; +export const DEFAULT_COLOR_MAP_VALUE_KEY = 'HEX' as ColorMapColorKey; /** Converts a color map array to a lookup map for quick access */ export function colorMapToLookup( From a51d185502a29ae867ff49b0b508f78317b3e1bf Mon Sep 17 00:00:00 2001 From: edlu77 Date: Thu, 26 Sep 2024 14:26:19 -0400 Subject: [PATCH 18/50] Increase testing and doc coverage --- ...reate-visualization-page.component.spec.ts | 7 +++++++ .../create-visualization-page.component.ts | 19 +++++++++++++++++++ 2 files changed, 26 insertions(+) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts index 30f54fcc3..04e0d6c71 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.spec.ts @@ -156,6 +156,13 @@ describe('CreateVisualizationPageComponent', () => { }); }); + describe('hasValidData()', () => { + it('checks for valid data', async () => { + instance.setNodes(sampleNodes); + expect(instance.hasValidData()).toBeTruthy(); + }); + }); + describe('setCustomColorMap()', () => { it('shows error if invalid color map file type', async () => { const loader = TestbedHarnessEnvironment.documentRootLoader(fixture); diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index 397ba6ea9..ba34c2f0e 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -97,7 +97,9 @@ export class CreateVisualizationPageComponent { /** Visualization data service */ private readonly dataService = inject(VisualizationDataService); + /** Cell type headers to match for preselection */ private readonly acceptableCellTypeHeaders = ['celltype', 'cell type', 'cell_type']; + /** Ontology ID headers to match for preselection */ private readonly acceptableOntologyHeaders = [ 'ontologyid', 'cellontologyid', @@ -171,6 +173,7 @@ export class CreateVisualizationPageComponent { /** Whether to show organize data tooltip */ organizeDataInfoOpen = false; + /** Whether to show parameters tooltip */ parametersInfoOpen = false; /** Whether to show metadata info tooltip */ @@ -185,6 +188,7 @@ export class CreateVisualizationPageComponent { /** Cell types included in uploaded data */ cellTypes = [DEFAULT_NODE_TARGET_VALUE]; + /** Headers for node data */ dataHeaders: string[] = []; /** Node CSV load error */ @@ -211,6 +215,7 @@ export class CreateVisualizationPageComponent { return this.getErrorActionMessage(this.customColorMapLoadError, 'color map'); } + /** Error message for missing data columns */ get columnErrorActionMessage(): string | undefined { if (!this.nodes) { return undefined; @@ -253,6 +258,10 @@ export class CreateVisualizationPageComponent { }); } + /** + * Sets node data headers for visualization form + * @param nodes Node data entries + */ private setHeaders(nodes: NodeEntry[]): void { this.dataHeaders = nodes[0] ? Object.keys(nodes[0]) : []; this.visualizationForm.controls['headers'].setValue({ @@ -264,6 +273,12 @@ export class CreateVisualizationPageComponent { }); } + /** + * If a header in the data matches one of the preselected options for a field, return that header + * @param headers Headers in uploaded data + * @param field Field to look for matches + * @returns selected header + */ private preSelectedHeader(headers: string[], field: string): string | null { if (field === 'x' || field === 'y' || field === 'z') { return headers.find((h) => h.toLowerCase() === field) || null; @@ -300,6 +315,10 @@ export class CreateVisualizationPageComponent { return !!(nodes && nodes.length > 0 && cellTypeHeader in nodes[0]); } + /** + * Determines whether all required fields have been provided + * @returns true if all required data has been filled in + */ hasValidData(): boolean { const { xAxis, yAxis, cellType } = this.visualizationForm.controls['headers'].value; const { nodeTargetValue, pixelSizeX, pixelSizeY, pixelSizeZ, distanceThreshold } = From 3fe780c7673f6ce64f3adbcc684f2b6095e646dd Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Thu, 26 Sep 2024 14:41:54 -0400 Subject: [PATCH 19/50] feat: :rocket: Deploy storybook builds under /ui[--staging]/storybook --- .github/workflows/production-build.yml | 1 + .github/workflows/staging-build.yml | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/production-build.yml b/.github/workflows/production-build.yml index ab25b7f67..94874c296 100644 --- a/.github/workflows/production-build.yml +++ b/.github/workflows/production-build.yml @@ -37,6 +37,7 @@ jobs: - name: Deploy to S3 run: | aws s3 sync --delete deploy/apps/ s3://${{ secrets.AWS_S3_BUCKET_NAME }}/ui/ + aws s3 sync deploy/storybook/ s3://${{ secrets.AWS_S3_BUCKET_NAME }}/ui/storybook/ aws cloudfront create-invalidation --distribution-id ${{ secrets.AWS_DISTRIBUTION_ID }} --paths "/ui/*" aws cloudfront create-invalidation --distribution-id ${{ secrets.AWS_HUMANATLAS_IO_DISTRIBUTION_ID }} --paths "/*" diff --git a/.github/workflows/staging-build.yml b/.github/workflows/staging-build.yml index 1a75ee0a8..af2e41be4 100644 --- a/.github/workflows/staging-build.yml +++ b/.github/workflows/staging-build.yml @@ -37,6 +37,7 @@ jobs: - name: Deploy to S3 run: | aws s3 sync --delete deploy/apps/ s3://${{ secrets.AWS_S3_BUCKET_NAME }}/ui--staging/ + aws s3 sync deploy/storybook/ s3://${{ secrets.AWS_S3_BUCKET_NAME }}/ui--staging/storybook/ aws cloudfront create-invalidation --distribution-id ${{ secrets.AWS_DISTRIBUTION_ID }} --paths "/ui--staging/*" - name: Publish From 17bd9c88fd244983f03dfb5bb05444dfacc8fa8e Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Thu, 26 Sep 2024 14:51:51 -0400 Subject: [PATCH 20/50] chore: Enable storybook builds for staging/production --- .github/workflows/production-build.yml | 1 - .github/workflows/staging-build.yml | 1 - 2 files changed, 2 deletions(-) diff --git a/.github/workflows/production-build.yml b/.github/workflows/production-build.yml index 94874c296..af73f4037 100644 --- a/.github/workflows/production-build.yml +++ b/.github/workflows/production-build.yml @@ -25,7 +25,6 @@ jobs: app-configuration: production nx-command: run-many build-compodoc: false - build-storybook: false - name: Configure AWS credentials uses: aws-actions/configure-aws-credentials@v1 diff --git a/.github/workflows/staging-build.yml b/.github/workflows/staging-build.yml index af2e41be4..97f5ce905 100644 --- a/.github/workflows/staging-build.yml +++ b/.github/workflows/staging-build.yml @@ -25,7 +25,6 @@ jobs: app-configuration: staging nx-command: run-many build-compodoc: false - build-storybook: false - name: Configure AWS credentials uses: aws-actions/configure-aws-credentials@v1 From 4ff2d40654d9383f18482336a5c7ae151b1a12f4 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Thu, 26 Sep 2024 16:27:05 -0400 Subject: [PATCH 21/50] create error indicator in design system --- libs/design-system/error-indicator/README.md | 3 ++ .../error-indicator/ng-package.json | 5 +++ .../error-indicator/src/index.ts | 1 + .../src/lib/error-indicator.component.html | 6 ++++ .../src/lib/error-indicator.component.scss | 17 ++++++++++ .../src/lib/error-indicator.component.spec.ts | 15 +++++++++ .../lib/error-indicator.component.stories.ts | 33 +++++++++++++++++++ .../src/lib/error-indicator.component.ts | 17 ++++++++++ tsconfig.base.json | 3 ++ 9 files changed, 100 insertions(+) create mode 100644 libs/design-system/error-indicator/README.md create mode 100644 libs/design-system/error-indicator/ng-package.json create mode 100644 libs/design-system/error-indicator/src/index.ts create mode 100644 libs/design-system/error-indicator/src/lib/error-indicator.component.html create mode 100644 libs/design-system/error-indicator/src/lib/error-indicator.component.scss create mode 100644 libs/design-system/error-indicator/src/lib/error-indicator.component.spec.ts create mode 100644 libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts create mode 100644 libs/design-system/error-indicator/src/lib/error-indicator.component.ts diff --git a/libs/design-system/error-indicator/README.md b/libs/design-system/error-indicator/README.md new file mode 100644 index 000000000..ebdb5ad05 --- /dev/null +++ b/libs/design-system/error-indicator/README.md @@ -0,0 +1,3 @@ +# @hra-ui/design-system/error-indicator + +Secondary entry point of `@hra-ui/design-system`. It can be used by importing from `@hra-ui/design-system/error-indicator`. diff --git a/libs/design-system/error-indicator/ng-package.json b/libs/design-system/error-indicator/ng-package.json new file mode 100644 index 000000000..c781f0df4 --- /dev/null +++ b/libs/design-system/error-indicator/ng-package.json @@ -0,0 +1,5 @@ +{ + "lib": { + "entryFile": "src/index.ts" + } +} diff --git a/libs/design-system/error-indicator/src/index.ts b/libs/design-system/error-indicator/src/index.ts new file mode 100644 index 000000000..4e7c37667 --- /dev/null +++ b/libs/design-system/error-indicator/src/index.ts @@ -0,0 +1 @@ +export * from './lib/error-indicator.component'; diff --git a/libs/design-system/error-indicator/src/lib/error-indicator.component.html b/libs/design-system/error-indicator/src/lib/error-indicator.component.html new file mode 100644 index 000000000..e12d533c4 --- /dev/null +++ b/libs/design-system/error-indicator/src/lib/error-indicator.component.html @@ -0,0 +1,6 @@ +error +
+ @for (error of errors(); track error) { +
{{ error }}
+ } +
diff --git a/libs/design-system/error-indicator/src/lib/error-indicator.component.scss b/libs/design-system/error-indicator/src/lib/error-indicator.component.scss new file mode 100644 index 000000000..26c8beed3 --- /dev/null +++ b/libs/design-system/error-indicator/src/lib/error-indicator.component.scss @@ -0,0 +1,17 @@ +:host { + display: flex; + width: fit-content; + padding: 0.5rem 0.75rem; + border-radius: 0.25rem; + color: var(--sys-on-error-container); + background-color: color-mix(in srgb, var(--sys-error-container) 80%, transparent); + + mat-icon { + margin-right: 0.5rem; + color: var(--sys-error); + } + .error { + font: var(--sys-label-large); + letter-spacing: var(--sys-label-large-text-tracking); + } +} diff --git a/libs/design-system/error-indicator/src/lib/error-indicator.component.spec.ts b/libs/design-system/error-indicator/src/lib/error-indicator.component.spec.ts new file mode 100644 index 000000000..4af763010 --- /dev/null +++ b/libs/design-system/error-indicator/src/lib/error-indicator.component.spec.ts @@ -0,0 +1,15 @@ +import { render } from '@testing-library/angular'; +import { ErrorIndicatorComponent } from './error-indicator.component'; +import { screen } from '@testing-library/dom'; +describe('ErrorIndicatorComponent', () => { + it('Error should be visible in the indicator', async () => { + const errors: string[] = ['Error 1']; + await render(ErrorIndicatorComponent, { + componentInputs: { + errors, + }, + }); + + expect(screen.getByText('Error 1')).toBeInTheDocument(); + }); +}); diff --git a/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts b/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts new file mode 100644 index 000000000..67cfedb0c --- /dev/null +++ b/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts @@ -0,0 +1,33 @@ +import { applicationConfig, Meta, StoryObj } from '@storybook/angular'; +import { provideDesignSystem } from '../../../src'; +import { ErrorIndicatorComponent } from './error-indicator.component'; + +const meta: Meta = { + component: ErrorIndicatorComponent, + title: 'ErrorIndicatorComponent', + parameters: { + design: { + type: 'figma', + url: 'https://www.figma.com/design/BCEJn9KCIbBJ5MzqnojKQp/Design-System-Components?node-id=5-842', + }, + }, + decorators: [ + applicationConfig({ + providers: [provideDesignSystem()], + }), + ], +}; +export default meta; +type Story = StoryObj; + +export const SingleError: Story = { + args: { + errors: ['Please upload a dataset.'], + }, +}; + +export const MultipleErrors: Story = { + args: { + errors: ['Required columns missing: Column Name, Column Name', 'Please upload a file with all required columns.'], + }, +}; diff --git a/libs/design-system/error-indicator/src/lib/error-indicator.component.ts b/libs/design-system/error-indicator/src/lib/error-indicator.component.ts new file mode 100644 index 000000000..ecf42bf41 --- /dev/null +++ b/libs/design-system/error-indicator/src/lib/error-indicator.component.ts @@ -0,0 +1,17 @@ +import { ChangeDetectionStrategy, Component, input } from '@angular/core'; +import { CommonModule } from '@angular/common'; +import { MatIconModule } from '@angular/material/icon'; + +/** Error Indicator component */ +@Component({ + selector: 'hra-error-indicator', + standalone: true, + imports: [CommonModule, MatIconModule], + templateUrl: './error-indicator.component.html', + styleUrl: './error-indicator.component.scss', + changeDetection: ChangeDetectionStrategy.OnPush, +}) +export class ErrorIndicatorComponent { + /** List of errors to be shown in the indicator */ + readonly errors = input(); +} diff --git a/tsconfig.base.json b/tsconfig.base.json index 0995373b6..ef6854d28 100644 --- a/tsconfig.base.json +++ b/tsconfig.base.json @@ -89,6 +89,9 @@ "@hra-ui/design-system/dialog": [ "libs/design-system/dialog/src/index.ts" ], + "@hra-ui/design-system/error-indicator": [ + "libs/design-system/error-indicator/src/index.ts" + ], "@hra-ui/design-system/footer": [ "libs/design-system/footer/src/index.ts" ], From ec74e77f6f3171252099bf3d12891203a62aed32 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Thu, 26 Sep 2024 22:17:44 -0400 Subject: [PATCH 22/50] Fix test --- .../cde-visualization/cde-visualization.component.spec.ts | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts index 258011ec3..9b151b9b5 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts @@ -282,23 +282,23 @@ describe('CdeVisualizationComponent', () => { ...sampleData, nodes: [ { - cell_type: 'a', + 'Cell Type': 'a', x: 0, y: 1, }, { - cell_type: 'b', + 'Cell Type': 'b', x: 0, y: 2, }, { - cell_type: 'c', + 'Cell Type': 'c', x: 0, y: 3, }, ], colorMap: sampleColorMap, - nodeTargetKey: 'cell_type', + nodeTargetKey: 'Cell Type', }, }); From 9623aa5868a8098f53362f8493d50018b0c4409a Mon Sep 17 00:00:00 2001 From: edlu77 Date: Thu, 26 Sep 2024 22:59:08 -0400 Subject: [PATCH 23/50] Fix sonarcloud issues --- .../create-visualization-page.component.html | 4 ++-- .../create-visualization-page.component.ts | 8 +++----- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index 15b48b684..7da2c47e6 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -50,7 +50,7 @@

Template

- +
@@ -371,7 +371,7 @@

@if (useCustomColorMap) { -

Required Columns Optional Columns
+
diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index ba34c2f0e..b39e2ea5d 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -226,11 +226,9 @@ export class CreateVisualizationPageComponent { const ctError = cellType ? undefined : 'Cell Type'; const errorColumns = [xError, yError, ctError].filter((e) => !!e); - const columnErrorMessage = - errorColumns.length > 0 - ? `Please select the required column headers: ${[xError, yError, ctError].filter((e) => !!e).join(', ')}` - : undefined; - return columnErrorMessage; + return errorColumns.length > 0 + ? `Please select the required column headers: ${[xError, yError, ctError].filter((e) => !!e).join(', ')}` + : undefined; } /** Current nodes */ From 4a422844bd78e45e31d5b13691d340eaef39c302 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Fri, 27 Sep 2024 10:48:39 -0400 Subject: [PATCH 24/50] update design url in story --- .../src/lib/error-indicator.component.stories.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts b/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts index 67cfedb0c..60cc1b6fa 100644 --- a/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts +++ b/libs/design-system/error-indicator/src/lib/error-indicator.component.stories.ts @@ -8,7 +8,7 @@ const meta: Meta = { parameters: { design: { type: 'figma', - url: 'https://www.figma.com/design/BCEJn9KCIbBJ5MzqnojKQp/Design-System-Components?node-id=5-842', + url: 'https://www.figma.com/design/BCEJn9KCIbBJ5MzqnojKQp/Explorer-Components?node-id=1294-4977', }, }, decorators: [ From fb919c2e3d5b73e33e3dfe2b325dfc34ff4b8a1f Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 27 Sep 2024 10:57:15 -0400 Subject: [PATCH 25/50] Add ontologyId to submitted data --- apps/cde-ui/example-data/nodes.csv | 5738 ++++++++--------- .../example-data/nodes_renamed_columns.csv | 5738 ++++++++--------- .../nodes_slightly_renamed_columns.csv | 5738 ++++++++--------- .../create-visualization-page.component.ts | 23 +- 4 files changed, 8619 insertions(+), 8618 deletions(-) diff --git a/apps/cde-ui/example-data/nodes.csv b/apps/cde-ui/example-data/nodes.csv index 558557f60..4711a8ba7 100644 --- a/apps/cde-ui/example-data/nodes.csv +++ b/apps/cde-ui/example-data/nodes.csv @@ -1,2869 +1,2869 @@ -x,y,z,Cell Type -188.5,342.5,10,T-Killer -136.6,161.4,20,T-Killer -437.5,363.5,20,T-Killer -203.5,512.0,20,T-Killer -155.579,204.895,0,T-Helper -107.5,223.5,0,T-Helper -180.593,226.519,0,T-Helper -188.5,226.778,0,T-Helper -198.579,231.895,0,T-Helper -478.5,232.0,0,T-Helper -191.0,236.0,0,T-Helper 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+348.5,395.5,11,DDB2,2859 +520.895,395.579,11,DDB2,2860 +134.5,502.5,11,DDB2,2861 +365.5,388,18,DDB2,2862 +176,109,20,DDB2,2863 +155.5,133.5,20,DDB2,2864 +102.5,251.5,20,DDB2,2865 +133.905,378.381,20,DDB2,2866 +439.846,378.231,20,DDB2,2867 +193,501.5,20,DDB2,2868 diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index b39e2ea5d..ecd10968b 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -263,27 +263,26 @@ export class CreateVisualizationPageComponent { private setHeaders(nodes: NodeEntry[]): void { this.dataHeaders = nodes[0] ? Object.keys(nodes[0]) : []; this.visualizationForm.controls['headers'].setValue({ - xAxis: this.preSelectedHeader(this.dataHeaders, 'x'), - yAxis: this.preSelectedHeader(this.dataHeaders, 'y'), - cellType: this.preSelectedHeader(this.dataHeaders, 'cellType'), - zAxis: this.preSelectedHeader(this.dataHeaders, 'z'), - ontologyId: this.preSelectedHeader(this.dataHeaders, 'ontologyId'), + xAxis: this.preSelectedHeader('x'), + yAxis: this.preSelectedHeader('y'), + cellType: this.preSelectedHeader('cellType'), + zAxis: this.preSelectedHeader('z'), + ontologyId: this.preSelectedHeader('ontologyId'), }); } /** * If a header in the data matches one of the preselected options for a field, return that header - * @param headers Headers in uploaded data * @param field Field to look for matches * @returns selected header */ - private preSelectedHeader(headers: string[], field: string): string | null { - if (field === 'x' || field === 'y' || field === 'z') { - return headers.find((h) => h.toLowerCase() === field) || null; + private preSelectedHeader(field: string): string | null { + if (['x', 'y', 'z'].includes(field)) { + return this.dataHeaders.find((h) => h.toLowerCase() === field) || null; } else if (field === 'cellType') { - return headers.find((h) => this.acceptableCellTypeHeaders.includes(h.toLowerCase())) || null; + return this.dataHeaders.find((h) => this.acceptableCellTypeHeaders.includes(h.toLowerCase())) || null; } else if (field === 'ontologyId') { - return headers.find((h) => this.acceptableOntologyHeaders.includes(h.toLowerCase())) || null; + return this.dataHeaders.find((h) => this.acceptableOntologyHeaders.includes(h.toLowerCase())) || null; } else { return null; } @@ -409,6 +408,7 @@ export class CreateVisualizationPageComponent { const yKey = (headers?.yAxis || '') as NodeTargetKey; const zKey = (headers?.zAxis || '') as NodeTargetKey; const ctKey = (headers?.cellType || '') as NodeTargetKey; + const idKey = (headers?.ontologyId || '') as NodeTargetKey; const convertedHeaderNodes = (nullishRemovedData.nodes = nullishRemovedData.nodes ? nullishRemovedData.nodes.map( @@ -418,6 +418,7 @@ export class CreateVisualizationPageComponent { y: node[yKey] as unknown as number, z: node[zKey] as unknown as number, [ntKey]: node[ctKey], + [idKey]: node[idKey], }) as NodeEntry, ) : []); From 82000fc4ebfb5fe154c12158ce1a4f3501b2df56 Mon Sep 17 00:00:00 2001 From: Bhushan Khope <53601863+bhushankhope@users.noreply.github.com> Date: Fri, 27 Sep 2024 15:18:24 -0400 Subject: [PATCH 26/50] Body UI wrapper (#740) * create body ui wrapper * added outputs to body ui * improve test coverage * add new inputs to body ui * refactor body ui library * improve test coverage for body ui library * add transform for bounds input * Update app.component.ts Remove console.log * add redirects file * added preview config in project.json * update base href * update main path in project.json * update static file path * update project config * restore wrong config changes * add base href to staging, prod and dev * Update styles.scss --------- Co-authored-by: Daniel Bolin --- apps/body-ui-e2e/.eslintrc.json | 10 + apps/body-ui-e2e/cypress.config.ts | 7 + apps/body-ui-e2e/project.json | 29 +++ apps/body-ui-e2e/src/e2e/app.cy.ts | 13 ++ apps/body-ui-e2e/src/fixtures/example.json | 5 + apps/body-ui-e2e/src/support/app.po.ts | 1 + apps/body-ui-e2e/src/support/commands.ts | 35 +++ apps/body-ui-e2e/src/support/e2e.ts | 17 ++ apps/body-ui-e2e/tsconfig.json | 17 ++ apps/body-ui/.eslintrc.json | 33 +++ apps/body-ui/jest.config.ts | 22 ++ apps/body-ui/project.json | 104 +++++++++ apps/body-ui/public/favicon.ico | Bin 0 -> 15086 bytes apps/body-ui/src/_redirects | 1 + apps/body-ui/src/index.html | 15 ++ apps/body-ui/src/main.ts | 8 + apps/body-ui/src/styles.scss | 5 + apps/body-ui/src/test-setup.ts | 8 + apps/body-ui/tsconfig.app.json | 10 + apps/body-ui/tsconfig.editor.json | 6 + apps/body-ui/tsconfig.json | 32 +++ apps/body-ui/tsconfig.spec.json | 11 + libs/ccf-body-ui/.eslintrc.json | 4 +- libs/ccf-body-ui/jest.config.ts | 22 ++ libs/ccf-body-ui/karma.conf.js | 43 ---- libs/ccf-body-ui/project.json | 9 +- libs/ccf-body-ui/src/ccf-body-ui.spec.ts | 6 - .../src/lib/body-ui/body-ui.component.html | 1 + .../src/lib/body-ui/body-ui.component.scss | 0 .../src/lib/body-ui/body-ui.component.spec.ts | 134 +++++++++++ .../src/lib/body-ui/body-ui.component.ts | 220 ++++++++++++++++++ libs/ccf-body-ui/src/public-api.ts | 1 + libs/ccf-body-ui/src/test-setup.ts | 9 + libs/ccf-body-ui/src/test.ts | 11 - libs/ccf-body-ui/tsconfig.spec.json | 8 +- nx.json | 5 + 36 files changed, 791 insertions(+), 71 deletions(-) create mode 100644 apps/body-ui-e2e/.eslintrc.json create mode 100644 apps/body-ui-e2e/cypress.config.ts create mode 100644 apps/body-ui-e2e/project.json create mode 100644 apps/body-ui-e2e/src/e2e/app.cy.ts create mode 100644 apps/body-ui-e2e/src/fixtures/example.json create mode 100644 apps/body-ui-e2e/src/support/app.po.ts create mode 100644 apps/body-ui-e2e/src/support/commands.ts create mode 100644 apps/body-ui-e2e/src/support/e2e.ts create mode 100644 apps/body-ui-e2e/tsconfig.json create mode 100644 apps/body-ui/.eslintrc.json create mode 100644 apps/body-ui/jest.config.ts create mode 100644 apps/body-ui/project.json create mode 100644 apps/body-ui/public/favicon.ico create mode 100644 apps/body-ui/src/_redirects create mode 100644 apps/body-ui/src/index.html create mode 100644 apps/body-ui/src/main.ts create mode 100644 apps/body-ui/src/styles.scss create mode 100644 apps/body-ui/src/test-setup.ts create mode 100644 apps/body-ui/tsconfig.app.json create mode 100644 apps/body-ui/tsconfig.editor.json create mode 100644 apps/body-ui/tsconfig.json create mode 100644 apps/body-ui/tsconfig.spec.json create mode 100644 libs/ccf-body-ui/jest.config.ts delete mode 100644 libs/ccf-body-ui/karma.conf.js delete mode 100644 libs/ccf-body-ui/src/ccf-body-ui.spec.ts create mode 100644 libs/ccf-body-ui/src/lib/body-ui/body-ui.component.html create mode 100644 libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss create mode 100644 libs/ccf-body-ui/src/lib/body-ui/body-ui.component.spec.ts create mode 100644 libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts create mode 100644 libs/ccf-body-ui/src/test-setup.ts delete mode 100644 libs/ccf-body-ui/src/test.ts diff --git a/apps/body-ui-e2e/.eslintrc.json b/apps/body-ui-e2e/.eslintrc.json new file mode 100644 index 000000000..696cb8b12 --- /dev/null +++ b/apps/body-ui-e2e/.eslintrc.json @@ -0,0 +1,10 @@ +{ + "extends": ["plugin:cypress/recommended", "../../.eslintrc.json"], + "ignorePatterns": ["!**/*"], + "overrides": [ + { + "files": ["*.ts", "*.tsx", "*.js", "*.jsx"], + "rules": {} + } + ] +} diff --git a/apps/body-ui-e2e/cypress.config.ts b/apps/body-ui-e2e/cypress.config.ts new file mode 100644 index 000000000..7df58bdcf --- /dev/null +++ b/apps/body-ui-e2e/cypress.config.ts @@ -0,0 +1,7 @@ +import { nxE2EPreset } from '@nx/cypress/plugins/cypress-preset'; + +import { defineConfig } from 'cypress'; + +export default defineConfig({ + e2e: { ...nxE2EPreset(__filename, { cypressDir: 'src' }), baseUrl: 'http://localhost:4200' }, +}); diff --git a/apps/body-ui-e2e/project.json b/apps/body-ui-e2e/project.json new file mode 100644 index 000000000..e356206f1 --- /dev/null +++ b/apps/body-ui-e2e/project.json @@ -0,0 +1,29 @@ +{ + "name": "body-ui-e2e", + "$schema": "../../node_modules/nx/schemas/project-schema.json", + "projectType": "application", + "sourceRoot": "apps/body-ui-e2e/src", + "tags": [], + "implicitDependencies": ["body-ui"], + "targets": { + "e2e": { + "executor": "@nx/cypress:cypress", + "options": { + "cypressConfig": "apps/body-ui-e2e/cypress.config.ts", + "testingType": "e2e", + "devServerTarget": "body-ui:serve:development" + }, + "configurations": { + "production": { + "devServerTarget": "body-ui:serve:production" + }, + "ci": { + "devServerTarget": "body-ui:serve-static" + } + } + }, + "lint": { + "executor": "@nx/eslint:lint" + } + } +} diff --git a/apps/body-ui-e2e/src/e2e/app.cy.ts b/apps/body-ui-e2e/src/e2e/app.cy.ts new file mode 100644 index 000000000..a2f8ad732 --- /dev/null +++ b/apps/body-ui-e2e/src/e2e/app.cy.ts @@ -0,0 +1,13 @@ +import { getGreeting } from '../support/app.po'; + +describe('body-ui-e2e', () => { + beforeEach(() => cy.visit('/')); + + it('should display welcome message', () => { + // Custom command example, see `../support/commands.ts` file + cy.login('my-email@something.com', 'myPassword'); + + // Function helper example, see `../support/app.po.ts` file + getGreeting().contains(/Welcome/); + }); +}); diff --git a/apps/body-ui-e2e/src/fixtures/example.json b/apps/body-ui-e2e/src/fixtures/example.json new file mode 100644 index 000000000..02e425437 --- /dev/null +++ b/apps/body-ui-e2e/src/fixtures/example.json @@ -0,0 +1,5 @@ +{ + "name": "Using fixtures to represent data", + "email": "hello@cypress.io", + "body": "Fixtures are a great way to mock data for responses to routes" +} diff --git a/apps/body-ui-e2e/src/support/app.po.ts b/apps/body-ui-e2e/src/support/app.po.ts new file mode 100644 index 000000000..329342469 --- /dev/null +++ b/apps/body-ui-e2e/src/support/app.po.ts @@ -0,0 +1 @@ +export const getGreeting = () => cy.get('h1'); diff --git a/apps/body-ui-e2e/src/support/commands.ts b/apps/body-ui-e2e/src/support/commands.ts new file mode 100644 index 000000000..c421a3c47 --- /dev/null +++ b/apps/body-ui-e2e/src/support/commands.ts @@ -0,0 +1,35 @@ +/// + +// *********************************************** +// This example commands.ts shows you how to +// create various custom commands and overwrite +// existing commands. +// +// For more comprehensive examples of custom +// commands please read more here: +// https://on.cypress.io/custom-commands +// *********************************************** + +// eslint-disable-next-line @typescript-eslint/no-namespace +declare namespace Cypress { + // eslint-disable-next-line @typescript-eslint/no-unused-vars + interface Chainable { + login(email: string, password: string): void; + } +} + +// -- This is a parent command -- +Cypress.Commands.add('login', (email, password) => { + console.log('Custom command example: Login', email, password); +}); +// +// -- This is a child command -- +// Cypress.Commands.add("drag", { prevSubject: 'element'}, (subject, options) => { ... }) +// +// +// -- This is a dual command -- +// Cypress.Commands.add("dismiss", { prevSubject: 'optional'}, (subject, options) => { ... }) +// +// +// -- This will overwrite an existing command -- +// Cypress.Commands.overwrite("visit", (originalFn, url, options) => { ... }) diff --git a/apps/body-ui-e2e/src/support/e2e.ts b/apps/body-ui-e2e/src/support/e2e.ts new file mode 100644 index 000000000..1c1a9e772 --- /dev/null +++ b/apps/body-ui-e2e/src/support/e2e.ts @@ -0,0 +1,17 @@ +// *********************************************************** +// This example support/e2e.ts is processed and +// loaded automatically before your test files. +// +// This is a great place to put global configuration and +// behavior that modifies Cypress. +// +// You can change the location of this file or turn off +// automatically serving support files with the +// 'supportFile' configuration option. +// +// You can read more here: +// https://on.cypress.io/configuration +// *********************************************************** + +// Import commands.ts using ES2015 syntax: +import './commands'; diff --git a/apps/body-ui-e2e/tsconfig.json b/apps/body-ui-e2e/tsconfig.json new file mode 100644 index 000000000..e28de1d79 --- /dev/null +++ b/apps/body-ui-e2e/tsconfig.json @@ -0,0 +1,17 @@ +{ + "extends": "../../tsconfig.base.json", + "compilerOptions": { + "allowJs": true, + "outDir": "../../dist/out-tsc", + "module": "commonjs", + "types": ["cypress", "node"], + "sourceMap": false, + "forceConsistentCasingInFileNames": true, + "strict": true, + "noImplicitOverride": true, + "noPropertyAccessFromIndexSignature": true, + "noImplicitReturns": true, + "noFallthroughCasesInSwitch": true + }, + "include": ["**/*.ts", "**/*.js", "cypress.config.ts", "**/*.cy.ts", "**/*.cy.js", "**/*.d.ts"] +} diff --git a/apps/body-ui/.eslintrc.json b/apps/body-ui/.eslintrc.json new file mode 100644 index 000000000..437641b9a --- /dev/null +++ b/apps/body-ui/.eslintrc.json @@ -0,0 +1,33 @@ +{ + "extends": ["../../.eslintrc.json"], + "ignorePatterns": ["!**/*"], + "overrides": [ + { + "files": ["*.ts"], + "extends": ["plugin:@nx/angular", "plugin:@angular-eslint/template/process-inline-templates"], + "rules": { + "@angular-eslint/directive-selector": [ + "error", + { + "type": "attribute", + "prefix": "app", + "style": "camelCase" + } + ], + "@angular-eslint/component-selector": [ + "error", + { + "type": "element", + "prefix": "app", + "style": "kebab-case" + } + ] + } + }, + { + "files": ["*.html"], + "extends": ["plugin:@nx/angular-template"], + "rules": {} + } + ] +} diff --git a/apps/body-ui/jest.config.ts b/apps/body-ui/jest.config.ts new file mode 100644 index 000000000..5ed277347 --- /dev/null +++ b/apps/body-ui/jest.config.ts @@ -0,0 +1,22 @@ +/* eslint-disable */ +export default { + displayName: 'body-ui', + preset: '../../jest.preset.js', + setupFilesAfterEnv: ['/src/test-setup.ts'], + coverageDirectory: '../../coverage/apps/body-ui', + transform: { + '^.+\\.(ts|mjs|js|html)$': [ + 'jest-preset-angular', + { + tsconfig: '/tsconfig.spec.json', + stringifyContentPathRegex: '\\.(html|svg)$', + }, + ], + }, + transformIgnorePatterns: ['node_modules/(?!.*\\.mjs$)'], + snapshotSerializers: [ + 'jest-preset-angular/build/serializers/no-ng-attributes', + 'jest-preset-angular/build/serializers/ng-snapshot', + 'jest-preset-angular/build/serializers/html-comment', + ], +}; diff --git a/apps/body-ui/project.json b/apps/body-ui/project.json new file mode 100644 index 000000000..1409258f4 --- /dev/null +++ b/apps/body-ui/project.json @@ -0,0 +1,104 @@ +{ + "name": "body-ui", + "$schema": "../../node_modules/nx/schemas/project-schema.json", + "projectType": "application", + "prefix": "app", + "sourceRoot": "apps/body-ui/src", + "tags": ["type:app"], + "targets": { + "build": { + "executor": "@angular-devkit/build-angular:browser-esbuild", + "outputs": ["{options.outputPath}"], + "options": { + "buildOptimizer": false, + "outputPath": "dist/apps/body-ui", + "index": "apps/body-ui/src/index.html", + "main": "apps/body-ui/src/main.ts", + "polyfills": ["zone.js"], + "tsConfig": "apps/body-ui/tsconfig.app.json", + "inlineStyleLanguage": "scss", + "assets": [ + { + "glob": "**/*", + "input": "apps/body-ui/public" + } + ], + "styles": ["apps/body-ui/src/styles.scss"], + "scripts": [] + }, + "configurations": { + "production": { + "baseHref": "/ui/body-ui/", + "budgets": [ + { + "type": "initial", + "maximumWarning": "500kb", + "maximumError": "1mb" + }, + { + "type": "anyComponentStyle", + "maximumWarning": "2kb", + "maximumError": "4kb" + } + ], + "outputHashing": "all" + }, + "development": { + "baseHref": "/", + "optimization": false, + "extractLicenses": false, + "sourceMap": true + }, + "staging": { + "baseHref": "/ui--staging/body-ui/", + "outputHashing": "none" + }, + "preview": { + "baseHref": "/apps/body-ui/", + "optimization": false, + "extractLicenses": false, + "sourceMap": true, + "namedChunks": true + } + }, + "defaultConfiguration": "production" + }, + "serve": { + "executor": "@angular-devkit/build-angular:dev-server", + "configurations": { + "production": { + "buildTarget": "body-ui:build:production" + }, + "development": { + "buildTarget": "body-ui:build:development" + } + }, + "defaultConfiguration": "development" + }, + "extract-i18n": { + "executor": "@angular-devkit/build-angular:extract-i18n", + "options": { + "buildTarget": "body-ui:build" + } + }, + "lint": { + "executor": "@nx/eslint:lint" + }, + "test": { + "executor": "@nx/jest:jest", + "outputs": ["{workspaceRoot}/coverage/{projectRoot}"], + "options": { + "jestConfig": "apps/body-ui/jest.config.ts" + } + }, + "serve-static": { + "executor": "@nx/web:file-server", + "options": { + "buildTarget": "body-ui:build", + "port": 4200, + "staticFilePath": "dist/apps/body-ui/browser", + "spa": true + } + } + } +} diff --git a/apps/body-ui/public/favicon.ico b/apps/body-ui/public/favicon.ico new file mode 100644 index 0000000000000000000000000000000000000000..317ebcb2336e0833a22dddf0ab287849f26fda57 GIT binary patch literal 15086 zcmeI332;U^%p|z7g|#(P)qFEA@4f!_@qOK2 z_lJl}!lhL!VT_U|uN7%8B2iKH??xhDa;*`g{yjTFWHvXn;2s{4R7kH|pKGdy(7z!K zgftM+Ku7~24TLlh(!g)gz|foI94G^t2^IO$uvX$3(OR0<_5L2sB)lMAMy|+`xodJ{ z_Uh_1m)~h?a;2W{dmhM;u!YGo=)OdmId_B<%^V^{ovI@y`7^g1_V9G}*f# zNzAtvou}I!W1#{M^@ROc(BZ! z+F!!_aR&Px3_reO(EW+TwlW~tv*2zr?iP7(d~a~yA|@*a89IUke+c472NXM0wiX{- zl`UrZC^1XYyf%1u)-Y)jj9;MZ!SLfd2Hl?o|80Su%Z?To_=^g_Jt0oa#CT*tjx>BI z16wec&AOWNK<#i0Qd=1O$fymLRoUR*%;h@*@v7}wApDl^w*h}!sYq%kw+DKDY)@&A z@9$ULEB3qkR#85`lb8#WZw=@})#kQig9oqy^I$dj&k4jU&^2(M3q{n1AKeGUKPFbr z1^<)aH;VsG@J|B&l>UtU#Ejv3GIqERzYgL@UOAWtW<{p#zy`WyJgpCy8$c_e%wYJL zyGHRRx38)HyjU3y{-4z6)pzb>&Q1pR)B&u01F-|&Gx4EZWK$nkUkOI|(D4UHOXg_- zw{OBf!oWQUn)Pe(=f=nt=zkmdjpO^o8ZZ9o_|4tW1ni+Un9iCW47*-ut$KQOww!;u z`0q)$s6IZO!~9$e_P9X!hqLxu`fpcL|2f^I5d4*a@Dq28;@2271v_N+5HqYZ>x;&O z05*7JT)mUe&%S0@UD)@&8SmQrMtsDfZT;fkdA!r(S=}Oz>iP)w=W508=Rc#nNn7ym z1;42c|8($ALY8#a({%1#IXbWn9-Y|0eDY$_L&j{63?{?AH{);EzcqfydD$@-B`Y3<%IIj7S7rK_N}je^=dEk%JQ4c z!tBdTPE3Tse;oYF>cnrapWq*o)m47X1`~6@(!Y29#>-#8zm&LXrXa(3=7Z)ElaQqj z-#0JJy3Fi(C#Rx(`=VXtJ63E2_bZGCz+QRa{W0e2(m3sI?LOcUBx)~^YCqZ{XEPX)C>G>U4tfqeH8L(3|pQR*zbL1 zT9e~4Tb5p9_G}$y4t`i*4t_Mr9QYvL9C&Ah*}t`q*}S+VYh0M6GxTTSXI)hMpMpIq zD1ImYqJLzbj0}~EpE-aH#VCH_udYEW#`P2zYmi&xSPs_{n6tBj=MY|-XrA;SGA_>y zGtU$?HXm$gYj*!N)_nQ59%lQdXtQZS3*#PC-{iB_sm+ytD*7j`D*k(P&IH2GHT}Eh z5697eQECVIGQAUe#eU2I!yI&%0CP#>%6MWV z@zS!p@+Y1i1b^QuuEF*13CuB zu69dve5k7&Wgb+^s|UB08Dr3u`h@yM0NTj4h7MnHo-4@xmyr7(*4$rpPwsCDZ@2be zRz9V^GnV;;?^Lk%ynzq&K(Aix`mWmW`^152Hoy$CTYVehpD-S1-W^#k#{0^L`V6CN+E z!w+xte;2vu4AmVNEFUOBmrBL>6MK@!O2*N|2=d|Y;oN&A&qv=qKn73lDD zI(+oJAdgv>Yr}8(&@ZuAZE%XUXmX(U!N+Z_sjL<1vjy1R+1IeHt`79fnYdOL{$ci7 z%3f0A*;Zt@ED&Gjm|OFTYBDe%bbo*xXAQsFz+Q`fVBH!N2)kaxN8P$c>sp~QXnv>b zwq=W3&Mtmih7xkR$YA)1Yi?avHNR6C99!u6fh=cL|KQ&PwF!n@ud^n(HNIImHD!h87!i*t?G|p0o+eelJ?B@A64_9%SBhNaJ64EvKgD&%LjLCYnNfc; 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+import { provideZoneChangeDetection } from '@angular/core'; +import { createCustomElement } from '@hra-ui/webcomponents'; +import { BodyUiComponent } from 'ccf-body-ui'; + +createCustomElement('hra-body-ui', BodyUiComponent, { + providers: [provideZoneChangeDetection({ eventCoalescing: true }), provideHttpClient()], +}); diff --git a/apps/body-ui/src/styles.scss b/apps/body-ui/src/styles.scss new file mode 100644 index 000000000..c40bb56ae --- /dev/null +++ b/apps/body-ui/src/styles.scss @@ -0,0 +1,5 @@ +/* You can add global styles to this file, and also import other style files */ + +body { + margin: 0; +} diff --git a/apps/body-ui/src/test-setup.ts b/apps/body-ui/src/test-setup.ts new file mode 100644 index 000000000..ab1eeeb33 --- /dev/null +++ b/apps/body-ui/src/test-setup.ts @@ -0,0 +1,8 @@ +// @ts-expect-error https://thymikee.github.io/jest-preset-angular/docs/getting-started/test-environment +globalThis.ngJest = { + testEnvironmentOptions: { + errorOnUnknownElements: true, + errorOnUnknownProperties: true, + }, +}; +import 'jest-preset-angular/setup-jest'; diff --git a/apps/body-ui/tsconfig.app.json b/apps/body-ui/tsconfig.app.json new file mode 100644 index 000000000..fff4a41d4 --- /dev/null +++ b/apps/body-ui/tsconfig.app.json @@ -0,0 +1,10 @@ +{ + "extends": "./tsconfig.json", + "compilerOptions": { + "outDir": "../../dist/out-tsc", + "types": [] + }, + "files": ["src/main.ts"], + "include": ["src/**/*.d.ts"], + "exclude": ["jest.config.ts", "src/**/*.test.ts", "src/**/*.spec.ts"] +} diff --git a/apps/body-ui/tsconfig.editor.json b/apps/body-ui/tsconfig.editor.json new file mode 100644 index 000000000..a8ac182c0 --- /dev/null +++ b/apps/body-ui/tsconfig.editor.json @@ -0,0 +1,6 @@ +{ + "extends": "./tsconfig.json", + "include": ["src/**/*.ts"], + "compilerOptions": {}, + "exclude": ["jest.config.ts", "src/**/*.test.ts", "src/**/*.spec.ts"] +} diff --git a/apps/body-ui/tsconfig.json b/apps/body-ui/tsconfig.json new file mode 100644 index 000000000..2f7d4b099 --- /dev/null +++ b/apps/body-ui/tsconfig.json @@ -0,0 +1,32 @@ +{ + "compilerOptions": { + "target": "es2022", + "forceConsistentCasingInFileNames": true, + "useDefineForClassFields": false, + "strict": true, + "noImplicitOverride": true, + "noPropertyAccessFromIndexSignature": true, + "noImplicitReturns": true, + "noFallthroughCasesInSwitch": true + }, + "files": [], + "include": [], + "references": [ + { + "path": "./tsconfig.editor.json" + }, + { + "path": "./tsconfig.app.json" + }, + { + "path": "./tsconfig.spec.json" + } + ], + "extends": "../../tsconfig.base.json", + "angularCompilerOptions": { + "enableI18nLegacyMessageIdFormat": false, + "strictInjectionParameters": true, + "strictInputAccessModifiers": true, + "strictTemplates": true + } +} diff --git a/apps/body-ui/tsconfig.spec.json b/apps/body-ui/tsconfig.spec.json new file mode 100644 index 000000000..2269b492d --- /dev/null +++ b/apps/body-ui/tsconfig.spec.json @@ -0,0 +1,11 @@ +{ + "extends": "./tsconfig.json", + "compilerOptions": { + "outDir": "../../dist/out-tsc", + "module": "commonjs", + "target": "es2016", + "types": ["jest", "node", "@testing-library/jest-dom"] + }, + "files": ["src/test-setup.ts"], + "include": ["jest.config.ts", "src/**/*.test.ts", "src/**/*.spec.ts", "src/**/*.d.ts"] +} diff --git a/libs/ccf-body-ui/.eslintrc.json b/libs/ccf-body-ui/.eslintrc.json index 285db045e..46454ca9d 100644 --- a/libs/ccf-body-ui/.eslintrc.json +++ b/libs/ccf-body-ui/.eslintrc.json @@ -9,7 +9,7 @@ "error", { "type": "element", - "prefix": "ccf", + "prefix": "hra", "style": "kebab-case" } ], @@ -17,7 +17,7 @@ "error", { "type": "attribute", - "prefix": "ccf", + "prefix": "hra", "style": "camelCase" } ] diff --git a/libs/ccf-body-ui/jest.config.ts b/libs/ccf-body-ui/jest.config.ts new file mode 100644 index 000000000..9eef19b82 --- /dev/null +++ b/libs/ccf-body-ui/jest.config.ts @@ -0,0 +1,22 @@ +/* eslint-disable */ +export default { + displayName: 'ccf-body-ui', + preset: '../../jest.preset.js', + setupFilesAfterEnv: ['/src/test-setup.ts', '@testing-library/jest-dom'], + coverageDirectory: '../../coverage/libs/ccf-body-ui', + transform: { + '^.+\\.(ts|mjs|js|html)$': [ + 'jest-preset-angular', + { + tsconfig: '/tsconfig.spec.json', + stringifyContentPathRegex: '\\.(html|svg)$', + }, + ], + }, + transformIgnorePatterns: ['node_modules/(?!.*\\.mjs$)'], + snapshotSerializers: [ + 'jest-preset-angular/build/serializers/no-ng-attributes', + 'jest-preset-angular/build/serializers/ng-snapshot', + 'jest-preset-angular/build/serializers/html-comment', + ], +}; diff --git a/libs/ccf-body-ui/karma.conf.js b/libs/ccf-body-ui/karma.conf.js deleted file mode 100644 index 7b27003bf..000000000 --- a/libs/ccf-body-ui/karma.conf.js +++ /dev/null @@ -1,43 +0,0 @@ -// Karma configuration file, see link for more information -// https://karma-runner.github.io/1.0/config/configuration-file.html - -module.exports = function (config) { - config.set({ - basePath: '', - frameworks: ['jasmine', '@angular-devkit/build-angular'], - plugins: [ - require('karma-jasmine'), - require('karma-chrome-launcher'), - require('karma-jasmine-html-reporter'), - require('karma-coverage-istanbul-reporter'), - require('@angular-devkit/build-angular/plugins/karma'), - ], - client: { - clearContext: false, // leave Jasmine Spec Runner output visible in browser - }, - coverageIstanbulReporter: { - dir: require('path').join(__dirname, '../../coverage/ccf-body-ui'), - reports: ['html', 'lcovonly', 'text-summary'], - fixWebpackSourcePaths: true, - thresholds: { - emitWarning: false, - global: { - lines: 20, - }, - }, - }, - reporters: ['progress', 'kjhtml', 'coverage-istanbul'], - port: 9876, - colors: true, - logLevel: config.LOG_INFO, - browsers: ['ChromeHeadless' + (require('is-wsl') ? 'WSL' : '')], - singleRun: true, - - customLaunchers: { - ChromeHeadlessWSL: { - base: 'ChromeHeadless', - flags: ['--no-sandbox', '--disable-features=VizDisplayCompositor'], - }, - }, - }); -}; diff --git a/libs/ccf-body-ui/project.json b/libs/ccf-body-ui/project.json index be30474a9..0351b5d89 100644 --- a/libs/ccf-body-ui/project.json +++ b/libs/ccf-body-ui/project.json @@ -19,13 +19,10 @@ } }, "test": { - "executor": "@angular-devkit/build-angular:karma", + "executor": "@nx/jest:jest", + "outputs": ["{workspaceRoot}/coverage/{projectRoot}"], "options": { - "main": "libs/ccf-body-ui/src/test.ts", - "tsConfig": "libs/ccf-body-ui/tsconfig.spec.json", - "karmaConfig": "libs/ccf-body-ui/karma.conf.js", - "codeCoverage": true, - "codeCoverageExclude": ["**/src/test.ts", "**/*.module.ts"] + "jestConfig": "libs/ccf-body-ui/jest.config.ts" } }, "lint": { diff --git a/libs/ccf-body-ui/src/ccf-body-ui.spec.ts b/libs/ccf-body-ui/src/ccf-body-ui.spec.ts deleted file mode 100644 index 7c114a027..000000000 --- a/libs/ccf-body-ui/src/ccf-body-ui.spec.ts +++ /dev/null @@ -1,6 +0,0 @@ -describe('ccf-body-ui', () => { - // Temporary noop test - it('passes', () => { - expect(true).toBeTruthy(); - }); -}); diff --git a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.html b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.html new file mode 100644 index 000000000..d03820a75 --- /dev/null +++ b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.html @@ -0,0 +1 @@ + diff --git a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss new file mode 100644 index 000000000..e69de29bb diff --git a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.spec.ts b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.spec.ts new file mode 100644 index 000000000..3f758c940 --- /dev/null +++ b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.spec.ts @@ -0,0 +1,134 @@ +import { provideHttpClient } from '@angular/common/http'; +import { HttpTestingController, provideHttpClientTesting } from '@angular/common/http/testing'; +import { ErrorHandler } from '@angular/core'; +import { TestBed } from '@angular/core/testing'; +import { SpatialSceneNode } from '@hra-api/ng-client'; +import { render, screen } from '@testing-library/angular'; +import { BodyUI, NodeClickEvent } from '../body-ui'; +import { BodyUiComponent, XYZTriplet } from './body-ui.component'; +import { Subject } from 'rxjs'; + +jest.mock('../body-ui.ts', () => ({ + BodyUI: jest.fn().mockImplementation(() => ({ + deck: { + setProps: jest.fn(), + finalize: jest.fn(), + }, + initialize: jest.fn().mockResolvedValue(undefined), + finalize: jest.fn(), + setScene: jest.fn(), + setZoom: jest.fn(), + nodeClick$: new Subject(), + nodeHoverStart$: new Subject(), + nodeHoverStop$: new Subject(), + sceneRotation$: new Subject(), + nodeDrag$: new Subject(), + })), +})); + +describe('BodyUiComponent', () => { + const sampleSpatialSceneNode: SpatialSceneNode = {}; + const providers = [provideHttpClient(), provideHttpClientTesting()]; + + function getBodyUi(): BodyUI { + return jest.mocked(BodyUI).mock.results[0].value; + } + + beforeEach(() => { + jest.clearAllMocks(); + }); + + it('should render a canvas element', async () => { + await render(BodyUiComponent, { providers }); + + const canvasElement = screen.getByRole('img'); + + expect(canvasElement).toBeTruthy(); + expect(canvasElement.tagName.toLowerCase()).toBe('canvas'); + }); + + it('should set zoom according to the bounds', async () => { + const bounds: XYZTriplet = { x: 0, y: 0, z: 0 }; + const { + fixture: { componentInstance: component }, + } = await render(BodyUiComponent, { + providers, + inputs: { + bounds: bounds, + }, + }); + + component.zoomToBounds(bounds); + expect(getBodyUi().setZoom).toHaveBeenCalled(); + }); + + it('it should return array as it is when input is not string', async () => { + const scenes: SpatialSceneNode[] = []; + const { fixture } = await render(BodyUiComponent, { + providers, + inputs: { + scene: scenes, + }, + }); + + await fixture.whenStable(); + expect(getBodyUi().setScene).toHaveBeenCalledWith(scenes); + }); + + it('it fetch the scene data and return when a url is passed as scene input', async () => { + const URL = 'https://example.com'; + const { fixture } = await render(BodyUiComponent, { + providers, + inputs: { + scene: URL, + }, + }); + + const controller = TestBed.inject(HttpTestingController); + const req = controller.expectOne(URL); + req.flush([sampleSpatialSceneNode]); + + await fixture.whenStable(); + expect(getBodyUi().setScene).toHaveBeenCalledWith([sampleSpatialSceneNode]); + }); + + it('it should throw error if response is of wrong type', async () => { + const URL = 'https://example.com'; + const errorHandler = { handleError: jest.fn() }; + const { fixture } = await render(BodyUiComponent, { + providers: [...providers, { provide: ErrorHandler, useValue: errorHandler }], + inputs: { + scene: URL, + }, + }); + + const controller = TestBed.inject(HttpTestingController); + const req = controller.expectOne(URL); + req.flush('Error Data'); + + await fixture.whenStable(); + expect(getBodyUi().setScene).not.toHaveBeenCalledWith([sampleSpatialSceneNode]); + expect(errorHandler.handleError).toHaveBeenCalled(); + }); + + it('outputs should emit value', async () => { + const event: NodeClickEvent = { + node: { + name: 'test', + }, + ctrlClick: true, + }; + const nodeClick = jest.fn(); + const { fixture } = await render(BodyUiComponent, { + providers, + on: { + nodeClick, + }, + }); + await fixture.whenStable(); + + const nodeClick$ = getBodyUi().nodeClick$ as Subject; + nodeClick$.next(event); + expect(nodeClick).toHaveBeenCalledWith(event); + }); +}); diff --git a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts new file mode 100644 index 000000000..7e37328e4 --- /dev/null +++ b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts @@ -0,0 +1,220 @@ +import { HttpClient } from '@angular/common/http'; +import { + booleanAttribute, + Component, + computed, + effect, + ElementRef, + ErrorHandler, + inject, + input, + numberAttribute, + output, + OutputEmitterRef, + Signal, + viewChild, +} from '@angular/core'; +import { SpatialSceneNode } from '@hra-api/ng-client'; +import { derivedAsync } from 'ngxtension/derived-async'; +import { catchError, map, Observable, of, Subscription } from 'rxjs'; +import { z } from 'zod'; +import { BodyUI, NodeClickEvent, NodeDragEvent } from '../body-ui'; + +/** Interface for bounds */ +export interface XYZTriplet { + x: T; + y: T; + z: T; +} + +/** Type for setter methods of the BodyUI */ +type SetterMethods = keyof { + [P in keyof BodyUI as BodyUI[P] extends (v: ValueT) => void ? P : never]: BodyUI[P]; +}; + +/** Parses the input if it is a JSON String */ +function tryParseJson(value: unknown): unknown { + try { + if (typeof value === 'string') { + return JSON.parse(value); + } + } catch { + // Ignore errors + } + + return value; +} + +/** Utility function to use input data to set to relevant body ui setter */ +function connectInput( + bodyUi: Signal, + source: Signal, + setter: SetterMethods, +): void { + const value = source(); + if (value !== undefined) { + bodyUi()?.[setter](value as never); + } +} + +/** Utility function to use output data to set to relevant body ui subject */ +function connectOutput(out: OutputEmitterRef, source: Observable): Subscription { + return source.subscribe((value) => out.emit(value)); +} + +/** Zod for SPATIAL SCENE NODE */ +export const SPATIAL_SCENE_NODE = z + .object({}) + .passthrough() + .refine((obj): obj is SpatialSceneNode => true); + +/** Zod for SPATIAL SCENE NODE array */ +export const SPATIAL_SCENE_NODE_ARRAY = z.array(SPATIAL_SCENE_NODE); + +/** Preprocesses the scene input */ +const SCENE_INPUT = z.preprocess(tryParseJson, z.union([z.literal(''), z.string().url(), SPATIAL_SCENE_NODE_ARRAY])); +/** Bind scene input */ +const parseSceneInput = SCENE_INPUT.parse.bind(SCENE_INPUT); + +/** Preprocess the target input */ +const TARGET_INPUT = z.preprocess(tryParseJson, z.tuple([z.number(), z.number(), z.number()])); +/** Bind target input */ +const parseTargetInput = TARGET_INPUT.parse.bind(TARGET_INPUT); + +/** Preprocess the bounds input */ +const BOUNDS_INPUT = z.preprocess(tryParseJson, z.object({ x: z.number(), y: z.number(), z: z.number() })); + +/** Bind the bounds input */ +const parseBoundsInput = BOUNDS_INPUT.parse.bind(BOUNDS_INPUT); + +/** HRA Body UI Component */ +@Component({ + standalone: true, + imports: [], + selector: 'hra-body-ui', + templateUrl: './body-ui.component.html', + styleUrl: './body-ui.component.scss', +}) +export class BodyUiComponent { + /** Scene for the deck gl */ + readonly scene = input(undefined, { transform: parseSceneInput }); + + /** Rotation for the deck gl */ + readonly rotation = input(undefined, { transform: numberAttribute }); + /** Rotation X for the deck gl */ + readonly rotationX = input(undefined, { transform: numberAttribute }); + /** Zoom for the deck gl */ + readonly zoom = input(undefined, { transform: numberAttribute }); + /** Target for the deck gl */ + readonly target = input(undefined, { transform: parseTargetInput }); + /** Bounds for the deck gl */ + readonly bounds = input(undefined, { transform: parseBoundsInput }); + /** Camera for the deck gl */ + readonly camera = input(); + /** Flag for the interactive for deck gl */ + readonly interactive = input(true, { transform: booleanAttribute }); + + /** Output for rotation change */ + readonly rotationChange = output<[number, number]>(); + /** Output for node click */ + readonly nodeClick = output(); + /** Output for node drag */ + readonly nodeDrag = output(); + /** Output for node hover start */ + readonly nodeHoverStart = output(); + /** Output for node hover end */ + readonly nodeHoverStop = output(); + + /** Instance of HttpClient */ + private readonly http = inject(HttpClient); + /** Instance of Error Handler */ + private readonly errorHandler = inject(ErrorHandler); + + /** Instance of canvas element */ + private readonly canvas = viewChild.required>('canvas'); + /** Instance of BodyUI class */ + private readonly bodyUi = derivedAsync( + async () => { + const bodyUi = new BodyUI({ + id: 'bodyUI', + canvas: this.canvas().nativeElement, + zoom: 9.5, + target: [0, 0, 0], + rotation: 0, + minRotationX: -75, + maxRotationX: 75, + interactive: true, + camera: '', + }); + + await bodyUi.initialize(); + return bodyUi; + }, + { initialValue: undefined }, + ); + + /** Processed scene data for deck gl */ + private readonly sceneData = derivedAsync( + () => { + const value = this.scene(); + if (!value) { + return []; + } else if (typeof value !== 'string') { + return value; + } + + return this.http.get(value).pipe( + map((data) => SPATIAL_SCENE_NODE_ARRAY.parse(data)), + catchError((error) => { + this.errorHandler.handleError(error); + return of([]); + }), + ); + }, + { initialValue: [] }, + ); + + /** Returns the bounds zoom according to bounds input */ + private readonly boundsZoom = computed(() => { + const bounds = this.bounds(); + return bounds ? this.getBoundsZoom(bounds) : undefined; + }); + + /** Constructor for the component */ + constructor() { + effect(() => connectInput(this.bodyUi, this.sceneData, 'setScene')); + effect(() => connectInput(this.bodyUi, this.rotation, 'setRotation')); + effect(() => connectInput(this.bodyUi, this.rotationX, 'setRotationX')); + effect(() => connectInput(this.bodyUi, this.target, 'setTarget')); + effect(() => connectInput(this.bodyUi, this.boundsZoom, 'setZoom')); + + effect((onCleanup) => { + const bodyUi = this.bodyUi(); + if (bodyUi) { + const subscriptions = new Subscription(); + subscriptions.add(connectOutput(this.nodeClick, bodyUi.nodeClick$)); + subscriptions.add(connectOutput(this.nodeDrag, bodyUi.nodeDrag$)); + subscriptions.add(connectOutput(this.nodeHoverStart, bodyUi.nodeHoverStart$)); + subscriptions.add(connectOutput(this.nodeHoverStop, bodyUi.nodeHoverStop$)); + subscriptions.add(() => bodyUi.finalize()); + onCleanup(() => subscriptions.unsubscribe()); + } + }); + } + + /** Sets the deck gl zoom according to the provided bounds */ + zoomToBounds(bounds: XYZTriplet, margin = { x: 48, y: 48 }): void { + const zoom = this.getBoundsZoom(bounds, margin); + this.bodyUi()?.setZoom(zoom); + } + + /** Returns zoom value according to current bounds */ + private getBoundsZoom(bounds: XYZTriplet, margin = { x: 48, y: 48 }): number { + const { width, height } = this.canvas().nativeElement; + const pxRatio = window.devicePixelRatio; + return Math.min( + Math.log2((width - margin.x) / pxRatio / bounds.x), + Math.log2((height - margin.y) / pxRatio / bounds.y), + ); + } +} diff --git a/libs/ccf-body-ui/src/public-api.ts b/libs/ccf-body-ui/src/public-api.ts index f7d97d9e0..1af3a8201 100644 --- a/libs/ccf-body-ui/src/public-api.ts +++ b/libs/ccf-body-ui/src/public-api.ts @@ -7,6 +7,7 @@ */ export * from './lib/body-ui-layer'; export * from './lib/body-ui'; +export * from './lib/body-ui/body-ui.component'; export * from './lib/shared/spatial-scene-node'; export * from './lib/shared/ccf-spatial-jsonld'; diff --git a/libs/ccf-body-ui/src/test-setup.ts b/libs/ccf-body-ui/src/test-setup.ts new file mode 100644 index 000000000..82cfe9b70 --- /dev/null +++ b/libs/ccf-body-ui/src/test-setup.ts @@ -0,0 +1,9 @@ +// @ts-expect-error https://thymikee.github.io/jest-preset-angular/docs/getting-started/test-environment +globalThis.ngJest = { + testEnvironmentOptions: { + errorOnUnknownElements: true, + errorOnUnknownProperties: true, + }, +}; +import 'jest-preset-angular/setup-jest'; +import '@testing-library/jest-dom'; diff --git a/libs/ccf-body-ui/src/test.ts b/libs/ccf-body-ui/src/test.ts deleted file mode 100644 index e4e6ef81e..000000000 --- a/libs/ccf-body-ui/src/test.ts +++ /dev/null @@ -1,11 +0,0 @@ -// This file is required by karma.conf.js and loads recursively all the .spec and framework files - -import 'zone.js'; -import 'zone.js/testing'; -import { getTestBed } from '@angular/core/testing'; -import { BrowserDynamicTestingModule, platformBrowserDynamicTesting } from '@angular/platform-browser-dynamic/testing'; - -// First, initialize the Angular testing environment. -getTestBed().initTestEnvironment(BrowserDynamicTestingModule, platformBrowserDynamicTesting(), { - teardown: { destroyAfterEach: false }, -}); diff --git a/libs/ccf-body-ui/tsconfig.spec.json b/libs/ccf-body-ui/tsconfig.spec.json index 5b3e61112..7e19a99c6 100644 --- a/libs/ccf-body-ui/tsconfig.spec.json +++ b/libs/ccf-body-ui/tsconfig.spec.json @@ -2,8 +2,10 @@ "extends": "./tsconfig.json", "compilerOptions": { "outDir": "../../dist/out-tsc", - "types": ["jasmine", "node"] + "module": "commonjs", + "target": "es2016", + "types": ["jest", "node", "@testing-library/jest-dom"] }, - "files": ["src/test.ts"], - "include": ["**/*.spec.ts", "**/*.d.ts"] + "files": ["src/test-setup.ts"], + "include": ["jest.config.ts", "**/*.test.ts", "**/*.spec.ts", "**/*.d.ts"] } diff --git a/nx.json b/nx.json index 4d9ba0ef6..2327a2234 100644 --- a/nx.json +++ b/nx.json @@ -100,6 +100,11 @@ "cache": true, "dependsOn": ["^build"], "inputs": ["production", "^production"] + }, + "@angular-devkit/build-angular:application": { + "cache": true, + "dependsOn": ["^build"], + "inputs": ["production", "^production"] } }, "generators": { From df551b306cf8d74f588307b5929f3d4a1104901e Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 27 Sep 2024 16:27:50 -0400 Subject: [PATCH 27/50] Renaming and tweaks --- .../cde-visualization.component.html | 8 ++++---- .../cde-visualization.component.ts | 14 ++++++------- .../histogram/histogram.component.spec.ts | 16 +++++++-------- .../histogram/histogram.component.ts | 20 +++++++++---------- .../lib/components/violin/violin.component.ts | 12 +++++------ 5 files changed, 35 insertions(+), 35 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html index 2acdea8f8..4b19b0ec8 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html @@ -37,15 +37,15 @@ #visualization > - + diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts index 79d5002dd..a4e5ce23c 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts @@ -264,13 +264,13 @@ export class CdeVisualizationComponent { ); /** Computed distances between nodes */ - readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); + protected readonly distances = computed(() => this.computeDistances(), { equal: emptyArrayEquals }); /** Data for the histogram visualization */ - readonly data = computed(() => this.computeData(), { equal: emptyArrayEquals }); + protected readonly filteredDistances = computed(() => this.computeFilteredDistances(), { equal: emptyArrayEquals }); /** Colors for the histogram visualization */ - readonly colors = computed(() => this.computeColors(), { equal: emptyArrayEquals }); + protected readonly filteredColors = computed(() => this.computeFilteredColors(), { equal: emptyArrayEquals }); /** Setup component */ constructor() { @@ -314,7 +314,7 @@ export class CdeVisualizationComponent { } /** Compute distances between nodes based on edges */ - computeDistances(): DistanceEntry[] { + private computeDistances(): DistanceEntry[] { const nodes = this.loadedNodes(); const edges = this.loadedEdges(); if (nodes.length === 0 || edges.length === 0) { @@ -336,17 +336,17 @@ export class CdeVisualizationComponent { } /** Compute data for the violin visualization */ - computeData(): DistanceEntry[] { + private computeFilteredDistances(): DistanceEntry[] { const selection = new Set(this.cellTypesSelection()); if (selection.size === 0) { return []; } - return this.computeDistances().filter(({ type }) => selection.has(type)); + return this.distances().filter(({ type }) => selection.has(type)); } /** Compute colors for the violin visualization */ - computeColors(): string[] { + private computeFilteredColors(): string[] { return this.filteredCellTypes() .sort((a, b) => (a.name < b.name ? -1 : a.name === b.name ? 0 : 1)) .map(({ color }) => rgbToHex(color)); diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts b/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts index 331f7e161..e17024cd7 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts @@ -59,8 +59,8 @@ describe('HistogramComponent', () => { it('should render the histogram using vega', async () => { const { fixture } = await setup({ componentInputs: { - computedData: sampleData, - computedColors: [], + data: sampleData, + colors: [], filteredCellTypes: [], selectedCellType: sampleNodes[0][nodeTargetKey], }, @@ -74,8 +74,8 @@ describe('HistogramComponent', () => { it('should set empty data when input data is empty', async () => { const { fixture } = await setup({ componentInputs: { - computedData: [], - computedColors: [], + data: [], + colors: [], filteredCellTypes: [], selectedCellType: sampleNodes[0][nodeTargetKey], }, @@ -88,8 +88,8 @@ describe('HistogramComponent', () => { it('should download in the specified format', async () => { await setup({ componentInputs: { - computedData: [], - computedColors: [], + data: [], + colors: [], filteredCellTypes: [], selectedCellType: '', }, @@ -112,8 +112,8 @@ describe('HistogramComponent', () => { fixture: { componentInstance: instance }, } = await setup({ componentInputs: { - computedData: [], - computedColors: [], + data: [], + colors: [], filteredCellTypes: [], selectedCellType: '', }, diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts b/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts index 7cc4ad4a5..587e6910e 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.ts @@ -35,7 +35,7 @@ import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-la import * as HISTOGRAM_SPEC from './histogram.vl.json'; interface UpdateColorData { - type: CellTypeEntry; + entry: CellTypeEntry; color: Rgb; } @@ -138,10 +138,10 @@ const DYNAMIC_COLOR_RANGE = Array(DYNAMIC_COLOR_RANGE_LENGTH) }) export class HistogramComponent { /** Data for the violin visualization */ - readonly computedData = input.required(); + readonly data = input.required(); /** Colors for the violin visualization */ - readonly computedColors = input.required(); + readonly colors = input.required(); readonly filteredCellTypes = input.required(); @@ -162,6 +162,9 @@ export class HistogramComponent { /** Label for the total cell type */ protected readonly totalCellTypeLabel = ALL_CELLS_TYPE; + /** Color for the total cell type */ + protected readonly totalCellTypeColor = signal([0, 0, 0], { equal: colorEquals }); + /** Reference to the document object */ private readonly document = inject(DOCUMENT); @@ -180,10 +183,10 @@ export class HistogramComponent { readonly updateColor = output(); /** Effect for updating view data */ - protected readonly viewDataRef = effect(() => this.view()?.data('data', this.computedData()).run()); + protected readonly viewDataRef = effect(() => this.view()?.data('data', this.data()).run()); /** Effect for updating view colors */ - protected readonly viewColorsRef = effect(() => this.view()?.signal('colors', this.computedColors()).run()); + protected readonly viewColorsRef = effect(() => this.view()?.signal('colors', this.colors()).run()); /** Effect for creating the Vega view */ protected readonly viewCreateRef = effect( @@ -214,8 +217,8 @@ export class HistogramComponent { draft.config.padding.right = EXPORT_IMAGE_PADDING; draft.config.padding.left = EXPORT_IMAGE_PADDING; draft.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; - draft.data.values = this.computedData(); - draft.encoding.color.scale.range = this.computedColors(); + draft.data.values = this.data(); + draft.encoding.color.scale.range = this.colors(); }); const el = this.renderer.createElement('div'); @@ -234,9 +237,6 @@ export class HistogramComponent { await Promise.all(loadPromises); } - /** Color for the total cell type */ - protected readonly totalCellTypeColor = signal([0, 0, 0], { equal: colorEquals }); - /** Reset the color of the total cell type */ resetAllCellsColor(): void { this.totalCellTypeColor.set([0, 0, 0]); diff --git a/libs/cde-visualization/src/lib/components/violin/violin.component.ts b/libs/cde-visualization/src/lib/components/violin/violin.component.ts index 1447c232a..e076480e6 100644 --- a/libs/cde-visualization/src/lib/components/violin/violin.component.ts +++ b/libs/cde-visualization/src/lib/components/violin/violin.component.ts @@ -124,10 +124,10 @@ export class ViolinComponent { infoOpen = false; /** Data for the violin visualization */ - readonly computedData = input.required(); + readonly data = input.required(); /** Colors for the violin visualization */ - readonly computedColors = input.required(); + readonly colors = input.required(); /** Reference to the document object */ private readonly document = inject(DOCUMENT); @@ -145,11 +145,11 @@ export class ViolinComponent { private readonly view = signal(undefined); /** Effect for updating view data */ - protected readonly viewDataRef = effect(() => this.view()?.data('data', this.computedData()).run()); + protected readonly viewDataRef = effect(() => this.view()?.data('data', this.data()).run()); /** Effect for updating view colors */ protected readonly viewColorsRef = effect(() => { - this.view()?.signal('colors', this.computedColors()).run(); + this.view()?.signal('colors', this.colors()).run(); this.view()?.resize(); }); @@ -184,7 +184,7 @@ export class ViolinComponent { for (const layer of draft.spec.layer) { if (layer.encoding.color.legend === null) { layer.encoding.color.legend = EXPORT_IMAGE_LEGEND_CONFIG; - layer.encoding.color.scale = { range: this.computedColors() }; + layer.encoding.color.scale = { range: this.colors() }; } } draft.spec.height = EXPORT_IMAGE_HEIGHT; @@ -192,7 +192,7 @@ export class ViolinComponent { draft.config.padding.top = EXPORT_IMAGE_PADDING; draft.config.padding.right = EXPORT_IMAGE_PADDING; draft.config.padding.left = EXPORT_IMAGE_PADDING; - draft.data.values = this.computedData(); + draft.data.values = this.data(); }); const el = this.renderer.createElement('div'); From e99f0624c0126925e5061d884b0b8358e8f6375d Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 27 Sep 2024 16:31:01 -0400 Subject: [PATCH 28/50] Renaming --- .../lib/components/histogram/histogram.component.html | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.html b/libs/cde-visualization/src/lib/components/histogram/histogram.component.html index 7529e405c..220768bf5 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.html +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.html @@ -58,13 +58,13 @@ (colorPickerOpen)="colorPicker.set($event)" > - @for (type of filteredCellTypes(); track type.name) { + @for (entry of filteredCellTypes(); track entry.name) { } From 03d1f507aea849067250593806cad47572e8bb01 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Fri, 27 Sep 2024 18:36:17 -0400 Subject: [PATCH 29/50] Set up design system theming --- ...te-visualization-page.component.theme.scss | 164 +++++++++--------- apps/cde-ui/src/styles.scss | 81 ++++----- 2 files changed, 123 insertions(+), 122 deletions(-) diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index fb5bf0bee..7a8042a87 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -1,95 +1,95 @@ -@use 'sass:map'; -@use '@angular/material' as mat; -@use '../../../styles/constants/palettes' as palettes; -@use '../../../styles/breakpoints' as breakpoints; - -$gray-palette: map.get(palettes.$palettes, 'gray'); -$blue-palette: map.get(palettes.$palettes, 'blue'); - -@mixin color($theme) { - cde-create-visualization-page { - h1, - h2, - h3, - h4 { - color: mat.get-theme-color($theme, accent, darker); - } - - .page-nav .nav { - a { - color: mat.get-theme-color($theme, primary, 700); - } +// @use 'sass:map'; +// @use '@angular/material' as mat; +// @use '../../../styles/constants/palettes' as palettes; +// @use '../../../styles/breakpoints' as breakpoints; + +// $gray-palette: map.get(palettes.$palettes, 'gray'); +// $blue-palette: map.get(palettes.$palettes, 'blue'); + +// @mixin color($theme) { +cde-create-visualization-page { + h1, + h2, + h3, + h4 { + // color: mat.get-theme-color($theme, accent, darker); + } - mat-icon, - span { - color: map.get($gray-palette, 700); - } + .page-nav .nav { + a { + color: var(--sys-on-background); } - .card { - background-color: white; + mat-icon, + span { + // color: map.get($gray-palette, 700); + } + } - .header { - .step-number { - background-color: map.get($blue-palette, 800); - color: white; - } + .card { + background-color: white; - .use-template { - color: mat.get-theme-color($theme, primary, 700); - } + .header { + .step-number { + // background-color: map.get($blue-palette, 800); + color: white; } - } - .data-upload { - td { - color: map.get($gray-palette, 700); + .use-template { + // color: mat.get-theme-color($theme, primary, 700); } } + } - .color-config { - mat-button-toggle-group { - border-color: map.get($gray-palette, 600); - --mat-standard-button-toggle-text-color: #{mat.get-theme-color($theme, accent, darker)}; - --mat-standard-button-toggle-selected-state-background-color: rgb( - from #{mat.get-theme-color($theme, primary, 600)} r g b / 0.24 - ); - } + .data-upload { + td { + // color: map.get($gray-palette, 700); + } + } - mat-button-toggle { - &:first-child { - border-color: map.get($gray-palette, 600); - } - } + .color-config { + mat-button-toggle-group { + // border-color: map.get($gray-palette, 600); + // --mat-standard-button-toggle-text-color: #{mat.get-theme-color($theme, accent, darker)}; + // --mat-standard-button-toggle-selected-state-background-color: rgb( + // from #{mat.get-theme-color($theme, primary, 600)} r g b / 0.24 + // ); + } - .use-template { - color: mat.get-theme-color($theme, primary, 700); + mat-button-toggle { + &:first-child { + // border-color: map.get($gray-palette, 600); } } - .metadata { - --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; + .use-template { + // color: mat.get-theme-color($theme, primary, 700); } } - .info-tooltip-panel { - background-color: white; - color: map.get($gray-palette, 600); + .metadata { + // --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; } +} - mat-form-field { - --mdc-filled-text-field-container-color: #{map.get($blue-palette, 500)}; - --mdc-filled-text-field-focus-label-text-color: #{mat.get-theme-color($theme, primary, darker)}; - --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; - --mat-select-enabled-arrow-color: #{map.get($gray-palette, 700)}; - --mat-select-focused-arrow-color: #{mat.get-theme-color($theme, primary, darker)}; - } +.info-tooltip-panel { + background-color: white; + // color: map.get($gray-palette, 600); +} + +mat-form-field { + // --mdc-filled-text-field-container-color: #{map.get($blue-palette, 500)}; + // --mdc-filled-text-field-focus-label-text-color: #{mat.get-theme-color($theme, primary, darker)}; + // --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; + // --mat-select-enabled-arrow-color: #{map.get($gray-palette, 700)}; + // --mat-select-focused-arrow-color: #{mat.get-theme-color($theme, primary, darker)}; + // } .select-panel { - --mat-option-selected-state-layer-color: #{mat.get-theme-color($theme, accent, lighter)}; - --mat-option-label-text-color: #{map.get($gray-palette, 700)}; - --mat-option-selected-state-label-text-color: #{mat.get-theme-color($theme, accent, darker)}; - --mat-minimal-pseudo-checkbox-selected-checkmark-color: #{mat.get-theme-color($theme, primary, 700)}; + // --mat-option-selected-state-layer-color: #{mat.get-theme-color($theme, accent, lighter)}; + // --mat-option-label-text-color: #{map.get($gray-palette, 700)}; + // --mat-option-selected-state-label-text-color: #{mat.get-theme-color($theme, accent, darker)}; + // --mat-minimal-pseudo-checkbox-selected-checkmark-color: #{mat.get-theme-color($theme, primary, 700)}; } .visualize-notification { @@ -98,23 +98,23 @@ $blue-palette: map.get(palettes.$palettes, 'blue'); .upload-errors { .error-message { - color: #{mat.get-theme-color($theme, primary, darker)}; + // color: #{mat.get-theme-color($theme, primary, darker)}; } .error-instructions { - color: #{map.get($gray-palette, 700)}; + // color: #{map.get($gray-palette, 700)}; } } -} + // } -@mixin typography($theme) { -} + // @mixin typography($theme) { + // } -@mixin theme($theme) { - @if mat.theme-has($theme, color) { - @include color($theme); - } + // @mixin theme($theme) { + // @if mat.theme-has($theme, color) { + // @include color($theme); + // } - @if mat.theme-has($theme, typography) { - @include typography($theme); - } + // @if mat.theme-has($theme, typography) { + // @include typography($theme); + // } } diff --git a/apps/cde-ui/src/styles.scss b/apps/cde-ui/src/styles.scss index d8ac7521c..15d46c199 100644 --- a/apps/cde-ui/src/styles.scss +++ b/apps/cde-ui/src/styles.scss @@ -1,16 +1,17 @@ -@use './styles/cta' as cta; -@use './styles/global/resets'; -@use './styles/global/fonts'; -@use './styles/material-theming'; +// @use './styles/cta' as cta; +// @use './styles/global/resets'; +// @use './styles/global/fonts'; +// @use './styles/material-theming'; @use 'light-theme'; @use 'theming'; +@use '../src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss' as create-visualization; + +@mixin theme($theme) { + @include create-visualization.theme($theme); +} // TODO Update and switch to design system theming -// html { -// @include theming.theme(light-theme.$theme); -// } -// Only enabled for the footer at the moment -hra-footer { +html { @include theming.theme(light-theme.$theme); } @@ -33,43 +34,43 @@ a { text-decoration: none; } -.cta-filled { - @include cta.filledDefault(); +// .cta-filled { +// @include cta.filledDefault(); - &:hover { - @include cta.filledHover(); - } +// &:hover { +// @include cta.filledHover(); +// } - &:active { - @include cta.filledActive(); - } +// &:active { +// @include cta.filledActive(); +// } - &:focus-visible { - --mdc-filled-button-label-text-color: rgba(32, 30, 61, 1); - color: var(--mdc-filled-button-label-text-color); - } +// &:focus-visible { +// --mdc-filled-button-label-text-color: rgba(32, 30, 61, 1); +// color: var(--mdc-filled-button-label-text-color); +// } - &:focus-visible::after { - @include cta.filledFocus(); - } -} +// &:focus-visible::after { +// @include cta.filledFocus(); +// } +// } -.cta-flat { - @include cta.flatDefault(); +// .cta-flat { +// @include cta.flatDefault(); - &:hover { - @include cta.flatHover(); - } +// &:hover { +// @include cta.flatHover(); +// } - &:active { - @include cta.flatActive(); - } +// &:active { +// @include cta.flatActive(); +// } - &:focus-visible { - @include cta.flatFocus(); - } -} +// &:focus-visible { +// @include cta.flatFocus(); +// } +// } -.selected { - box-shadow: 0 -2px 0 #e00d3a inset; -} +// .selected { +// box-shadow: 0 -2px 0 #e00d3a inset; +// } From 7b5e71dfba8cf0f8f7e5f6874dcdde080450af57 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Mon, 30 Sep 2024 12:46:58 -0400 Subject: [PATCH 30/50] update cell type component --- libs/cde-visualization/src/index.ts | 9 ++- .../cell-types/cell-types.component.html | 77 ++++++++++++------- .../cell-types/cell-types.component.ts | 6 +- libs/cde-visualization/src/main.ts | 8 -- 4 files changed, 64 insertions(+), 36 deletions(-) delete mode 100644 libs/cde-visualization/src/main.ts diff --git a/libs/cde-visualization/src/index.ts b/libs/cde-visualization/src/index.ts index 7c8c4622e..adda4deb5 100644 --- a/libs/cde-visualization/src/index.ts +++ b/libs/cde-visualization/src/index.ts @@ -1,6 +1,7 @@ import { provideHttpClient } from '@angular/common/http'; import { importProvidersFrom } from '@angular/core'; import { provideAnimations } from '@angular/platform-browser/animations'; +import { provideDesignSystem } from '@hra-ui/design-system'; import { provideScrolling } from '@hra-ui/design-system/scrolling'; import { InputProps, createCustomElement } from '@hra-ui/webcomponents'; import { ColorPickerModule } from 'ngx-color-picker'; @@ -30,5 +31,11 @@ export type CdeVisualizationElementConstructor = Awaited Cell Types - info - -
- Show/hide specific cell types in the visualizations by clicking the checkboxes. Update individual cell type - visualization colors by clicking the cell type's color legend button. Download a color map CSV file of the current - cell types and HEX codes. -
- + + + + + + + + + + + + + + + + + -
Total Cell Types diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts index 8ab3d9a51..0442f6643 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts @@ -18,15 +18,17 @@ import { MatButtonModule } from '@angular/material/button'; import { MatCheckboxModule } from '@angular/material/checkbox'; import { MatIconModule } from '@angular/material/icon'; import { MatListModule } from '@angular/material/list'; +import { MatMenuModule } from '@angular/material/menu'; import { MatSort, MatSortModule } from '@angular/material/sort'; import { MatTableDataSource, MatTableModule } from '@angular/material/table'; +import { Rgb } from '@hra-ui/design-system/color-picker'; import { ScrollingModule } from '@hra-ui/design-system/scrolling'; import { ColorPickerModule } from 'ngx-color-picker'; import { map } from 'rxjs'; import { CellTypeEntry } from '../../models/cell-type'; -import { Rgb } from '@hra-ui/design-system/color-picker'; import { TOOLTIP_POSITION_RIGHT_SIDE } from '../../shared/tooltip-position'; import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-label.component'; +import { IconButtonSizeDirective } from '@hra-ui/design-system/icon-button'; /** * Cell Type Component @@ -46,6 +48,8 @@ import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-la OverlayModule, ColorPickerLabelComponent, ScrollingModule, + MatMenuModule, + IconButtonSizeDirective, ], templateUrl: './cell-types.component.html', styleUrl: './cell-types.component.scss', diff --git a/libs/cde-visualization/src/main.ts b/libs/cde-visualization/src/main.ts deleted file mode 100644 index 0b105e070..000000000 --- a/libs/cde-visualization/src/main.ts +++ /dev/null @@ -1,8 +0,0 @@ -import { provideHttpClient } from '@angular/common/http'; -import { provideScrolling } from '@hra-ui/design-system/scrolling'; -import { createCustomElement } from '@hra-ui/webcomponents'; -import { CdeVisualizationComponent } from './lib/cde-visualization/cde-visualization.component'; - -createCustomElement('cde-visualization-wc', CdeVisualizationComponent, { - providers: [provideHttpClient(), provideScrolling()], -}); From 946d2a5d8ff798f646c6b5f4dcb0e7b09e67e2d6 Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Mon, 30 Sep 2024 13:58:03 -0400 Subject: [PATCH 31/50] build(body-ui): :construction_worker: Update build executor (#747) --- .vscode/settings.json | 3 ++- apps/body-ui/project.json | 31 ++++++++++++++++++------------- 2 files changed, 20 insertions(+), 14 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index e3a41041c..8a2aa6c80 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -11,6 +11,7 @@ "ftu-ui", "services", "ccf-organ-info", - "design-system" + "design-system", + "body-ui" ] } diff --git a/apps/body-ui/project.json b/apps/body-ui/project.json index 1409258f4..af9ade3f9 100644 --- a/apps/body-ui/project.json +++ b/apps/body-ui/project.json @@ -7,13 +7,15 @@ "tags": ["type:app"], "targets": { "build": { - "executor": "@angular-devkit/build-angular:browser-esbuild", - "outputs": ["{options.outputPath}"], + "executor": "@nx/angular:application", + "outputs": ["{options.outputPath.base}"], "options": { - "buildOptimizer": false, - "outputPath": "dist/apps/body-ui", + "outputPath": { + "base": "dist/apps/body-ui", + "browser": "." + }, "index": "apps/body-ui/src/index.html", - "main": "apps/body-ui/src/main.ts", + "browser": "apps/body-ui/src/main.ts", "polyfills": ["zone.js"], "tsConfig": "apps/body-ui/tsconfig.app.json", "inlineStyleLanguage": "scss", @@ -24,7 +26,12 @@ } ], "styles": ["apps/body-ui/src/styles.scss"], - "scripts": [] + "scripts": [], + "define": { + "define": "undefined" + }, + "outputHashing": "none", + "allowedCommonJsDependencies": ["*"] }, "configurations": { "production": { @@ -32,16 +39,15 @@ "budgets": [ { "type": "initial", - "maximumWarning": "500kb", - "maximumError": "1mb" + "maximumWarning": "1mb", + "maximumError": "2mb" }, { "type": "anyComponentStyle", "maximumWarning": "2kb", "maximumError": "4kb" } - ], - "outputHashing": "all" + ] }, "development": { "baseHref": "/", @@ -50,8 +56,7 @@ "sourceMap": true }, "staging": { - "baseHref": "/ui--staging/body-ui/", - "outputHashing": "none" + "baseHref": "/ui--staging/body-ui/" }, "preview": { "baseHref": "/apps/body-ui/", @@ -64,7 +69,7 @@ "defaultConfiguration": "production" }, "serve": { - "executor": "@angular-devkit/build-angular:dev-server", + "executor": "@nx/angular:dev-server", "configurations": { "production": { "buildTarget": "body-ui:build:production" From 5f5899d4072fc547d0e66a38c8862bf3df8a44f5 Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Mon, 30 Sep 2024 15:05:55 -0400 Subject: [PATCH 32/50] refactor(body-ui): Tweak body ui styles --- libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss | 3 +++ libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts | 2 ++ 2 files changed, 5 insertions(+) diff --git a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss index e69de29bb..5d4e87f30 100644 --- a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss +++ b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.scss @@ -0,0 +1,3 @@ +:host { + display: block; +} diff --git a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts index 7e37328e4..ba7d68585 100644 --- a/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts +++ b/libs/ccf-body-ui/src/lib/body-ui/body-ui.component.ts @@ -13,6 +13,7 @@ import { OutputEmitterRef, Signal, viewChild, + ViewEncapsulation, } from '@angular/core'; import { SpatialSceneNode } from '@hra-api/ng-client'; import { derivedAsync } from 'ngxtension/derived-async'; @@ -94,6 +95,7 @@ const parseBoundsInput = BOUNDS_INPUT.parse.bind(BOUNDS_INPUT); selector: 'hra-body-ui', templateUrl: './body-ui.component.html', styleUrl: './body-ui.component.scss', + encapsulation: ViewEncapsulation.ShadowDom, }) export class BodyUiComponent { /** Scene for the deck gl */ From 55a66309711c38c3f94838805352231f447b4d6c Mon Sep 17 00:00:00 2001 From: Bhushan Khope <53601863+bhushankhope@users.noreply.github.com> Date: Mon, 30 Sep 2024 15:06:20 -0400 Subject: [PATCH 33/50] create menu size directive (#749) --- .../src/lib/directives/menu-size.directive.ts | 36 ++++++++++++++++ .../lib/menu-demo/menu-demo.component.html | 4 +- .../src/lib/menu-demo/menu-demo.component.ts | 3 +- .../menu-styles/menu-styles.component.scss | 41 ++++++++++--------- 4 files changed, 61 insertions(+), 23 deletions(-) create mode 100644 libs/design-system/menu/src/lib/directives/menu-size.directive.ts diff --git a/libs/design-system/menu/src/lib/directives/menu-size.directive.ts b/libs/design-system/menu/src/lib/directives/menu-size.directive.ts new file mode 100644 index 000000000..828cc1041 --- /dev/null +++ b/libs/design-system/menu/src/lib/directives/menu-size.directive.ts @@ -0,0 +1,36 @@ +import { Directive, effect, inject, input } from '@angular/core'; +import { MatMenu } from '@angular/material/menu'; + +/** Type for Menu Sizes */ +export type MenuSize = 'small' | 'medium' | 'large'; + +/** Menu Size Directive */ +@Directive({ + selector: '[hraMenuSize]', + standalone: true, +}) +export class MenuSizeDirective { + /** Size of menu to use */ + readonly size = input('medium', { alias: 'hraMenuSize' }); + + /** Instance of Mat Menu */ + protected readonly menu = inject(MatMenu); + + /** Cleanup the previous panel class and assign the current */ + constructor() { + effect((onCleanup) => { + const { menu } = this; + const cls = ` ${this.size()}`; + menu.panelClass = this.getPanelClass() + cls; + + onCleanup(() => (menu.panelClass = this.getPanelClass().replace(cls, ''))); + }); + } + + /** Utility function to get the panel class because they dont have the getter for panelClass in mat menu */ + private getPanelClass(): string { + // WARNING: Pulling from internals since panelClass doesn't have a getter. + // May break in the future! + return (this.menu as unknown as { _previousPanelClass: string })._previousPanelClass; + } +} diff --git a/libs/design-system/menu/src/lib/menu-demo/menu-demo.component.html b/libs/design-system/menu/src/lib/menu-demo/menu-demo.component.html index 6fa777c8c..e2390144f 100644 --- a/libs/design-system/menu/src/lib/menu-demo/menu-demo.component.html +++ b/libs/design-system/menu/src/lib/menu-demo/menu-demo.component.html @@ -7,7 +7,7 @@ more_vert - + @for (option of menuOptions(); track option) { @if (option.expandedOptions) { - + - + - +
} @else { - +
-
- Home - chevron_right - Create Visualization -
+ +

Create a Cell Distance Visualization

- 1 + Upload Data [cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

- Use the template to format single-cell spatial feature tables for exploration. The cell type column can - include damage and proliferation markers. -

+
- Template - +

Required Columns Supported Format
@@ -89,7 +88,7 @@

- 2 + Organize Data [cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

Verify column headers and edit as needed. Select optional column headers.

+

@@ -119,7 +118,13 @@

X Axis - + @for (option of dataHeaders; track option) { {{ option }} } @@ -128,7 +133,13 @@

Y Axis - + @for (option of dataHeaders; track option) { {{ option }} } @@ -137,7 +148,13 @@

Cell Type - + @for (option of dataHeaders; track option) { {{ option }} } @@ -148,9 +165,7 @@

@if (columnErrorActionMessage) {
error -
- {{ columnErrorActionMessage }} -
+ {{ columnErrorActionMessage }}
} @@ -159,7 +174,13 @@

Z Axis - + @for (option of dataHeaders; track option) { {{ option }} } @@ -168,7 +189,13 @@

Cell Ontology ID - + @for (option of dataHeaders; track option) { {{ option }} } @@ -179,7 +206,7 @@

- 3 +
Configure Parameters
[cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

Anchor Cell Type

-

- The anchor cell type represents the cell type to which the nearest cell distance distributions should be - computed and visualized. Euclidian distance is used to compute the distance between two cells. -

-

- “Endothelial” is used as the default anchor cell type. If an “Endothelial” cell label is not present, the - first listed cell type label is used as the anchor cell type. -

-

Distance Threshold (µm)

-

Configure the distance threshold to modify visualizations for analysis.

-

Pixel Size (µm/pixel)

-

- Pixel size is used as a scaling factor to convert coordinates to micrometers. Use 1 if coordinates are already - in micrometers. -

+

@@ -222,6 +234,7 @@

Anchor Cell Type

- 4 +
Optional: Add Metadata
[cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

- Information in these fields will not change the visualization output. Metadata may be helpful for taking - screenshots of the uploaded data and resulting visualizations in the Visualization App. -

+

@@ -298,7 +308,13 @@

Organ - + @for (organ of organs(); track organ) { {{ organ.label | titlecase }} } @@ -307,7 +323,13 @@

Sex - + Male Female @@ -326,7 +348,7 @@

- 5 +
Optional: Configure Colors
[cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

- Use default colors or customize the visualization by uploading a preferred color map CSV file. Cell type - colors may be changed individually while exploring the visualization in the Visualization App. -

+

- - Use Default Colors - Upload Color Map + + Use Default Colors + Upload Color Map @if (useCustomColorMap) { @@ -405,7 +429,7 @@

- 6 +
Visualize Cell Distance Data
[cdkConnectedOverlayViewportMargin]="8" [cdkConnectedOverlayPush]="true" > -

Data on the Create Visualization page cannot be modified after a visualization is generated.

+

@@ -439,14 +463,14 @@

diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index 7589a5512..8750d560d 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -1,5 +1,3 @@ -@use '../../../styles/breakpoints' as breakpoints; - :host { display: block; min-width: 545px; @@ -15,30 +13,22 @@ padding: 3rem 1rem 6rem; gap: 3rem; align-items: center; - - @include breakpoints.breakpoint('large', 'x-large', 'xx-large', 'xxx-large') { - max-width: 53.5rem; - align-items: flex-start; - padding: 3rem 0rem 6rem; - } + max-width: 53.5rem; + align-items: flex-start; + padding: 3rem 0rem 6rem; } .page-nav { - margin-bottom: -0.6rem; - width: 100%; + margin-bottom: -0.5rem; .nav { - display: flex; - align-items: center; margin-bottom: 1.5rem; - - & > :not(mat-icon) { - padding: 0.375rem 0.5rem; - } } .title { margin: 0; + font: var(--sys-display-small); + letter-spacing: var(--sys-display-small-tracking); } } @@ -53,25 +43,20 @@ display: flex; align-items: center; height: 2.5rem; - margin-bottom: 0; + margin: 0; .step-number { - display: flex; - width: 2rem; - height: 2rem; - border-radius: 50%; - justify-content: center; - align-items: center; margin-right: 0.75rem; - font-size: 1rem; } .card-title { margin-right: 0.75rem; + font: var(--sys-title-large); } .info { margin: 0.25rem; + cursor: pointer; } } } @@ -86,7 +71,8 @@ th, td { - font-weight: 500; + font: var(--sys-label-large); + font-weight: var(--sys-label-large-weight); padding-left: 1rem; text-align: left; min-width: 216px; @@ -98,14 +84,6 @@ } } - .use-template { - --mdc-text-button-label-text-size: 14px; - --mat-text-button-with-icon-horizontal-padding: 1rem; - --mdc-text-button-label-text-tracking: 0.02em; - --mat-text-button-icon-offset: 0.75rem; - --mdc-text-button-container-height: 2.5rem; - } - .data-upload { display: grid; grid: @@ -126,6 +104,7 @@ display: grid; grid: 'subheader subheader'; column-gap: 1.5rem; + font: var(--sys-label-large); } .required-headers { @@ -135,26 +114,6 @@ .subheader { grid-area: subheader; } - - .error { - display: flex; - align-items: center; - gap: 0.5rem; - margin-bottom: 2rem; - background-color: rgb(from #ffdcc4 r g b / 0.8); - padding: 0.5rem 0.75rem; - border-radius: 0.25rem; - - .alert { - color: #bc4f00; - } - - .error-messages { - display: flex; - flex-direction: column; - color: #2f1400; - } - } } .parameters { @@ -209,9 +168,6 @@ mat-button-toggle-group { grid-area: toggle; - --mat-standard-button-toggle-label-text-size: 1rem; - --mat-standard-button-toggle-height: 2.5rem; - --mat-standard-button-toggle-label-text-weight: 500; mat-button-toggle { width: 50%; @@ -230,39 +186,9 @@ } .visualize { - .visualize-notification { - display: flex; - align-items: center; - gap: 0.5rem; - margin: 2rem 0; - background-color: rgb(from #ffdcc4 r g b / 0.8); - padding: 0.5rem 0.75rem; - border-radius: 0.25rem; - - .alert { - color: #bc4f00; - } - - .span { - display: flex; - flex-direction: column; - color: #2f1400; - } - } - .visualize-button { - display: flex; - --mdc-filled-button-label-text-size: 1rem; - --mat-filled-button-horizontal-padding: 1.5rem; - --mdc-filled-button-label-text-tracking: 0.02em; - --mat-filled-button-icon-spacing: 0.75rem; - --mat-filled-button-icon-offset: -0.375rem; - margin-top: 2rem; - mat-icon { - font-size: 1.5rem; - height: 1.5rem; - width: 1.5rem; + margin-left: 0.25rem; } } } @@ -270,13 +196,6 @@ ::ng-deep mat-form-field { margin: 1rem 0; - --mat-form-field-container-height: 3rem; - --mat-form-field-filled-with-label-container-padding-top: 1.25rem; - --mat-form-field-filled-with-label-container-padding-bottom: 0.25rem; - --mat-form-field-container-text-size: 14px; - --mat-form-field-container-text-line-height: 21px; - --mdc-filled-text-field-label-text-size: 14px; - --mdc-filled-text-field-label-text-weight: 500; .mdc-floating-label { line-height: 18px !important; @@ -292,27 +211,20 @@ } } -::ng-deep .info-tooltip-panel { - display: flex; - flex-direction: column; - max-width: 28rem; - min-width: 21rem; - padding: 0.75rem 1rem; - box-shadow: 0 0.3125rem 1rem 0 #201e3d3d; - border-radius: 0.5rem; - - p:last-child { - margin: 0; - } +::ng-deep .select-panel { + font: var(--sys-label-large); + // border-radius: 0.5rem !important; + // box-shadow: 0 5px 0.25rem 0 #201e3d29 !important; + // padding: 1rem 0 !important; } -::ng-deep .select-panel { - --mat-option-label-text-size: 1rem; - --mat-option-label-text-line-height: 1.5rem; - --mat-option-label-text-weight: 500; - --mat-option-label-text-font: Metropolis; - --mat-option-label-text-tracking: normal; - border-radius: 0.5rem !important; - box-shadow: 0 5px 0.25rem 0 #201e3d29 !important; - padding: 1rem 0 !important; +.visualize-notification, +.error { + display: flex; + align-items: center; + gap: 0.5rem; + margin: 2rem 0; + padding: 0.5rem 0.75rem; + border-radius: 0.25rem; + font: var(--sys-label-large); } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index 7a8042a87..4ce4daccb 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -1,120 +1,49 @@ -// @use 'sass:map'; -// @use '@angular/material' as mat; -// @use '../../../styles/constants/palettes' as palettes; -// @use '../../../styles/breakpoints' as breakpoints; - -// $gray-palette: map.get(palettes.$palettes, 'gray'); -// $blue-palette: map.get(palettes.$palettes, 'blue'); - -// @mixin color($theme) { cde-create-visualization-page { - h1, - h2, - h3, - h4 { - // color: mat.get-theme-color($theme, accent, darker); - } - - .page-nav .nav { - a { - color: var(--sys-on-background); - } - - mat-icon, - span { - // color: map.get($gray-palette, 700); + .page-nav { + .title { + color: var(--sys-secondary); } } .card { - background-color: white; - - .header { - .step-number { - // background-color: map.get($blue-palette, 800); - color: white; - } - - .use-template { - // color: mat.get-theme-color($theme, primary, 700); - } - } + background-color: var(--sys-surface-container-low); } .data-upload { + th { + color: var(--sys-secondary); + } td { - // color: map.get($gray-palette, 700); + color: var(--sys-primary); } } .color-config { mat-button-toggle-group { - // border-color: map.get($gray-palette, 600); - // --mat-standard-button-toggle-text-color: #{mat.get-theme-color($theme, accent, darker)}; - // --mat-standard-button-toggle-selected-state-background-color: rgb( - // from #{mat.get-theme-color($theme, primary, 600)} r g b / 0.24 - // ); + border-color: var(--sys-primary); + --mat-standard-button-toggle-text-color: var(--sys-secondary); + --mat-standard-button-toggle-selected-state-text-color: var(--sys-secondary); + --mat-standard-button-toggle-selected-state-background-color: rgb(from var(--sys-tertiary) r g b / 0.2); } mat-button-toggle { &:first-child { - // border-color: map.get($gray-palette, 600); + border-color: var(--sys-primary); } } - - .use-template { - // color: mat.get-theme-color($theme, primary, 700); - } - } - - .metadata { - // --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; } } .info-tooltip-panel { - background-color: white; - // color: map.get($gray-palette, 600); + background-color: var(--sys-on-primary); } -mat-form-field { - // --mdc-filled-text-field-container-color: #{map.get($blue-palette, 500)}; - // --mdc-filled-text-field-focus-label-text-color: #{mat.get-theme-color($theme, primary, darker)}; - // --mdc-filled-text-field-label-text-color: #{map.get($gray-palette, 700)}; - // --mat-select-enabled-arrow-color: #{map.get($gray-palette, 700)}; - // --mat-select-focused-arrow-color: #{mat.get-theme-color($theme, primary, darker)}; - // } - - .select-panel { - // --mat-option-selected-state-layer-color: #{mat.get-theme-color($theme, accent, lighter)}; - // --mat-option-label-text-color: #{map.get($gray-palette, 700)}; - // --mat-option-selected-state-label-text-color: #{mat.get-theme-color($theme, accent, darker)}; - // --mat-minimal-pseudo-checkbox-selected-checkmark-color: #{mat.get-theme-color($theme, primary, 700)}; - } - - .visualize-notification { - color: #4b4b5e; - } +.visualize-notification, +.error { + color: var(--sys-on-error-container); + background-color: rgb(from var(--sys-error-container) r g b / 0.8); - .upload-errors { - .error-message { - // color: #{mat.get-theme-color($theme, primary, darker)}; - } - .error-instructions { - // color: #{map.get($gray-palette, 700)}; - } + .alert { + color: var(--sys-error); } - // } - - // @mixin typography($theme) { - // } - - // @mixin theme($theme) { - // @if mat.theme-has($theme, color) { - // @include color($theme); - // } - - // @if mat.theme-has($theme, typography) { - // @include typography($theme); - // } } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index ecd10968b..c6b23ec2d 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -2,7 +2,6 @@ import { OverlayModule } from '@angular/cdk/overlay'; import { CommonModule } from '@angular/common'; import { ChangeDetectionStrategy, Component, inject, input, viewChild } from '@angular/core'; import { FormBuilder, ReactiveFormsModule, Validators } from '@angular/forms'; -import { MatButtonModule } from '@angular/material/button'; import { MatButtonToggleModule } from '@angular/material/button-toggle'; import { MatFormFieldModule } from '@angular/material/form-field'; import { MatIconModule } from '@angular/material/icon'; @@ -23,6 +22,8 @@ import { NodeTargetKey, TOOLTIP_POSITION_BELOW, } from '@hra-ui/cde-visualization'; +import { BreadcrumbsComponent } from '@hra-ui/design-system/breadcrumbs'; +import { ButtonModule } from '@hra-ui/design-system/button'; import { FooterComponent } from '@hra-ui/design-system/footer'; import { ParseError } from 'papaparse'; @@ -32,6 +33,8 @@ import { HeaderComponent } from '../../components/header/header.component'; import { VisualizationDataService } from '../../services/visualization-data-service/visualization-data.service'; import { validateInteger } from '../../shared/form-validators/is-integer'; import { OrganEntry } from '../../shared/resolvers/organs/organs.resolver'; +import { StepIndicatorComponent } from '@hra-ui/design-system/step-indicator'; +import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; /** Error when missing required columns in uploaded csv */ export interface MissingKeyError { @@ -61,7 +64,6 @@ function optionalValue(): T | null { ReactiveFormsModule, RouterModule, - MatButtonModule, MatButtonToggleModule, MatFormFieldModule, MatIconModule, @@ -74,6 +76,10 @@ function optionalValue(): T | null { HeaderComponent, MarkEmptyFormControlDirective, OverlayModule, + ButtonModule, + BreadcrumbsComponent, + StepIndicatorComponent, + TooltipCardComponent, ], templateUrl: './create-visualization-page.component.html', styleUrl: './create-visualization-page.component.scss', @@ -168,6 +174,53 @@ export class CreateVisualizationPageComponent { /** Tooltip position config */ readonly tooltipPosition = TOOLTIP_POSITION_BELOW; + readonly tooltips: TooltipContent[][] = [ + [ + { + description: + 'Use the template to format single-cell spatial feature tables for exploration. The cell type column can include damage and proliferation markers.', + }, + ], + [ + { + description: 'Verify column headers and edit as needed. Select optional column headers.', + }, + ], + [ + { + title: 'Anchor Cell Type', + description: + 'The anchor cell type represents the cell type to which the nearest cell distance distributions should be computed and visualized. Euclidian distance is used to compute the distance between two cells. \n“Endothelial” is used as the default anchor cell type. If an “Endothelial” cell label is not present, the first listed cell type label is used as the anchor cell type.', + }, + { + title: 'Distance Threshold (µm)', + description: 'Configure the distance threshold to modify visualizations for analysis.', + }, + { + title: 'Pixel Size (µm/pixel)', + description: + 'Pixel size is used as a scaling factor to convert coordinates to micrometers. Use 1 if coordinates are already in micrometers.', + }, + ], + [ + { + description: + 'Information in these fields will not change the visualization output. Metadata may be helpful for taking screenshots of the uploaded data and resulting visualizations in the Visualization App.', + }, + ], + [ + { + description: + 'Use default colors or customize the visualization by uploading a preferred color map CSV file. Cell type colors may be changed individually while exploring the visualization in the Visualization App.', + }, + ], + [ + { + description: 'Data on the Create Visualization page cannot be modified after a visualization is generated.', + }, + ], + ]; + /** Whether to show upload info tooltip */ uploadInfoOpen = false; /** Whether to show organize data tooltip */ diff --git a/apps/cde-ui/src/styles.scss b/apps/cde-ui/src/styles.scss index 15d46c199..f1f22da29 100644 --- a/apps/cde-ui/src/styles.scss +++ b/apps/cde-ui/src/styles.scss @@ -6,9 +6,9 @@ @use 'theming'; @use '../src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss' as create-visualization; -@mixin theme($theme) { - @include create-visualization.theme($theme); -} +// @mixin theme($theme) { +// @include create-visualization.theme($theme); +// } // TODO Update and switch to design system theming html { @@ -26,13 +26,13 @@ input[type='number'] { -moz-appearance: textfield; /* Firefox */ } -body { - margin: 0; -} +// body { +// margin: 0; +// } -a { - text-decoration: none; -} +// a { +// text-decoration: none; +// } // .cta-filled { // @include cta.filledDefault(); diff --git a/apps/cde-ui/src/styles/_creation-page-typographies.scss b/apps/cde-ui/src/styles/_creation-page-typographies.scss deleted file mode 100644 index 2866c19df..000000000 --- a/apps/cde-ui/src/styles/_creation-page-typographies.scss +++ /dev/null @@ -1,9 +0,0 @@ -@use '@angular/material' as mat; - -$create-vis: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2rem, 3rem, 500, $letter-spacing: -1.25px), - $headline-6: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $subtitle-1: mat.m2-define-typography-level(1.25rem, 1.875rem, 500), - $body-2: mat.m2-define-typography-level(1rem, 1.5rem, 500), -); diff --git a/apps/cde-ui/src/styles/_cta.scss b/apps/cde-ui/src/styles/_cta.scss deleted file mode 100644 index b97dfd34b..000000000 --- a/apps/cde-ui/src/styles/_cta.scss +++ /dev/null @@ -1,70 +0,0 @@ -$corner-width: 0.9375rem; -$corner-height: 0.8125rem; -$border-width: 0.25rem; -$x-multiplier: 0.373; -$y-multiplier: 0.4566; - -@mixin flatDefault() { - color: rgba(178, 10, 47, 1); - background-color: transparent; - border: none; - outline: none; -} - -@mixin flatHover() { - color: rgba(142, 8, 37, 1); -} - -@mixin flatActive() { - color: rgba(106, 6, 28, 1); -} - -@mixin flatFocus() { - color: rgba(32, 30, 61, 1); - outline: solid 0.25rem rgba(224, 13, 58, 1); - background-color: white; -} - -@mixin filledDefault() { - position: relative; - z-index: 0; - background-color: rgba(224, 13, 58, 1); - color: white; - border: none; - border-radius: 0 !important; - clip-path: polygon( - /* Bottom left */ 0 100%, - /* Top left */ 0 0, - /* Top right */ 100% 0%, - /* Bottom right y-axis */ 100% calc(100% - $corner-height), - /* Bottom right x-axis */ calc(100% - $corner-width) 100% - ); -} - -@mixin filledHover() { - --mdc-filled-button-container-color: rgba(178, 10, 47, 1); - background-color: var(--mdc-filled-button-container-color); -} - -@mixin filledActive() { - --mdc-filled-button-container-color: rgba(142, 8, 37, 1); - background-color: var(--mdc-filled-button-container-color); -} - -@mixin filledFocus() { - content: ''; - position: absolute; - inset: 0; - z-index: -1; - /* approximately tan((90 - theta) / 2) */ - padding: 0.15625rem 1.5rem; - line-height: 2.15625rem; - background-color: white; - clip-path: polygon( - /* Bottom left */ $border-width calc(100% - $border-width), - /* Top left */ $border-width $border-width, - /* Top right */ calc(100% - $border-width) $border-width, - /* Bottom right y-axis */ calc(100% - $border-width) calc(100% - $corner-height - $border-width * $y-multiplier), - /* Bottom right x-axis */ calc(100% - $corner-width - $border-width * $x-multiplier) calc(100% - $border-width) - ); -} diff --git a/apps/cde-ui/src/styles/_landing-page-typographies.scss b/apps/cde-ui/src/styles/_landing-page-typographies.scss deleted file mode 100644 index 5c1309d51..000000000 --- a/apps/cde-ui/src/styles/_landing-page-typographies.scss +++ /dev/null @@ -1,47 +0,0 @@ -@use '@angular/material' as mat; - -$xx-small: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2rem, 3rem, 500, $letter-spacing: -1.25px), - $headline-6: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $subtitle-1: mat.m2-define-typography-level(0.875rem, 1.3125rem, 400, $letter-spacing: 0.005em), - $body-1: mat.m2-define-typography-level(1.125rem, 1.6875rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $body-2: mat.m2-define-typography-level(0.875rem, 1.3125rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $button: mat.m2-define-typography-level(0.6875rem, 1.03125rem, 500, $letter-spacing: 0.002em), -); - -$x-small: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2rem, 3rem, 500, $letter-spacing: -1.25px), - $headline-6: mat.m2-define-typography-level(1.75rem, 2.625rem, 500), - $subtitle-1: mat.m2-define-typography-level(0.875rem, 1.3125rem, 400, $letter-spacing: 0.005em), - $body-1: mat.m2-define-typography-level(1.125rem, 1.6875rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $body-2: mat.m2-define-typography-level(1rem, 1.5rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $button: mat.m2-define-typography-level(0.6875rem, 1.03125rem, 500, $letter-spacing: 0.002em), -); - -$small: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2.375rem, 3.5625rem, 500, $letter-spacing: -1.75px), - $headline-6: mat.m2-define-typography-level(1.75rem, 2.625rem, 500), - $subtitle-1: mat.m2-define-typography-level(1.25rem, 1.875rem, 400, $letter-spacing: 0.013em), - $body-1: mat.m2-define-typography-level(1.125rem, 1.6875rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $body-2: mat.m2-define-typography-level(1rem, 1.5rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $button: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), -); - -$medium: $small; - -$large: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2.625rem, 3.9375rem, 500, $letter-spacing: -1.25px), - $headline-6: mat.m2-define-typography-level(2rem, 3rem, 500), - $subtitle-1: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $body-1: mat.m2-define-typography-level(1.125rem, 1.6875rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $body-2: mat.m2-define-typography-level(1rem, 1.5rem, 400, 'Nunito Sans', $letter-spacing: 0.5px), - $button: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), -); - -$x-large: $large; -$xx-large: $x-large; -$xxx-large: $xx-large; diff --git a/apps/cde-ui/src/styles/_material-theming.scss b/apps/cde-ui/src/styles/_material-theming.scss deleted file mode 100644 index 6fd9dc2f1..000000000 --- a/apps/cde-ui/src/styles/_material-theming.scss +++ /dev/null @@ -1,76 +0,0 @@ -@use '@angular/material' as mat; -@use './themable-sections/header' as header-section; -@use './themable-sections/main' as main-section; -@use './themable-sections/create-visualization' as create-visualization-section; -@use './themes/header' as header-theme; -@use './themes/main' as main-theme; -@use './typographies' as typographies; -@use './landing-page-typographies' as landing-page-typographies; -@use './creation-page-typographies' as creation-page-typographies; -@use './breakpoints' as breakpoints; - -$_theme: main-theme.$theme; - -@include mat.core(); -@include mat.core-theme($_theme); -@include mat.typography-hierarchy($_theme); - -// Add theme mixin for material components here! -@include mat.button-theme($_theme); -@include mat.button-toggle-theme($_theme); -@include mat.card-theme($_theme); -@include mat.divider-theme($_theme); -@include mat.form-field-theme($_theme); -@include mat.icon-theme($_theme); -@include mat.progress-bar-theme($_theme); -@include mat.select-theme($_theme); -@include mat.snack-bar-theme($_theme); - -// Add section theme mixins here! -@include header-section.theme($_theme); -@include main-section.theme($_theme); -@include create-visualization-section.theme($_theme); - -// Typography -@include breakpoints.breakpoint('xx-small') { - @include main-section.typography(landing-page-typographies.$xx-small); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); -} - -@include breakpoints.breakpoint('x-small') { - @include main-section.typography(landing-page-typographies.$x-small); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); -} - -@include breakpoints.breakpoint('small', 'medium') { - @include main-section.typography(landing-page-typographies.$small); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); -} - -@include breakpoints.breakpoint('large') { - @include main-section.typography(landing-page-typographies.$large); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); -} - -@include breakpoints.breakpoint('x-large') { - @include main-section.typography(landing-page-typographies.$x-large); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); -} - -@include breakpoints.breakpoint('xx-large', 'xxx-large') { - @include main-section.typography(landing-page-typographies.$xx-large); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); -} - -.mat-typography:has(cde-visualization-page) { - @include main-section.typography(landing-page-typographies.$xx-large); - @include create-visualization-section.typography(creation-page-typographies.$create-vis); - @include mat.typography-hierarchy( - mat.m2-define-light-theme( - ( - typography: typographies.$xx-large, - density: 0, - ) - ) - ); -} diff --git a/apps/cde-ui/src/styles/_typographies.scss b/apps/cde-ui/src/styles/_typographies.scss deleted file mode 100644 index cde2e2537..000000000 --- a/apps/cde-ui/src/styles/_typographies.scss +++ /dev/null @@ -1,49 +0,0 @@ -@use '@angular/material' as mat; - -$xx-small: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $headline-6: mat.m2-define-typography-level(0.9375rem, 1.40625rem, 500), - $subtitle-1: mat.m2-define-typography-level(0.875rem, 1.3125rem, 400, $letter-spacing: 0.005em), - $body-1: mat.m2-define-typography-level(0.75rem, 1.3125rem, 400, $letter-spacing: 0.005em), - $body-2: mat.m2-define-typography-level(0.6875rem, 1.03125rem, 500, $letter-spacing: 0.002em), - $button: mat.m2-define-typography-level(0.6875rem, 1.03125rem, 500, $letter-spacing: 0.002em), -); - -$x-small: $xx-small; - -$small: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2rem, 3rem, 500), - $headline-6: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $subtitle-1: mat.m2-define-typography-level(1.25rem, 1.875rem, 400, $letter-spacing: 0.013em), - $body-1: mat.m2-define-typography-level(1.25rem, 1.875rem, 400, $letter-spacing: 0.013em), - $body-2: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), - $button: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), -); - -$medium: $small; - -$large: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2rem, 3rem, 500), - $headline-6: mat.m2-define-typography-level(2rem, 3rem, 500), - $subtitle-1: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $body-1: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), - $body-2: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), - $button: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), -); - -$x-large: mat.m2-define-rem-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(2.625rem, 3.9375rem, 500, $letter-spacing: 0.0325em), - $headline-6: mat.m2-define-typography-level(2rem, 3rem, 500), - $subtitle-1: mat.m2-define-typography-level(1.5rem, 2.25rem, 500), - $body-1: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), - $body-2: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), - $button: mat.m2-define-typography-level(1.125rem, 1.6875rem, 500), - $caption: mat.m2-define-typography-level(0.875rem, 1.3125rem, 500, $letter-spacing: 0.02em), -); - -$xx-large: $x-large; -$xxx-large: $xx-large; diff --git a/apps/cde-ui/src/styles/global/_fonts.scss b/apps/cde-ui/src/styles/global/_fonts.scss deleted file mode 100644 index f9f639a99..000000000 --- a/apps/cde-ui/src/styles/global/_fonts.scss +++ /dev/null @@ -1,28 +0,0 @@ -@use '@fontsource/material-symbols-outlined'; -@use '@fontsource/material-symbols-rounded'; -@use '@fontsource/metropolis/400.css' as Metropolis400; -@use '@fontsource/metropolis/500.css' as Metropolis500; -@use '@fontsource/nunito-sans'; - -/* As per https://fontsource.org/docs/getting-started/material-symbols */ -.material-symbols-outlined, -.material-symbols-rounded { - font-weight: 300; - font-style: normal; - font-size: 1.5rem; - display: inline-block; - line-height: 1; - text-transform: none; - letter-spacing: normal; - word-wrap: normal; - white-space: nowrap; - direction: ltr; -} - -.material-symbols-outlined { - font-family: 'Material Symbols Outlined'; -} - -.material-symbols-rounded { - font-family: 'Material Symbols Rounded'; -} diff --git a/apps/cde-ui/src/styles/global/_resets.scss b/apps/cde-ui/src/styles/global/_resets.scss deleted file mode 100644 index 312256dda..000000000 --- a/apps/cde-ui/src/styles/global/_resets.scss +++ /dev/null @@ -1,12 +0,0 @@ -@use 'normalize.css/normalize.css'; - -// Box sizing reset -html { - box-sizing: border-box; -} - -*, -*:before, -*:after { - box-sizing: inherit; -} diff --git a/apps/cde-ui/src/styles/themable-sections/_create-visualization.scss b/apps/cde-ui/src/styles/themable-sections/_create-visualization.scss deleted file mode 100644 index ebd1aa7e6..000000000 --- a/apps/cde-ui/src/styles/themable-sections/_create-visualization.scss +++ /dev/null @@ -1,16 +0,0 @@ -@use '@angular/material' as mat; -@use '../../app/pages/create-visualization-page/create-visualization-page.component.theme.scss' as create-visualization; - -@mixin theme($theme) { - @include create-visualization.theme($theme); -} - -@mixin typography($typography) { - @include mat.button-typography($typography); - @include mat.button-toggle-typography($typography); - @include mat.form-field-typography($typography); - @include mat.select-typography($typography); - - @include mat.typography-hierarchy($typography); - @include create-visualization.typography($typography); -} diff --git a/apps/cde-ui/src/styles/themable-sections/_header.scss b/apps/cde-ui/src/styles/themable-sections/_header.scss deleted file mode 100644 index df07992dc..000000000 --- a/apps/cde-ui/src/styles/themable-sections/_header.scss +++ /dev/null @@ -1,5 +0,0 @@ -@use '../../app/components/header/header.component.theme.scss' as header; - -@mixin theme($theme) { - @include header.theme($theme); -} diff --git a/apps/cde-ui/src/styles/themable-sections/_main.scss b/apps/cde-ui/src/styles/themable-sections/_main.scss deleted file mode 100644 index c5645ea03..000000000 --- a/apps/cde-ui/src/styles/themable-sections/_main.scss +++ /dev/null @@ -1,11 +0,0 @@ -@use '../../app/pages/landing-page/landing-page.component.theme.scss' as landing-page; -@use '@angular/material' as mat; - -@mixin theme($theme) { - @include landing-page.theme($theme); -} - -@mixin typography($typography) { - @include mat.typography-hierarchy($typography); - @include landing-page.typography($typography); -} diff --git a/apps/cde-ui/src/styles/themes/_footer.scss b/apps/cde-ui/src/styles/themes/_footer.scss deleted file mode 100644 index a8ba89057..000000000 --- a/apps/cde-ui/src/styles/themes/_footer.scss +++ /dev/null @@ -1,19 +0,0 @@ -@use '@angular/material' as mat; - -$primary: mat.m2-define-palette(map.get(palettes.$palettes, 'red'), 700, 500, 900); -$accent: mat.m2-define-palette(map.get(palettes.$palettes, 'blue'), 900, 800, 900); - -$typography: mat.m2-define-typography-config( - $font-family: 'Metropolis', - $body-1: mat.m2-define-typography-level(18px, 27px, 500), - $caption: mat.m2-define-typography-level(15px, 22.5px, 400), -); - -$theme: ( - color: ( - primary: $primary, - accent: $accent, - ), - typography: $typography, - density: 0, -); diff --git a/apps/cde-ui/src/styles/themes/_header.scss b/apps/cde-ui/src/styles/themes/_header.scss deleted file mode 100644 index 132c34ec1..000000000 --- a/apps/cde-ui/src/styles/themes/_header.scss +++ /dev/null @@ -1,20 +0,0 @@ -@use 'sass:map'; -@use '@angular/material' as mat; -@use '../constants/palettes' as palettes; - -$primary: mat.m2-define-palette(map.get(palettes.$palettes, 'red'), 700, 500, 900); -$accent: mat.m2-define-palette(map.get(palettes.$palettes, 'blue'), 900, 800, 900); - -$typography: mat.m2-define-typography-config( - $font-family: 'Metropolis', - $button: mat.m2-define-typography-level(18px, 27px, 500), -); - -$theme: ( - color: ( - primary: $primary, - accent: $accent, - ), - typography: $typography, - density: 0, -); diff --git a/apps/cde-ui/src/styles/themes/_main.scss b/apps/cde-ui/src/styles/themes/_main.scss deleted file mode 100644 index d85e24afb..000000000 --- a/apps/cde-ui/src/styles/themes/_main.scss +++ /dev/null @@ -1,28 +0,0 @@ -@use 'sass:map'; -@use '@angular/material' as mat; -@use '../constants/palettes' as palettes; - -$primary: mat.m2-define-palette(map.get(palettes.$palettes, 'red'), 600, 500, 900); -$accent: mat.m2-define-palette(map.get(palettes.$palettes, 'blue'), 600, 500, 900); - -$typography: mat.m2-define-typography-config( - $font-family: 'Metropolis', - $headline-5: mat.m2-define-typography-level(72px, 90px, 500, $letter-spacing: -0.05em), - $headline-6: mat.m2-define-typography-level(42px, 52.5px, 500), - $subtitle-1: mat.m2-define-typography-level(24px, 36px, 500), - $body-1: mat.m2-define-typography-level(20px, 30px, 400, 'Nunito Sans', $letter-spacing: 0.07em), - $body-2: mat.m2-define-typography-level(18px, 27px, 400, 'Nunito Sans', $letter-spacing: 0.07em), - $button: mat.m2-define-typography-level(18px, 34.5px, 500), - $caption: mat.m2-define-typography-level(14px, 21px, 400, $letter-spacing: 0.005em), -); - -$theme: mat.m2-define-light-theme( - ( - color: ( - primary: $primary, - accent: $accent, - ), - typography: $typography, - density: 0, - ) -); diff --git a/libs/design-system/breadcrumbs/src/index.ts b/libs/design-system/breadcrumbs/src/index.ts index 864d08075..fb564b65b 100644 --- a/libs/design-system/breadcrumbs/src/index.ts +++ b/libs/design-system/breadcrumbs/src/index.ts @@ -1 +1,2 @@ export * from './lib/breadcrumbs-size/breadcrumbs-size.directive'; +export * from './lib/breadcrumbs/breadcrumbs.component'; diff --git a/libs/design-system/src/lib/providers.ts b/libs/design-system/src/lib/providers.ts index 5aa450962..a09335d83 100644 --- a/libs/design-system/src/lib/providers.ts +++ b/libs/design-system/src/lib/providers.ts @@ -7,6 +7,9 @@ import { provideMenu } from '@hra-ui/design-system/menu'; import { provideTrees } from '@hra-ui/design-system/tree'; import { provideScrolling } from '@hra-ui/design-system/scrolling'; import { provideTable } from '@hra-ui/design-system/table'; +import { provideSelect } from '@hra-ui/design-system/select'; +import { provideInput } from '@hra-ui/design-system/input'; +import { provideButtonToggle } from '@hra-ui/design-system/button-toggle'; /** * Returns design system providers @@ -25,5 +28,8 @@ export function provideDesignSystem(): EnvironmentProviders { provideScrolling(), provideMenu(), provideTable(), + provideSelect(), + provideInput(), + provideButtonToggle(), ]); } diff --git a/libs/design-system/tooltip-card/src/lib/tooltip-card.component.scss b/libs/design-system/tooltip-card/src/lib/tooltip-card.component.scss index 454f75cb1..ff6736682 100644 --- a/libs/design-system/tooltip-card/src/lib/tooltip-card.component.scss +++ b/libs/design-system/tooltip-card/src/lib/tooltip-card.component.scss @@ -16,6 +16,7 @@ .description { margin: 0 0 1rem; color: var(--sys-primary); + white-space: pre-line; } .section:last-child .description { From 60dac6aab4b6c1ba351760638b92b22b131ebd7f Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Tue, 1 Oct 2024 16:07:27 -0400 Subject: [PATCH 38/50] add links count to cell type table --- .../cde-visualization.component.html | 5 +- .../cde-visualization.component.scss | 2 +- .../cde-visualization.component.ts | 14 +++- .../cell-types/cell-types.component.html | 45 ++++++---- .../cell-types/cell-types.component.scss | 84 ++++++++++++++----- .../cell-types/cell-types.component.ts | 25 ++++-- .../color-picker-label.component.scss | 5 +- .../src/lib/models/cell-type.ts | 2 + .../services/file-saver/file-saver.service.ts | 6 +- libs/design-system/snackbar/src/index.ts | 2 +- 10 files changed, 136 insertions(+), 54 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html index 6786e3620..c1aa46618 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.html @@ -14,7 +14,10 @@ [(cellTypes)]="cellTypes" [(cellTypesSelection)]="cellTypesSelection" [selectedCellType]="selectedNodeTargetValue()" - (download)="downloadColorMap()" + (downloadColorMap)="downloadColorMap()" + (downloadNodes)="downloadNodes()" + (downloadEdges)="downloadEdges()" + (resetAllColors)="histogram.resetAllCellsColor(); resetCellTypes()" #cellTypesTable >

diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss index e353b76ce..ea77a241b 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.scss @@ -44,7 +44,7 @@ :host { width: 100%; display: grid; - grid-template-columns: 21rem minmax(59rem, calc(100vw - 21rem)); + grid-template-columns: 22.75rem minmax(59rem, calc(100vw - 21rem)); grid-template-rows: 5.25rem minmax(calc(900px - 5.25rem), calc(100vh - 5.25rem)); grid-template-areas: 'header header' diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts index 02cf471b1..9366b0be3 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.ts @@ -12,22 +12,22 @@ import { signal, ViewContainerRef, } from '@angular/core'; +import { rgbToHex } from '@hra-ui/design-system/color-picker'; import { CellTypesComponent } from '../components/cell-types/cell-types.component'; import { HistogramComponent } from '../components/histogram/histogram.component'; import { MetadataComponent } from '../components/metadata/metadata.component'; import { NodeDistVisualizationComponent } from '../components/node-dist-visualization/node-dist-visualization.component'; import { VisualizationHeaderComponent } from '../components/visualization-header/visualization-header.component'; import { CellTypeEntry } from '../models/cell-type'; -import { rgbToHex } from '@hra-ui/design-system/color-picker'; import { ColorMapColorKey, ColorMapEntry, + colorMapToLookup, ColorMapTypeKey, DEFAULT_COLOR_MAP_KEY, DEFAULT_COLOR_MAP_VALUE_KEY, - colorMapToLookup, } from '../models/color-map'; -import { DEFAULT_MAX_EDGE_DISTANCE, EdgeEntry } from '../models/edge'; +import { DEFAULT_MAX_EDGE_DISTANCE, EdgeEntry, EdgeIndex } from '../models/edge'; import { Metadata } from '../models/metadata'; import { DEFAULT_NODE_TARGET_KEY, NodeEntry, NodeTargetKey, selectNodeTargetValue } from '../models/node'; import { ColorMapFileLoaderService } from '../services/data/color-map-loader.service'; @@ -206,6 +206,7 @@ export class CdeVisualizationComponent { /** Computed cell types from loaded nodes */ readonly cellTypesFromNodes = computed(() => { const nodes = this.loadedNodes(); + const edges = this.loadedEdges(); const targetKey = this.nodeTypeKey(); const defaultColorGenerator = createColorGenerator(); const cellTypeByName: Record = {}; @@ -215,11 +216,18 @@ export class CdeVisualizationComponent { cellTypeByName[name] ??= { name, count: 0, + outgoingEdgeCount: 0, color: this.colorMapLookup().get(name) ?? defaultColorGenerator(), }; cellTypeByName[name].count += 1; } + for (const edge of edges) { + const node = nodes[edge[EdgeIndex.SourceNode]]; + const name = node[targetKey]; + cellTypeByName[name].outgoingEdgeCount += 1; + } + return Object.values(cellTypeByName); }); diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index 6c322e5b9..58a235a26 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -1,4 +1,4 @@ - + Cell Types - - - + - - - -
- Total Cell Types +
{{ selection().length }} + Total Cell Types
-
- Total Cells +
{{ totalCellCount() | number }} + Total Cells
- -

+ + - + + + + + + + diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss index fd93b0028..c6a7ae7a6 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss @@ -36,25 +36,25 @@ $blue-theme: mat.m2-define-light-theme( border-color: map.get(map.get(palettes.$palettes, 'blue'), 600); $button-text-color: map.get(map.get(palettes.$palettes, 'blue'), 900); --mat-table-background-color: white; - --mdc-checkbox-unselected-icon-color: #201e3d; - --mat-sort-arrow-color: #201e3d; + --mdc-checkbox-unselected-icon-color: var(--sys-secondary); + --mdc-checkbox-selected-icon-color: var(--sys-secondary); + --mdc-checkbox-selected-checkmark-color: var(--sys-secondary); + --mdc-checkbox-state-layer-size: 28px; + --mat-sort-arrow-color: var(--sys-secondary); --mat-table-row-item-container-height: 1.75rem; --mat-table-row-item-outline-width: 0; --mat-table-header-headline-color: var(--mat-sort-arrow-color); --mdc-filled-button-container-height: 2rem; --mat-table-header-container-height: 2rem; + --mat-menu-item-label-text-color: var(--sys-primary); span.cell-types-label { + font: var(--sys-label-medium); + letter-spacing: var(--sys-label-medium-tracking); grid-area: cell-types; - font-size: 1rem; - height: 2rem; display: flex; align-items: center; gap: 0.25rem; - - mat-icon { - margin: 2px; - } } button.download-csv { @@ -71,23 +71,25 @@ $blue-theme: mat.m2-define-light-theme( } } - .mat-caption, - .total-ct-label { - grid-area: total-cell-types; + .total-ct-label, + .total-cells { + font: var(--sys-label-small); + letter-spacing: var(--sys-label-medium-tracking); span { display: block; - color: #4b4b5e; + color: var(--sys-primary); + font: var(--sys-label-medium); } } + .mat-caption, + .total-ct-label { + grid-area: total-cell-types; + } + .total-cells { grid-area: total-cells; - - span { - color: #4b4b5e; - text-align: right; - } } .table-overflow-container { @@ -97,7 +99,27 @@ $blue-theme: mat.m2-define-light-theme( table { ::ng-deep { + .mat-mdc-menu-content { + color: var(--sys-primary); + } + thead { + tr { + font: var(--sys-label-small); + .mat-mdc-checkbox { + .mdc-checkbox__background { + background-color: white; + } + } + } + .mat-sort-header-container { + max-width: 6rem; + .mat-sort-header-content { + font: var(--sys-label-small); + color: var(--sys-secondary); + } + } + .mat-sort-header-arrow { opacity: 1 !important; transform: none !important; @@ -107,14 +129,22 @@ $blue-theme: mat.m2-define-light-theme( --mat-sort-arrow-color: #4b4b5e; justify-content: flex-end; margin-right: 0.25rem; - color: #4b4b5e; + color: var(--sys-primary); } } tbody tr td.mdc-data-table__cell:last-child { text-align: end; - padding-right: 0.25rem; - color: #4b4b5e; + padding-right: 1.65rem; + color: var(--sys-primary); + font: var(--sys-label-small); + } + + tbody { + tr, + td { + font: var(--sys-label-small); + } } tr:has(.anchor) { @@ -141,6 +171,16 @@ $blue-theme: mat.m2-define-light-theme( border-bottom: solid #d5dbe3 0.0625rem; } } + + tr { + .mat-mdc-checkbox { + &.mat-mdc-checkbox-checked { + .mdc-checkbox__background { + background-color: white; + } + } + } + } } tr { @@ -172,3 +212,7 @@ $blue-theme: mat.m2-define-light-theme( } } } + +::ng-deep .mat-mdc-menu-content button { + color: var(--sys-primary); +} diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts index 65bc6ca70..5b60f4c47 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts @@ -19,17 +19,18 @@ import { MatCheckboxModule } from '@angular/material/checkbox'; import { MatIconModule } from '@angular/material/icon'; import { MatListModule } from '@angular/material/list'; import { MatMenuModule } from '@angular/material/menu'; +import { MatSnackBarModule } from '@angular/material/snack-bar'; import { MatSort, MatSortModule } from '@angular/material/sort'; import { MatTableDataSource, MatTableModule } from '@angular/material/table'; import { Rgb } from '@hra-ui/design-system/color-picker'; +import { IconButtonSizeDirective } from '@hra-ui/design-system/icon-button'; import { ScrollingModule } from '@hra-ui/design-system/scrolling'; +import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; import { ColorPickerModule } from 'ngx-color-picker'; import { map } from 'rxjs'; import { CellTypeEntry } from '../../models/cell-type'; import { TOOLTIP_POSITION_RIGHT_SIDE } from '../../shared/tooltip-position'; import { ColorPickerLabelComponent } from '../color-picker-label/color-picker-label.component'; -import { IconButtonSizeDirective } from '@hra-ui/design-system/icon-button'; -import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; /** * Cell Type Component @@ -52,6 +53,7 @@ import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tool MatMenuModule, IconButtonSizeDirective, TooltipCardComponent, + MatSnackBarModule, ], templateUrl: './cell-types.component.html', styleUrl: './cell-types.component.scss', @@ -66,11 +68,20 @@ export class CellTypesComponent { /** Currently selected cell type */ readonly selectedCellType = input(''); - /** Output event for download action */ - readonly download = output(); + /** Output event for download colormap action */ + readonly downloadColorMap = output(); + + /** Output event for download edges action */ + readonly downloadNodes = output(); + + /** Output event for download edges action */ + readonly downloadEdges = output(); + + /** Output event for reset color */ + readonly resetAllColors = output(); /** Columns to be displayed in the table */ - protected readonly columns = ['select', 'name', 'count']; + protected readonly columns = ['select', 'cellType', 'count', 'links']; /** Tooltip position configuration */ protected readonly tooltipPosition = TOOLTIP_POSITION_RIGHT_SIDE; @@ -86,6 +97,9 @@ export class CellTypesComponent { }, ]; + /** Flag to toggle cell links row visibility */ + hideCellLinkData = false; + /** Bind sort state to data source */ protected readonly sortBindRef = effect(() => (this.dataSource.sort = this.sort())); @@ -98,6 +112,7 @@ export class CellTypesComponent { /** Bind data source to cell types */ protected readonly dataSourceBindRef = effect(() => { this.dataSource.data = this.cellTypes(); + console.log(this.cellTypes()); this.cdr.markForCheck(); }); diff --git a/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss b/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss index 64fcd5c01..e83ad0d4f 100644 --- a/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss +++ b/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss @@ -29,14 +29,15 @@ } .label { + font: var(--sys-label-small); + color: var(--sys-secondary); cursor: pointer; display: block; white-space: nowrap; - max-width: 10.5rem; + max-width: 8.25rem; text-overflow: ellipsis; overflow: hidden; flex-grow: 0; - font-weight: 500; } } diff --git a/libs/cde-visualization/src/lib/models/cell-type.ts b/libs/cde-visualization/src/lib/models/cell-type.ts index 944d9cc2b..a1d087cc2 100644 --- a/libs/cde-visualization/src/lib/models/cell-type.ts +++ b/libs/cde-visualization/src/lib/models/cell-type.ts @@ -6,6 +6,8 @@ export interface CellTypeEntry { name: string; /** Count of instances for this cell type */ count: number; + /** Count of number of outgoing edges */ + outgoingEdgeCount: number; /** RGB color associated with this cell type */ color: Rgb; } diff --git a/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts b/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts index 948eb86bc..5c413684f 100644 --- a/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts +++ b/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts @@ -1,6 +1,6 @@ import { DOCUMENT } from '@angular/common'; import { inject, Injectable } from '@angular/core'; -import { MatSnackBar } from '@angular/material/snack-bar'; +import { SnackbarService } from '@hra-ui/design-system/snackbar'; import { unparse, UnparseConfig, UnparseObject } from 'papaparse'; /** @@ -14,7 +14,7 @@ export class FileSaverService { private readonly document = inject(DOCUMENT); /** Injects the MatSnackBar service for notifications */ - private readonly snackbar = inject(MatSnackBar); + private readonly snackbar = inject(SnackbarService); /** Saves a file from a URL with a given filename */ save(url: string, filename: string): void { @@ -28,7 +28,7 @@ export class FileSaverService { document.body.appendChild(linkEl); linkEl.dispatchEvent(new MouseEvent('click')); document.body.removeChild(linkEl); - this.snackbar.open('File downloaded', undefined, { duration: 1000, panelClass: 'download-snackbar-panel' }); + this.snackbar.open('File downloaded', '', false, 'end', { duration: 1000 }); } /** Saves a Blob as a file with a given filename */ diff --git a/libs/design-system/snackbar/src/index.ts b/libs/design-system/snackbar/src/index.ts index 555147194..dadfc4312 100644 --- a/libs/design-system/snackbar/src/index.ts +++ b/libs/design-system/snackbar/src/index.ts @@ -1 +1 @@ -export * from './lib/snackbar.component'; +export * from './lib/snackbar.service'; From 7a7cc08481aff5f27d3307951e30029ac0f61cc3 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Tue, 1 Oct 2024 19:01:23 -0400 Subject: [PATCH 39/50] More style updates --- .../file-upload/file-upload.component.scss | 53 +---------- .../create-visualization-page.component.html | 53 ++++++----- .../create-visualization-page.component.scss | 91 ++++++++----------- ...te-visualization-page.component.theme.scss | 37 ++++---- .../create-visualization-page.component.ts | 6 ++ apps/cde-ui/src/styles.scss | 58 ------------ libs/design-system/button-toggle/src/index.ts | 1 + libs/design-system/select/src/index.ts | 1 + 8 files changed, 93 insertions(+), 207 deletions(-) diff --git a/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss b/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss index e0d0129f4..fb016619b 100644 --- a/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss +++ b/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss @@ -1,43 +1,4 @@ -@use 'sass:map'; -// @use '@angular/material' as mat; -// @use '../../../styles/constants/palettes' as palettes; - -// $blue: mat.m2-define-palette(map.get(palettes.$palettes, 'blue'), 500, 600, 800, 900); -// $blue-theme: mat.m2-define-light-theme( -// ( -// color: ( -// primary: $blue, -// accent: $blue, -// ), -// ) -// ); - -// $gray: mat.m2-define-palette(map.get(palettes.$palettes, 'gray'), 500, 600, 700); -// $gray-theme: mat.m2-define-light-theme( -// ( -// color: ( -// primary: $gray, -// accent: $gray, -// ), -// ) -// ); -// $red: mat.m2-define-palette(map.get(palettes.$palettes, 'red'), 500, 600, 700); -// $red-theme: mat.m2-define-light-theme( -// ( -// color: ( -// primary: $red, -// accent: $red, -// ), -// ) -// ); - :host { - // --mdc-filled-button-label-text-size: 1rem; - // --mat-filled-button-horizontal-padding: 0.5rem; - // --mdc-filled-button-label-text-tracking: 0.02em; - // --mat-filled-button-icon-spacing: 0.25rem; - // @include mat.button-color($blue-theme); - .upload-success { height: 2.5rem; display: flex; @@ -64,21 +25,16 @@ .error { display: flex; - align-items: center; gap: 0.5rem; margin-bottom: 2rem; - background-color: rgb(from #ffdcc4 r g b / 0.8); padding: 0.5rem 0.75rem; border-radius: 0.25rem; - - .alert { - color: #bc4f00; - } + font: var(--sys-label-large); + width: fit-content; .error-messages { display: flex; flex-direction: column; - color: #2f1400; } } @@ -98,11 +54,6 @@ } .use-template { - // --mdc-text-button-label-text-size: 1rem; - // --mat-text-button-with-icon-horizontal-padding: 0rem; - // --mdc-text-button-label-text-tracking: 0.02em; - // --mat-text-button-icon-spacing: 0.25rem; - &.loaded { margin-top: 1.5rem; } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index 59a2bb86b..e07e36c9a 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -1,4 +1,9 @@ - +
- +
NameCell Type - Count{{ element.count.toLocaleString() }}#Cells{{ element.count.toLocaleString() }}#Links{{ element.outgoingEdgeCount.toLocaleString() }}
@@ -116,13 +121,12 @@

Required: Verify column headers - + X Axis @for (option of dataHeaders; track option) { @@ -131,13 +135,12 @@

- + Y Axis @for (option of dataHeaders; track option) { @@ -146,13 +149,13 @@

- + Cell Type @for (option of dataHeaders; track option) { @@ -172,13 +175,12 @@

Optional: Add column headers - + Z Axis @for (option of dataHeaders; track option) { @@ -187,13 +189,12 @@

- + Cell Ontology ID @for (option of dataHeaders; track option) { @@ -231,13 +232,12 @@

- + Anchor Cell Type @for (type of cellTypes; track type) { @@ -306,13 +306,12 @@

- + Organ @for (organ of organs(); track organ) { @@ -321,13 +320,12 @@

- + Sex Male @@ -386,9 +384,10 @@

Use Default Colors Upload Color Map diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss index 8750d560d..1cfcd8fa7 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.scss @@ -5,14 +5,23 @@ background-position: center; background-size: cover; + hra-nav-header { + border-bottom: 1px solid var(--sys-outline); + } + + ::ng-deep .app-logo .app-description { + border-radius: 2px; + width: fit-content; + padding: 0 4px; + font: 500 10px/1rem Metropolis !important; + } + .content { display: flex; flex-direction: column; width: 100%; margin: 0 auto; - padding: 3rem 1rem 6rem; gap: 3rem; - align-items: center; max-width: 53.5rem; align-items: flex-start; padding: 3rem 0rem 6rem; @@ -43,7 +52,7 @@ display: flex; align-items: center; height: 2.5rem; - margin: 0; + margin: 0 0 2rem 0; .step-number { margin-right: 0.75rem; @@ -67,7 +76,6 @@ table { grid-area: table; - margin: 0.5rem 0; th, td { @@ -84,6 +92,21 @@ } } + .visualize-notification, + .error { + display: flex; + gap: 0.5rem; + margin: 2rem 0; + padding: 0.5rem 0.75rem; + border-radius: 0.25rem; + font: var(--sys-label-large); + width: fit-content; + } + + // mat-form-field { + // margin: 1rem 0; + // } + .data-upload { display: grid; grid: @@ -93,6 +116,10 @@ grid-template-rows: auto auto auto; row-gap: 2rem; + .header { + margin-bottom: 0; + } + .upload-csv { grid-area: upload-csv; } @@ -107,12 +134,13 @@ font: var(--sys-label-large); } - .required-headers { - margin-bottom: 1rem; + .optional-headers { + margin-top: 2rem; } .subheader { grid-area: subheader; + margin-bottom: 1rem; } } @@ -121,6 +149,7 @@ display: grid; grid: '. .'; column-gap: 1.5rem; + margin-bottom: 2rem; } .parameters-2 { @@ -132,19 +161,16 @@ .metadata { display: grid; - gap: 0.5rem; column-gap: 1.5rem; grid: 'header header'; .header { grid-area: header; - margin-bottom: 0; } } .color-config { display: grid; - row-gap: 2rem; grid: 'header header' 'toggle toggle' / auto 1fr; @@ -159,6 +185,7 @@ table { width: 66%; + margin-top: 2rem; th, td { @@ -168,20 +195,11 @@ mat-button-toggle-group { grid-area: toggle; - - mat-button-toggle { - width: 50%; - border-width: 0; - - &:first-child { - border-right-width: 1px; - border-style: solid; - } - } } .upload-colormap { grid-area: upload-colormap; + margin-top: 2rem; } } @@ -193,38 +211,3 @@ } } } - -::ng-deep mat-form-field { - margin: 1rem 0; - - .mdc-floating-label { - line-height: 18px !important; - } - - .mat-mdc-text-field-wrapper { - border-radius: 4px 4px 0 0; - padding: 0 1rem; - } - - .mat-mdc-form-field-subscript-wrapper { - display: none; - } -} - -::ng-deep .select-panel { - font: var(--sys-label-large); - // border-radius: 0.5rem !important; - // box-shadow: 0 5px 0.25rem 0 #201e3d29 !important; - // padding: 1rem 0 !important; -} - -.visualize-notification, -.error { - display: flex; - align-items: center; - gap: 0.5rem; - margin: 2rem 0; - padding: 0.5rem 0.75rem; - border-radius: 0.25rem; - font: var(--sys-label-large); -} diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index 4ce4daccb..0b1f07024 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -5,17 +5,20 @@ cde-create-visualization-page { } } + .app-description { + color: var(--sys-on-tertiary-fixed) !important; + background: rgb(from var(--sys-on-tertiary-container) r g b / 0.08); + } + .card { background-color: var(--sys-surface-container-low); } - .data-upload { - th { - color: var(--sys-secondary); - } - td { - color: var(--sys-primary); - } + th { + color: var(--sys-secondary); + } + td { + color: var(--sys-primary); } .color-config { @@ -32,18 +35,18 @@ cde-create-visualization-page { } } } + + .visualize-notification, + .error { + color: var(--sys-on-error-container); + background-color: rgb(from var(--sys-error-container) r g b / 0.8); + + .alert { + color: var(--sys-error); + } + } } .info-tooltip-panel { background-color: var(--sys-on-primary); } - -.visualize-notification, -.error { - color: var(--sys-on-error-container); - background-color: rgb(from var(--sys-error-container) r g b / 0.8); - - .alert { - color: var(--sys-error); - } -} diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index c6b23ec2d..ccf594058 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -35,6 +35,9 @@ import { validateInteger } from '../../shared/form-validators/is-integer'; import { OrganEntry } from '../../shared/resolvers/organs/organs.resolver'; import { StepIndicatorComponent } from '@hra-ui/design-system/step-indicator'; import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; +import { ToggleButtonSizeDirective } from '@hra-ui/design-system/button-toggle'; +import { NavHeaderComponent } from '@hra-ui/design-system/nav-header'; +import { SelectSizeDirective } from '@hra-ui/design-system/select'; /** Error when missing required columns in uploaded csv */ export interface MissingKeyError { @@ -80,6 +83,9 @@ function optionalValue(): T | null { BreadcrumbsComponent, StepIndicatorComponent, TooltipCardComponent, + ToggleButtonSizeDirective, + SelectSizeDirective, + NavHeaderComponent, ], templateUrl: './create-visualization-page.component.html', styleUrl: './create-visualization-page.component.scss', diff --git a/apps/cde-ui/src/styles.scss b/apps/cde-ui/src/styles.scss index f1f22da29..d407dd3c2 100644 --- a/apps/cde-ui/src/styles.scss +++ b/apps/cde-ui/src/styles.scss @@ -1,16 +1,7 @@ -// @use './styles/cta' as cta; -// @use './styles/global/resets'; -// @use './styles/global/fonts'; -// @use './styles/material-theming'; @use 'light-theme'; @use 'theming'; @use '../src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss' as create-visualization; -// @mixin theme($theme) { -// @include create-visualization.theme($theme); -// } - -// TODO Update and switch to design system theming html { @include theming.theme(light-theme.$theme); } @@ -25,52 +16,3 @@ input::-webkit-inner-spin-button { input[type='number'] { -moz-appearance: textfield; /* Firefox */ } - -// body { -// margin: 0; -// } - -// a { -// text-decoration: none; -// } - -// .cta-filled { -// @include cta.filledDefault(); - -// &:hover { -// @include cta.filledHover(); -// } - -// &:active { -// @include cta.filledActive(); -// } - -// &:focus-visible { -// --mdc-filled-button-label-text-color: rgba(32, 30, 61, 1); -// color: var(--mdc-filled-button-label-text-color); -// } - -// &:focus-visible::after { -// @include cta.filledFocus(); -// } -// } - -// .cta-flat { -// @include cta.flatDefault(); - -// &:hover { -// @include cta.flatHover(); -// } - -// &:active { -// @include cta.flatActive(); -// } - -// &:focus-visible { -// @include cta.flatFocus(); -// } -// } - -// .selected { -// box-shadow: 0 -2px 0 #e00d3a inset; -// } diff --git a/libs/design-system/button-toggle/src/index.ts b/libs/design-system/button-toggle/src/index.ts index e194182f8..246ecf6a6 100644 --- a/libs/design-system/button-toggle/src/index.ts +++ b/libs/design-system/button-toggle/src/index.ts @@ -1 +1,2 @@ export * from './lib/providers'; +export * from './lib/button-toggle-size/button-toggle-size.directive'; diff --git a/libs/design-system/select/src/index.ts b/libs/design-system/select/src/index.ts index e194182f8..f0a35ba2d 100644 --- a/libs/design-system/select/src/index.ts +++ b/libs/design-system/select/src/index.ts @@ -1 +1,2 @@ export * from './lib/providers'; +export * from './lib/select-size/select-size.directive'; From 6422ebf06029f95c3e44b0071300de329386d91f Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 2 Oct 2024 00:08:43 -0400 Subject: [PATCH 40/50] Make styles closer to spec --- .../file-upload/file-upload.component.scss | 6 ----- .../create-visualization-page.component.html | 3 +-- .../create-visualization-page.component.scss | 22 ++++++++++------ ...reate-visualization-page.component.spec.ts | 2 +- ...te-visualization-page.component.theme.scss | 15 +++++------ .../create-visualization-page.component.ts | 25 ++++++++++--------- 6 files changed, 38 insertions(+), 35 deletions(-) diff --git a/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss b/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss index fb016619b..493f3df51 100644 --- a/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss +++ b/apps/cde-ui/src/app/components/file-upload/file-upload.component.scss @@ -52,10 +52,4 @@ font-size: 2rem; } } - - .use-template { - &.loaded { - margin-top: 1.5rem; - } - } } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html index e07e36c9a..52bebf107 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.html @@ -149,11 +149,10 @@

- + Cell Type { fixture.autoDetectChanges(); await new Promise((resolve) => setTimeout(resolve, 50)); expect(spy).toHaveBeenCalledTimes(0); - expect(instance.columnErrorActionMessage).toMatch(/Please select the required column headers: Cell Type/); + expect(instance.columnErrorActionMessage).toMatch(/Please select the required column header: Cell Type/); }); it('sets nodes', async () => { diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss index 0b1f07024..77ba3ef3e 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.theme.scss @@ -1,8 +1,8 @@ cde-create-visualization-page { - .page-nav { - .title { - color: var(--sys-secondary); - } + color: var(--sys-secondary); + + hra-nav-header { + background-color: var(--sys-surface-container-high) !important; } .app-description { @@ -12,11 +12,12 @@ cde-create-visualization-page { .card { background-color: var(--sys-surface-container-low); - } - th { - color: var(--sys-secondary); + .header { + --mat-icon-color: var(--sys-secondary); + } } + td { color: var(--sys-primary); } diff --git a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts index ccf594058..77f2a3974 100644 --- a/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts +++ b/apps/cde-ui/src/app/pages/create-visualization-page/create-visualization-page.component.ts @@ -24,7 +24,12 @@ import { } from '@hra-ui/cde-visualization'; import { BreadcrumbsComponent } from '@hra-ui/design-system/breadcrumbs'; import { ButtonModule } from '@hra-ui/design-system/button'; +import { ToggleButtonSizeDirective } from '@hra-ui/design-system/button-toggle'; import { FooterComponent } from '@hra-ui/design-system/footer'; +import { NavHeaderComponent } from '@hra-ui/design-system/nav-header'; +import { SelectSizeDirective } from '@hra-ui/design-system/select'; +import { StepIndicatorComponent } from '@hra-ui/design-system/step-indicator'; +import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; import { ParseError } from 'papaparse'; import { MarkEmptyFormControlDirective } from '../../components/empty-form-control/empty-form-control.directive'; @@ -33,11 +38,6 @@ import { HeaderComponent } from '../../components/header/header.component'; import { VisualizationDataService } from '../../services/visualization-data-service/visualization-data.service'; import { validateInteger } from '../../shared/form-validators/is-integer'; import { OrganEntry } from '../../shared/resolvers/organs/organs.resolver'; -import { StepIndicatorComponent } from '@hra-ui/design-system/step-indicator'; -import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; -import { ToggleButtonSizeDirective } from '@hra-ui/design-system/button-toggle'; -import { NavHeaderComponent } from '@hra-ui/design-system/nav-header'; -import { SelectSizeDirective } from '@hra-ui/design-system/select'; /** Error when missing required columns in uploaded csv */ export interface MissingKeyError { @@ -74,18 +74,18 @@ function optionalValue(): T | null { MatSelectModule, MatTableModule, + BreadcrumbsComponent, + ButtonModule, FileUploadComponent, FooterComponent, HeaderComponent, MarkEmptyFormControlDirective, + NavHeaderComponent, OverlayModule, - ButtonModule, - BreadcrumbsComponent, + SelectSizeDirective, StepIndicatorComponent, - TooltipCardComponent, ToggleButtonSizeDirective, - SelectSizeDirective, - NavHeaderComponent, + TooltipCardComponent, ], templateUrl: './create-visualization-page.component.html', styleUrl: './create-visualization-page.component.scss', @@ -180,6 +180,7 @@ export class CreateVisualizationPageComponent { /** Tooltip position config */ readonly tooltipPosition = TOOLTIP_POSITION_BELOW; + /** Tooltip content */ readonly tooltips: TooltipContent[][] = [ [ { @@ -286,7 +287,7 @@ export class CreateVisualizationPageComponent { const errorColumns = [xError, yError, ctError].filter((e) => !!e); return errorColumns.length > 0 - ? `Please select the required column headers: ${[xError, yError, ctError].filter((e) => !!e).join(', ')}` + ? `Please select the required column header${errorColumns.length === 1 ? '' : 's'}: ${[xError, yError, ctError].filter((e) => !!e).join(', ')}` : undefined; } @@ -523,7 +524,7 @@ export class CreateVisualizationPageComponent { private formatErrorMessage(error: ExtendedFileLoadError): string { switch (error.type) { case 'missing-key-error': - return `Required columns missing: ${error.keys.join(', ')}`; + return `Required column${error.keys.length === 1 ? '' : 's'} missing: ${error.keys.join(', ')}`; case 'type-error': return `Invalid file type: ${error.received}, expected csv`; From 8c34da149565a64d72387df63f888b4eff9d8d59 Mon Sep 17 00:00:00 2001 From: edlu77 Date: Wed, 2 Oct 2024 00:32:20 -0400 Subject: [PATCH 41/50] Remove redundant assets --- .../data/examples/example-csvs}/color_map.csv | 0 .../color_map_wrong_column_name.csv | 0 .../data/examples/example-csvs}/nodes.csv | 0 .../example-csvs}/nodes_renamed_columns.csv | 0 .../nodes_slightly_renamed_columns.csv | 0 .../src/assets/fonts/metropolis.medium.otf | Bin 23240 -> 0 bytes .../src/assets/fonts/metropolis.regular.otf | Bin 23124 -> 0 bytes .../src/assets/icons/settings_alert.svg | 3 -- apps/cde-ui/src/assets/icons/social/email.svg | 9 ----- .../src/assets/icons/social/email_large.svg | 9 ----- .../src/assets/icons/social/facebook.svg | 17 --------- .../assets/icons/social/facebook_large.svg | 17 --------- .../src/assets/icons/social/instagram.svg | 11 ------ .../assets/icons/social/instagram_large.svg | 11 ------ .../src/assets/icons/social/linkedin.svg | 7 ---- .../assets/icons/social/linkedin_large.svg | 7 ---- apps/cde-ui/src/assets/icons/social/x.svg | 4 --- .../src/assets/icons/social/x_large.svg | 4 --- .../src/assets/icons/social/youtube.svg | 12 ------- .../src/assets/icons/social/youtube_large.svg | 5 --- apps/cde-ui/src/assets/icons/upload.svg | 15 -------- apps/cde-ui/src/assets/logo/cde_logo.svg | 15 -------- apps/cde-ui/src/assets/logo/cifar.svg | 20 ----------- apps/cde-ui/src/assets/logo/hra_logo.svg | 33 ----------------- .../cde-ui/src/assets/logo/hra_logo_black.svg | 34 ------------------ apps/cde-ui/src/assets/logo/hra_small.svg | 15 -------- apps/cde-ui/src/assets/logo/iu.svg | 10 ------ apps/cde-ui/src/assets/logo/nih.svg | 4 --- 28 files changed, 262 deletions(-) rename apps/cde-ui/{example-data => src/assets/data/examples/example-csvs}/color_map.csv (100%) rename apps/cde-ui/{example-data => src/assets/data/examples/example-csvs}/color_map_wrong_column_name.csv (100%) rename apps/cde-ui/{example-data => src/assets/data/examples/example-csvs}/nodes.csv (100%) rename apps/cde-ui/{example-data => src/assets/data/examples/example-csvs}/nodes_renamed_columns.csv (100%) rename apps/cde-ui/{example-data => src/assets/data/examples/example-csvs}/nodes_slightly_renamed_columns.csv (100%) delete mode 100644 apps/cde-ui/src/assets/fonts/metropolis.medium.otf delete mode 100644 apps/cde-ui/src/assets/fonts/metropolis.regular.otf delete mode 100644 apps/cde-ui/src/assets/icons/settings_alert.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/email.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/email_large.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/facebook.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/facebook_large.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/instagram.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/instagram_large.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/linkedin.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/linkedin_large.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/x.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/x_large.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/youtube.svg delete mode 100644 apps/cde-ui/src/assets/icons/social/youtube_large.svg delete mode 100644 apps/cde-ui/src/assets/icons/upload.svg delete mode 100644 apps/cde-ui/src/assets/logo/cde_logo.svg delete mode 100644 apps/cde-ui/src/assets/logo/cifar.svg delete mode 100644 apps/cde-ui/src/assets/logo/hra_logo.svg delete mode 100644 apps/cde-ui/src/assets/logo/hra_logo_black.svg delete mode 100644 apps/cde-ui/src/assets/logo/hra_small.svg delete mode 100644 apps/cde-ui/src/assets/logo/iu.svg delete mode 100644 apps/cde-ui/src/assets/logo/nih.svg diff --git a/apps/cde-ui/example-data/color_map.csv b/apps/cde-ui/src/assets/data/examples/example-csvs/color_map.csv similarity index 100% rename from apps/cde-ui/example-data/color_map.csv rename to apps/cde-ui/src/assets/data/examples/example-csvs/color_map.csv diff --git a/apps/cde-ui/example-data/color_map_wrong_column_name.csv b/apps/cde-ui/src/assets/data/examples/example-csvs/color_map_wrong_column_name.csv similarity index 100% rename from apps/cde-ui/example-data/color_map_wrong_column_name.csv rename to apps/cde-ui/src/assets/data/examples/example-csvs/color_map_wrong_column_name.csv diff --git a/apps/cde-ui/example-data/nodes.csv b/apps/cde-ui/src/assets/data/examples/example-csvs/nodes.csv similarity index 100% rename from apps/cde-ui/example-data/nodes.csv rename to apps/cde-ui/src/assets/data/examples/example-csvs/nodes.csv diff --git a/apps/cde-ui/example-data/nodes_renamed_columns.csv b/apps/cde-ui/src/assets/data/examples/example-csvs/nodes_renamed_columns.csv similarity index 100% rename from apps/cde-ui/example-data/nodes_renamed_columns.csv rename to apps/cde-ui/src/assets/data/examples/example-csvs/nodes_renamed_columns.csv diff --git a/apps/cde-ui/example-data/nodes_slightly_renamed_columns.csv b/apps/cde-ui/src/assets/data/examples/example-csvs/nodes_slightly_renamed_columns.csv similarity index 100% rename from apps/cde-ui/example-data/nodes_slightly_renamed_columns.csv rename to apps/cde-ui/src/assets/data/examples/example-csvs/nodes_slightly_renamed_columns.csv diff --git a/apps/cde-ui/src/assets/fonts/metropolis.medium.otf b/apps/cde-ui/src/assets/fonts/metropolis.medium.otf deleted file mode 100644 index 239d69dc23299efaf89c57c0879b9c18a56919ed..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 23240 zcmdVCcR&=$vpC+fvoi}lx+?3U0<()*45*kBf&s;d85IK}3X&w7!BbD~^iI9=#4L&d z6~!!y5fdtAMa*IZMT}<;*NgnBXYtN^@AJOz{rh9-o|^9JINjA%)m`0x@ZkQa0!l9kCB&R*Y;5`E&TTPEaL%JXi zV$g`A;Nkv*nz{w`+ZKV4@C4q+288)fKEM2g4Mah_FgGaBe>^@QB|+RRaIJ$NK+M%n 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+++ /dev/null @@ -1,9 +0,0 @@ - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/email_large.svg b/apps/cde-ui/src/assets/icons/social/email_large.svg deleted file mode 100644 index 7624a60fe..000000000 --- a/apps/cde-ui/src/assets/icons/social/email_large.svg +++ /dev/null @@ -1,9 +0,0 @@ - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/facebook.svg b/apps/cde-ui/src/assets/icons/social/facebook.svg deleted file mode 100644 index c2683f86d..000000000 --- a/apps/cde-ui/src/assets/icons/social/facebook.svg +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/facebook_large.svg b/apps/cde-ui/src/assets/icons/social/facebook_large.svg deleted file mode 100644 index bf4bfdc43..000000000 --- a/apps/cde-ui/src/assets/icons/social/facebook_large.svg +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/instagram.svg b/apps/cde-ui/src/assets/icons/social/instagram.svg deleted file mode 100644 index ab3cd1360..000000000 --- a/apps/cde-ui/src/assets/icons/social/instagram.svg +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/instagram_large.svg b/apps/cde-ui/src/assets/icons/social/instagram_large.svg deleted file mode 100644 index 0bb67b58e..000000000 --- a/apps/cde-ui/src/assets/icons/social/instagram_large.svg +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/linkedin.svg b/apps/cde-ui/src/assets/icons/social/linkedin.svg deleted file mode 100644 index 40994c344..000000000 --- a/apps/cde-ui/src/assets/icons/social/linkedin.svg +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/linkedin_large.svg b/apps/cde-ui/src/assets/icons/social/linkedin_large.svg deleted file mode 100644 index 6a60bb43b..000000000 --- a/apps/cde-ui/src/assets/icons/social/linkedin_large.svg +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/x.svg b/apps/cde-ui/src/assets/icons/social/x.svg deleted file mode 100644 index d0f6c2043..000000000 --- a/apps/cde-ui/src/assets/icons/social/x.svg +++ /dev/null @@ -1,4 +0,0 @@ - - - - diff --git a/apps/cde-ui/src/assets/icons/social/x_large.svg b/apps/cde-ui/src/assets/icons/social/x_large.svg deleted file mode 100644 index fe9d7ea23..000000000 --- a/apps/cde-ui/src/assets/icons/social/x_large.svg +++ /dev/null @@ -1,4 +0,0 @@ - - - - diff --git a/apps/cde-ui/src/assets/icons/social/youtube.svg b/apps/cde-ui/src/assets/icons/social/youtube.svg deleted file mode 100644 index 92a33b819..000000000 --- a/apps/cde-ui/src/assets/icons/social/youtube.svg +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/icons/social/youtube_large.svg b/apps/cde-ui/src/assets/icons/social/youtube_large.svg deleted file mode 100644 index 305cacd97..000000000 --- a/apps/cde-ui/src/assets/icons/social/youtube_large.svg +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/apps/cde-ui/src/assets/icons/upload.svg b/apps/cde-ui/src/assets/icons/upload.svg deleted file mode 100644 index 5a238de7f..000000000 --- a/apps/cde-ui/src/assets/icons/upload.svg +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/cde_logo.svg b/apps/cde-ui/src/assets/logo/cde_logo.svg deleted file mode 100644 index ee0b60d9e..000000000 --- a/apps/cde-ui/src/assets/logo/cde_logo.svg +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/cifar.svg b/apps/cde-ui/src/assets/logo/cifar.svg deleted file mode 100644 index 6dfd3d901..000000000 --- a/apps/cde-ui/src/assets/logo/cifar.svg +++ /dev/null @@ -1,20 +0,0 @@ - - - - - - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/hra_logo.svg b/apps/cde-ui/src/assets/logo/hra_logo.svg deleted file mode 100644 index dc3ee658f..000000000 --- a/apps/cde-ui/src/assets/logo/hra_logo.svg +++ /dev/null @@ -1,33 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/hra_logo_black.svg b/apps/cde-ui/src/assets/logo/hra_logo_black.svg deleted file mode 100644 index 7bd9cad21..000000000 --- a/apps/cde-ui/src/assets/logo/hra_logo_black.svg +++ /dev/null @@ -1,34 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/hra_small.svg b/apps/cde-ui/src/assets/logo/hra_small.svg deleted file mode 100644 index 99ae65502..000000000 --- a/apps/cde-ui/src/assets/logo/hra_small.svg +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/iu.svg b/apps/cde-ui/src/assets/logo/iu.svg deleted file mode 100644 index 5b548b75b..000000000 --- a/apps/cde-ui/src/assets/logo/iu.svg +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/apps/cde-ui/src/assets/logo/nih.svg b/apps/cde-ui/src/assets/logo/nih.svg deleted file mode 100644 index 24e1666d7..000000000 --- a/apps/cde-ui/src/assets/logo/nih.svg +++ /dev/null @@ -1,4 +0,0 @@ - - - - From 9447f60797a67995cbc450381b2746cadebd2e21 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Wed, 2 Oct 2024 12:17:18 -0400 Subject: [PATCH 42/50] add toggle links column functionality --- .../cell-types/cell-types.component.html | 12 ++++-- .../cell-types/cell-types.component.scss | 14 +++++-- .../cell-types/cell-types.component.ts | 39 +++++++++++++++---- .../color-picker-label.component.scss | 2 +- 4 files changed, 50 insertions(+), 17 deletions(-) diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index 58a235a26..830fbbd82 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -14,7 +14,7 @@ Download arrow_right - @@ -58,6 +58,10 @@ {{ totalCellCount() | number }} Total Cells

+
+ {{ totalCellLinksCount() | number }} + Total Cell Links +
-

- + + diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss index c6a7ae7a6..1d106195e 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss @@ -24,7 +24,7 @@ $blue-theme: mat.m2-define-light-theme( display: grid; grid: 'cell-types . download' - 'total-cell-types . total-cells' + 'total-cell-types total-cells total-cell-links' 'table table table' 1fr / auto 1fr auto; align-items: start; @@ -72,7 +72,8 @@ $blue-theme: mat.m2-define-light-theme( } .total-ct-label, - .total-cells { + .total-cells, + .total-cell-links { font: var(--sys-label-small); letter-spacing: var(--sys-label-medium-tracking); @@ -90,6 +91,11 @@ $blue-theme: mat.m2-define-light-theme( .total-cells { grid-area: total-cells; + justify-self: center; + } + + .total-cell-links { + grid-area: total-cell-links; } .table-overflow-container { @@ -133,9 +139,9 @@ $blue-theme: mat.m2-define-light-theme( } } - tbody tr td.mdc-data-table__cell:last-child { + tbody tr td.mdc-data-table__cell:nth-last-child(-n + 2) { text-align: end; - padding-right: 1.65rem; + padding-right: 1.5rem; color: var(--sys-primary); font: var(--sys-label-small); } diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts index 5b60f4c47..adbaad9da 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts @@ -80,8 +80,11 @@ export class CellTypesComponent { /** Output event for reset color */ readonly resetAllColors = output(); + /** Base columns to be displayed in the table */ + private readonly baseColumns = ['select', 'cellType', 'count']; + /** Columns to be displayed in the table */ - protected readonly columns = ['select', 'cellType', 'count', 'links']; + protected columns = [...this.baseColumns, 'links']; /** Tooltip position configuration */ protected readonly tooltipPosition = TOOLTIP_POSITION_RIGHT_SIDE; @@ -98,7 +101,7 @@ export class CellTypesComponent { ]; /** Flag to toggle cell links row visibility */ - hideCellLinkData = false; + protected hideCellLinkData = false; /** Bind sort state to data source */ protected readonly sortBindRef = effect(() => (this.dataSource.sort = this.sort())); @@ -112,7 +115,6 @@ export class CellTypesComponent { /** Bind data source to cell types */ protected readonly dataSourceBindRef = effect(() => { this.dataSource.data = this.cellTypes(); - console.log(this.cellTypes()); this.cdr.markForCheck(); }); @@ -147,17 +149,25 @@ export class CellTypesComponent { } }); + /** Helper function to calculate the number of nodes or edges */ + protected readonly sumCounts = (count: number, entry: CellTypeEntry, key: 'count' | 'outgoingEdgeCount') => { + const value = this.isSelected(entry) ? entry[key] : 0; + return count + value; + }; + /** Computed total cell count based on selection */ protected totalCellCount = computed(() => { - const sumCounts = (count: number, entry: CellTypeEntry) => { - const value = this.isSelected(entry) ? entry.count : 0; - return count + value; - }; + // Grab dependency on current selection since selectionModel is used indirectly + this.selection(); + + return this.cellTypes().reduce((count, entry) => this.sumCounts(count, entry, 'count'), 0); + }); + protected totalCellLinksCount = computed(() => { // Grab dependency on current selection since selectionModel is used indirectly this.selection(); - return this.cellTypes().reduce(sumCounts, 0); + return this.cellTypes().reduce((count, entry) => this.sumCounts(count, entry, 'outgoingEdgeCount'), 0); }); /** Toggle state for cell types info */ @@ -212,4 +222,17 @@ export class CellTypesComponent { } while (sorter.direction !== 'desc'); } } + + private updateColumns() { + if (this.hideCellLinkData) { + this.columns = this.columns.filter((column) => column !== 'links'); + } else if (!this.columns.includes('links')) { + this.columns = [...this.baseColumns, 'links']; + } + } + + toggleLinksColumn(): void { + this.hideCellLinkData = !this.hideCellLinkData; + this.updateColumns(); + } } diff --git a/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss b/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss index e83ad0d4f..49996543e 100644 --- a/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss +++ b/libs/cde-visualization/src/lib/components/color-picker-label/color-picker-label.component.scss @@ -34,7 +34,7 @@ cursor: pointer; display: block; white-space: nowrap; - max-width: 8.25rem; + max-width: calc(100% - 3.5rem); text-overflow: ellipsis; overflow: hidden; flex-grow: 0; From 1b6778a05ef5bf7cc0082698afe65f6e5ef4e6f0 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Wed, 2 Oct 2024 13:20:09 -0400 Subject: [PATCH 43/50] compute columns based on the links visibility signal --- .../cell-types/cell-types.component.html | 28 ++++++++------- .../cell-types/cell-types.component.scss | 22 ++++++++++-- .../cell-types/cell-types.component.ts | 35 +++++++------------ 3 files changed, 48 insertions(+), 37 deletions(-) diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index 830fbbd82..6bd36af3e 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -15,8 +15,8 @@ arrow_right + + - + - - + +
Cell Type + Cell Type - #Cells#Cells {{ element.count.toLocaleString() }} Cell TypeCell Type - #Cells#Cells {{ element.count.toLocaleString() }} #Links#Links {{ element.outgoingEdgeCount.toLocaleString() }}
diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss index 1d106195e..ecaf5a5ad 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.scss @@ -48,6 +48,14 @@ $blue-theme: mat.m2-define-light-theme( --mat-table-header-container-height: 2rem; --mat-menu-item-label-text-color: var(--sys-primary); + &:not(:has(.total-cell-links)) { + grid: + 'cell-types . download' + 'total-cell-types . total-cells' + 'table table table' 1fr + / auto 1fr auto; + } + span.cell-types-label { font: var(--sys-label-medium); letter-spacing: var(--sys-label-medium-tracking); @@ -219,6 +227,16 @@ $blue-theme: mat.m2-define-light-theme( } } -::ng-deep .mat-mdc-menu-content button { - color: var(--sys-primary); +::ng-deep { + .mat-mdc-menu-content button { + color: var(--sys-primary); + } + + div.mat-mdc-menu-panel { + max-width: 308px; + &.info-sub-menu .mat-mdc-menu-content { + padding: 1rem 1rem; + color: var(--sys-primary); + } + } } diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts index adbaad9da..e2f410deb 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts @@ -11,6 +11,7 @@ import { input, model, output, + signal, viewChild, } from '@angular/core'; import { toSignal } from '@angular/core/rxjs-interop'; @@ -25,7 +26,7 @@ import { MatTableDataSource, MatTableModule } from '@angular/material/table'; import { Rgb } from '@hra-ui/design-system/color-picker'; import { IconButtonSizeDirective } from '@hra-ui/design-system/icon-button'; import { ScrollingModule } from '@hra-ui/design-system/scrolling'; -import { TooltipCardComponent, TooltipContent } from '@hra-ui/design-system/tooltip-card'; +import { TooltipCardComponent } from '@hra-ui/design-system/tooltip-card'; import { ColorPickerModule } from 'ngx-color-picker'; import { map } from 'rxjs'; import { CellTypeEntry } from '../../models/cell-type'; @@ -80,11 +81,14 @@ export class CellTypesComponent { /** Output event for reset color */ readonly resetAllColors = output(); - /** Base columns to be displayed in the table */ - private readonly baseColumns = ['select', 'cellType', 'count']; - /** Columns to be displayed in the table */ - protected columns = [...this.baseColumns, 'links']; + protected readonly columns = computed(() => { + if (this.hideCellLinkData()) { + return ['select', 'cellType', 'count']; + } else { + return ['select', 'cellType', 'count', 'links']; + } + }); /** Tooltip position configuration */ protected readonly tooltipPosition = TOOLTIP_POSITION_RIGHT_SIDE; @@ -93,15 +97,11 @@ export class CellTypesComponent { protected readonly sort = viewChild.required(MatSort); /** Content for Info Tooltip card */ - protected readonly infoToolTip: TooltipContent[] = [ - { - description: - 'Show/hide cell types in the visualization and plots. Hide cell links from this table view. Update colors for individual cell types. Download CSVs for the current configurations of cell types, cell links, and cell type color map formatting.', - }, - ]; + protected readonly infoToolTipDescription: string = + 'Show/hide cell types in the visualization and plots. Hide cell links from this table view. Update colors for individual cell types. Download CSVs for the current configurations of cell types, cell links, and cell type color map formatting.'; /** Flag to toggle cell links row visibility */ - protected hideCellLinkData = false; + protected hideCellLinkData = signal(false); /** Bind sort state to data source */ protected readonly sortBindRef = effect(() => (this.dataSource.sort = this.sort())); @@ -223,16 +223,7 @@ export class CellTypesComponent { } } - private updateColumns() { - if (this.hideCellLinkData) { - this.columns = this.columns.filter((column) => column !== 'links'); - } else if (!this.columns.includes('links')) { - this.columns = [...this.baseColumns, 'links']; - } - } - toggleLinksColumn(): void { - this.hideCellLinkData = !this.hideCellLinkData; - this.updateColumns(); + this.hideCellLinkData.set(!this.hideCellLinkData); } } From d57034583562d610a6db76f2e78a5b65427206cf Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Wed, 2 Oct 2024 13:47:12 -0400 Subject: [PATCH 44/50] fix toggle signal for cell links --- .../cde-visualization/cde-visualization.component.spec.ts | 6 ++++++ .../lib/components/cell-types/cell-types.component.html | 2 +- .../lib/components/cell-types/cell-types.component.spec.ts | 6 +++--- .../src/lib/components/cell-types/cell-types.component.ts | 7 ++++--- .../lib/components/histogram/histogram.component.spec.ts | 6 +++--- 5 files changed, 17 insertions(+), 10 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts index 258011ec3..98cefb6d7 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts @@ -307,16 +307,19 @@ describe('CdeVisualizationComponent', () => { name: 'a', count: 1, color: [0, 0, 0], + outgoingEdgeCount: 0, }, { name: 'b', count: 1, color: [0, 0, 1], + outgoingEdgeCount: 0, }, { name: 'c', count: 1, color: [0, 0, 2], + outgoingEdgeCount: 0, }, ]); }); @@ -336,16 +339,19 @@ describe('CdeVisualizationComponent', () => { name: 'a', count: 1, color: [112, 165, 168], + outgoingEdgeCount: 0, }, { name: 'b', count: 2, color: [205, 132, 144], + outgoingEdgeCount: 0, }, { name: 'c', count: 1, color: [116, 149, 174], + outgoingEdgeCount: 0, }, ]); }); diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index 6bd36af3e..64fd3f807 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -58,7 +58,7 @@ {{ totalCellCount() | number }} Total Cells -@if (!hideCellLinkData) { +@if (!hideCellLinkData()) {
{{ totalCellLinksCount() | number }} Total Cell Links diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.spec.ts b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.spec.ts index 5db548c61..f022e76e2 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.spec.ts +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.spec.ts @@ -7,9 +7,9 @@ import { CellTypesComponent } from './cell-types.component'; describe('CellTypesComponent', () => { const cellTypes: CellTypeEntry[] = [ - { name: 'Cell Type 1', count: 100, color: [0, 1, 2] }, - { name: 'Cell Type 2', count: 200, color: [3, 4, 5] }, - { name: 'Cell Type 3', count: 300, color: [6, 7, 8] }, + { name: 'Cell Type 1', count: 100, color: [0, 1, 2], outgoingEdgeCount: 0 }, + { name: 'Cell Type 2', count: 200, color: [3, 4, 5], outgoingEdgeCount: 0 }, + { name: 'Cell Type 3', count: 300, color: [6, 7, 8], outgoingEdgeCount: 0 }, ]; const cellTypesSelection = [cellTypes[0].name, cellTypes[1].name]; diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts index e2f410deb..af12d3ba3 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.ts @@ -97,8 +97,9 @@ export class CellTypesComponent { protected readonly sort = viewChild.required(MatSort); /** Content for Info Tooltip card */ - protected readonly infoToolTipDescription: string = - 'Show/hide cell types in the visualization and plots. Hide cell links from this table view. Update colors for individual cell types. Download CSVs for the current configurations of cell types, cell links, and cell type color map formatting.'; + protected readonly infoToolTipDescription: string = `Show/hide cell types in the visualization and plots. Hide cell links from this table view. + Update colors for individual cell types. Download CSVs for the current configurations of + cell types, cell links, and cell type color map formatting.`; /** Flag to toggle cell links row visibility */ protected hideCellLinkData = signal(false); @@ -224,6 +225,6 @@ export class CellTypesComponent { } toggleLinksColumn(): void { - this.hideCellLinkData.set(!this.hideCellLinkData); + this.hideCellLinkData.set(!this.hideCellLinkData()); } } diff --git a/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts b/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts index 132e23609..a5b8312a3 100644 --- a/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts +++ b/libs/cde-visualization/src/lib/components/histogram/histogram.component.spec.ts @@ -27,9 +27,9 @@ describe('HistogramComponent', () => { [2, 0, 4, 3, 4, 5, 6], ]; const sampleCellTypes: CellTypeEntry[] = [ - { name: 'a', count: 2, color: [0, 0, 0] }, - { name: 'b', count: 4, color: [0, 1, 2] }, - { name: 'c', count: 6, color: [0, 1, 3] }, + { name: 'a', count: 2, color: [0, 0, 0], outgoingEdgeCount: 0 }, + { name: 'b', count: 4, color: [0, 1, 2], outgoingEdgeCount: 0 }, + { name: 'c', count: 6, color: [0, 1, 3], outgoingEdgeCount: 0 }, ]; const sampleCellTypesSelection: string[] = [sampleCellTypes[0].name, sampleCellTypes[1].name]; From 6bfe69865e4dd567013fcf9c55ef857a7620fb53 Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Tue, 1 Oct 2024 16:01:20 -0400 Subject: [PATCH 45/50] fix(eui): Update api endpoint service to respect user provided database tokens --- .vscode/settings.json | 3 +- .../data-source/api-endpoint.service.ts | 101 ++++++++---------- 2 files changed, 48 insertions(+), 56 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 8a2aa6c80..bdaa61ed7 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -12,6 +12,7 @@ "services", "ccf-organ-info", "design-system", - "body-ui" + "body-ui", + "eui" ] } diff --git a/libs/ccf-shared/src/lib/services/data-source/api-endpoint.service.ts b/libs/ccf-shared/src/lib/services/data-source/api-endpoint.service.ts index a1e26a806..ff078ec82 100644 --- a/libs/ccf-shared/src/lib/services/data-source/api-endpoint.service.ts +++ b/libs/ccf-shared/src/lib/services/data-source/api-endpoint.service.ts @@ -1,7 +1,6 @@ -import { Injectable } from '@angular/core'; +import { inject, Injectable } from '@angular/core'; import { AggregateCount, - Filter as ApiFilter, DatabaseStatus, Filter, MinMax, @@ -13,15 +12,17 @@ import { V1Service, } from '@hra-api/ng-client'; import { Matrix4 } from '@math.gl/core'; -import { Observable, ReplaySubject, Subject, combineLatest, of } from 'rxjs'; +import { Observable, of, Subject } from 'rxjs'; import { debounceTime, delay, + distinctUntilChanged, endWith, filter, ignoreElements, map, repeat, + shareReplay, switchMap, take, tap, @@ -107,28 +108,34 @@ function filterToParams(filter?: Filter): FilterParams { }; } +function compareConfig(x: ApiEndpointDataSourceOptions, y: ApiEndpointDataSourceOptions): boolean { + if (x.remoteApiEndpoint !== y.remoteApiEndpoint || x.token !== y.token) { + return false; + } else if (x.token !== undefined) { + return true; + } else { + // Deep compare? + return x.filter === y.filter && x.dataSources === y.dataSources; + } +} + @Injectable({ providedIn: 'root', }) export class ApiEndpointDataSourceService implements DataSource { - private readonly initialized = new ReplaySubject(1); - - constructor( - private readonly api: V1Service, - private readonly globalConfig: GlobalConfigState, - ) { - this.getSessionToken() - .pipe( - tap((token) => globalConfig.patchConfig({ token })), - tap(buster$), - debounceTime(1), - ) - .subscribe(() => { - if (!this.initialized.closed) { - this.initialized.next(); - this.initialized.complete(); - } - }); + private readonly api = inject(V1Service); + private readonly globalConfig: GlobalConfigState = inject(GlobalConfigState); + private readonly config$ = this.globalConfig.config$.pipe( + map(cast()), + distinctUntilChanged(compareConfig), + debounceTime(10), + switchMap((config) => this.getSessionToken(config)), + tap(() => buster$.next(null)), + shareReplay(1), + ); + + constructor() { + this.config$.subscribe(); } getDatabaseStatus(): Observable { @@ -222,18 +229,14 @@ export class ApiEndpointDataSourceService implements DataSource { params?: P, reviver?: DataReviver, ): Observable { - const { api, globalConfig } = this; + const { api, config$ } = this; const requestParams: Record = { ...filterToParams(filter), ...params }; - return combineLatest([ - globalConfig.getOption('remoteApiEndpoint'), - globalConfig.getOption('token'), - this.initialized, - ]).pipe( - debounceTime(1), + return config$.pipe( + debounceTime(50), take(1), - tap(([endpoint, token]) => { - api.configuration.basePath = endpoint; + tap(({ remoteApiEndpoint, token }) => { + api.configuration.basePath = remoteApiEndpoint; if (token) { requestParams['token'] = token; } @@ -243,35 +246,23 @@ export class ApiEndpointDataSourceService implements DataSource { ); } - private getSessionToken(): Observable { - const { globalConfig } = this; - const dataSources = globalConfig.getOption('dataSources'); - const filter = globalConfig.getOption('filter'); - return combineLatest([dataSources, filter]).pipe( - debounceTime(50), - switchMap((args) => this.getSessionTokenImpl(...args)), - switchMap((token) => this.ensureDatabaseReady(token)), - ); - } + private getSessionToken(config: ApiEndpointDataSourceOptions): Observable { + if (config.token) { + return of(config); + } - private getSessionTokenImpl( - dataSources: string[] | undefined, - filter: Filter | undefined, - ): Observable { - if ((dataSources === undefined || dataSources.length === 0) && filter === undefined) { - return of(undefined); + const { remoteApiEndpoint, dataSources = [], filter } = config; + if (dataSources.length === 0 && filter === undefined) { + return of(config); } - const { api, globalConfig } = this; - const sessionTokenRequest = { - dataSources: dataSources ?? [], - filter: filter as ApiFilter, - }; + const { api } = this; + const sessionTokenRequest = { dataSources, filter }; + api.configuration.basePath = remoteApiEndpoint; - return globalConfig.getOption('remoteApiEndpoint').pipe( - tap((endpoint) => (api.configuration.basePath = endpoint)), - switchMap(() => api.sessionToken({ sessionTokenRequest })), - map(({ token }) => token), + return api.sessionToken({ sessionTokenRequest }).pipe( + switchMap(({ token }) => this.ensureDatabaseReady(token)), + map((token) => ({ ...config, token })), ); } From b1b9df97b4cfc8c80528acfed2f5dfc028fef631 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Wed, 2 Oct 2024 15:30:09 -0400 Subject: [PATCH 46/50] fix tests for downloads --- .../cde-visualization.component.spec.ts | 15 +++++++++------ .../cell-types/cell-types.component.html | 2 +- .../node-dist-visualization.component.spec.ts | 6 +++--- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts index 98cefb6d7..3c488f069 100644 --- a/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts +++ b/libs/cde-visualization/src/lib/cde-visualization/cde-visualization.component.spec.ts @@ -4,8 +4,10 @@ import userEvent from '@testing-library/user-event'; import { mockDeep } from 'jest-mock-extended'; import embed, { Result } from 'vega-embed'; -import { provideScrolling } from '@hra-ui/design-system/scrolling'; +import { TestbedHarnessEnvironment } from '@angular/cdk/testing/testbed'; +import { MatMenuHarness } from '@angular/material/menu/testing'; import { rgbToHex } from '@hra-ui/design-system/color-picker'; +import { provideScrolling } from '@hra-ui/design-system/scrolling'; import { ColorMapEntry, DEFAULT_COLOR_MAP_KEY, DEFAULT_COLOR_MAP_VALUE_KEY } from '../models/color-map'; import { EdgeEntry } from '../models/edge'; import { DEFAULT_NODE_TARGET_KEY, DEFAULT_NODE_TARGET_VALUE, NodeEntry } from '../models/node'; @@ -144,9 +146,7 @@ describe('CdeVisualizationComponent', () => { }); it('should update color map when downloadColorMap is called', async () => { - const { - fixture: { componentInstance: instance }, - } = await setup({ + const { fixture } = await setup({ componentInputs: { ...sampleData, nodes: sampleNodes, @@ -154,6 +154,7 @@ describe('CdeVisualizationComponent', () => { }, }); + const instance = fixture.componentInstance; const processedColorMap = instance .cellTypesAsColorMap() .map((entry) => ({ ...entry, [instance.colorMapValueKey()]: rgbToHex(entry[instance.colorMapValueKey()]) })); @@ -161,8 +162,10 @@ describe('CdeVisualizationComponent', () => { const fileSaver = TestBed.inject(FileSaverService); const fileSaveSpy = jest.spyOn(fileSaver, 'saveCsv').mockReturnValue(undefined); - const downloadColorMapButton = screen.getByText('CSV'); - await userEvent.click(downloadColorMapButton); + const loader = TestbedHarnessEnvironment.loader(fixture); + const menu = await loader.getHarness(MatMenuHarness); + + await menu.clickItem({ text: /Download/ }, { text: /Cell Color Map CSV/ }); expect(fileSaveSpy).toHaveBeenCalledWith(processedColorMap, 'color-map.csv'); }); diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index 64fd3f807..ffcd0c7e9 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -1,6 +1,6 @@ Cell Types - diff --git a/libs/cde-visualization/src/lib/components/node-dist-visualization/node-dist-visualization.component.spec.ts b/libs/cde-visualization/src/lib/components/node-dist-visualization/node-dist-visualization.component.spec.ts index 7cef99e51..90be09dbf 100644 --- a/libs/cde-visualization/src/lib/components/node-dist-visualization/node-dist-visualization.component.spec.ts +++ b/libs/cde-visualization/src/lib/components/node-dist-visualization/node-dist-visualization.component.spec.ts @@ -54,9 +54,9 @@ describe('NodeDistVisualizationComponent', () => { [2, 0, 4, 3, 4, 5, 6], ]; const sampleCellTypes: CellTypeEntry[] = [ - { name: 'a', count: 2, color: [0, 0, 0] }, - { name: 'b', count: 4, color: [0, 1, 2] }, - { name: 'c', count: 6, color: [0, 1, 3] }, + { name: 'a', count: 2, color: [0, 0, 0], outgoingEdgeCount: 0 }, + { name: 'b', count: 4, color: [0, 1, 2], outgoingEdgeCount: 0 }, + { name: 'c', count: 6, color: [0, 1, 3], outgoingEdgeCount: 0 }, ]; const sampleCellTypesSelection: string[] = [sampleCellTypes[0].name, sampleCellTypes[1].name]; From 457b4a4dbe3d545de6432807f4b3393517fc9354 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Wed, 2 Oct 2024 15:50:47 -0400 Subject: [PATCH 47/50] update snackbar timer --- .../src/lib/services/file-saver/file-saver.service.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts b/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts index 5c413684f..764486570 100644 --- a/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts +++ b/libs/cde-visualization/src/lib/services/file-saver/file-saver.service.ts @@ -28,7 +28,7 @@ export class FileSaverService { document.body.appendChild(linkEl); linkEl.dispatchEvent(new MouseEvent('click')); document.body.removeChild(linkEl); - this.snackbar.open('File downloaded', '', false, 'end', { duration: 1000 }); + this.snackbar.open('File downloaded', '', false, 'end', { duration: 5000 }); } /** Saves a Blob as a file with a given filename */ From 43c4ba3691bf23149bba31610cffa8fdabb6c0c0 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Wed, 2 Oct 2024 15:52:05 -0400 Subject: [PATCH 48/50] add noreferrer to link --- .../src/lib/components/cell-types/cell-types.component.html | 1 + 1 file changed, 1 insertion(+) diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index ffcd0c7e9..fcd6f668d 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -26,6 +26,7 @@ mat-menu-item href="https://github.com/hubmapconsortium/hra-ui/blob/main/apps/cde-visualization-wc/EMBEDDING.md" target="_blank" + rel="noopener noreferrer" > code Embed App From 49e7c43654ed9d088d407eaa408d66517363df53 Mon Sep 17 00:00:00 2001 From: Bhushan Khope Date: Tue, 8 Oct 2024 12:08:08 -0400 Subject: [PATCH 49/50] add micro tooltip to cell types module --- .../components/cell-types/cell-types.component.html | 10 ++++++++-- .../lib/components/cell-types/cell-types.component.ts | 3 ++- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html index fcd6f668d..ecce419ad 100644 --- a/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html +++ b/libs/cde-visualization/src/lib/components/cell-types/cell-types.component.html @@ -1,6 +1,12 @@ Cell Types - @@ -19,7 +25,7 @@ {{ hideCellLinkData() ? 'Show' : 'Hide' }} Cell Link Data Date: Thu, 10 Oct 2024 12:31:37 -0400 Subject: [PATCH 50/50] update padding and selected color for button toggle --- .../button-toggle-size.directive.ts | 6 +++- .../button-toggle-styles.component.scss | 32 +++++++++++++------ .../lib/button-toggle.component.stories.ts | 16 +++++----- 3 files changed, 36 insertions(+), 18 deletions(-) diff --git a/libs/design-system/button-toggle/src/lib/button-toggle-size/button-toggle-size.directive.ts b/libs/design-system/button-toggle/src/lib/button-toggle-size/button-toggle-size.directive.ts index 0350a3b8b..b2597f08e 100644 --- a/libs/design-system/button-toggle/src/lib/button-toggle-size/button-toggle-size.directive.ts +++ b/libs/design-system/button-toggle/src/lib/button-toggle-size/button-toggle-size.directive.ts @@ -1,7 +1,7 @@ import { computed, Directive, input } from '@angular/core'; /** Input options for icon button size */ -export type IconButtonSize = 'medium' | 'large'; +export type IconButtonSize = 'small' | 'medium' | 'large'; /** Interface for ButtonToggle Config */ interface ButtonToggleConfig { @@ -13,6 +13,10 @@ interface ButtonToggleConfig { /** Record of button sizes (number in rem) */ const BUTTON_CONFIG: Record = { + small: { + lineHeight: 18, + font: '--sys-label-small', + }, medium: { lineHeight: 21, font: '--sys-label-medium', diff --git a/libs/design-system/button-toggle/src/lib/button-toggle-styles/button-toggle-styles.component.scss b/libs/design-system/button-toggle/src/lib/button-toggle-styles/button-toggle-styles.component.scss index 4d3196477..f35f5b666 100644 --- a/libs/design-system/button-toggle/src/lib/button-toggle-styles/button-toggle-styles.component.scss +++ b/libs/design-system/button-toggle/src/lib/button-toggle-styles/button-toggle-styles.component.scss @@ -1,10 +1,13 @@ mat-button-toggle-group { --mat-standard-button-toggle-shape: 0.25rem; --mat-standard-button-toggle-divider-color: var(--sys-primary); - --mat-standard-button-toggle-selected-state-background-color: var(--sys-tertiary); - --mat-standard-button-toggle-selected-state-text-color: var(--sys-on-primary); + --mat-standard-button-toggle-selected-state-background-color: color-mix( + in srgb, + var(--sys-tertiary) 20%, + transparent + ); + --mat-standard-button-toggle-selected-state-text-color: var(--sys-secondary); --mat-standard-button-toggle-hover-state-layer-opacity: 0.04; - width: 100%; &.mat-button-toggle-group-appearance-standard { border: unset; @@ -13,6 +16,7 @@ mat-button-toggle-group { .mat-button-toggle { width: 100%; + font: inherit; &:active { --mat-standard-button-toggle-hover-state-layer-opacity: 0.08; @@ -20,24 +24,34 @@ mat-button-toggle-group { } .mat-button-toggle:not(.mat-button-toggle-checked) .mat-button-toggle-button { - padding: 0.5rem 1.15rem; + padding: 0.5rem 1rem; } .mat-button-toggle.mat-button-toggle-checked .mat-button-toggle-button { - padding: 0.5rem 0.2rem; + padding: 0.5rem 1rem; + } + + .mat-button-toggle-appearance-standard .mat-button-toggle-label-content { + padding: 0; } &[hraButtonToggleSize='medium'] { .mat-button-toggle:not(.mat-button-toggle-checked) .mat-button-toggle-button { - padding: 0.3438rem 1.15rem; + padding: 0.3438rem 0.5rem; } .mat-button-toggle.mat-button-toggle-checked .mat-button-toggle-button { - padding: 0.3438rem 0.2rem; + padding: 0.3438rem 0.5rem; } + } - .mat-button-toggle .mat-button-toggle-label-content { - vertical-align: middle; + &[hraButtonToggleSize='small'] { + .mat-button-toggle:not(.mat-button-toggle-checked) .mat-button-toggle-button { + padding: 0.3125rem 0.5rem; + } + + .mat-button-toggle.mat-button-toggle-checked .mat-button-toggle-button { + padding: 0.3125rem 0.5rem; } } } diff --git a/libs/design-system/button-toggle/src/lib/button-toggle.component.stories.ts b/libs/design-system/button-toggle/src/lib/button-toggle.component.stories.ts index b9d55f02e..619627f4c 100644 --- a/libs/design-system/button-toggle/src/lib/button-toggle.component.stories.ts +++ b/libs/design-system/button-toggle/src/lib/button-toggle.component.stories.ts @@ -29,7 +29,7 @@ export const SingleSelect: Story = { argTypes: { size: { control: 'select', - options: ['medium', 'large'], + options: ['small', 'medium', 'large'], }, }, render: (args) => ({ @@ -38,9 +38,9 @@ export const SingleSelect: Story = { - Button - Button - Button + Button + Button + Button `, }), @@ -53,7 +53,7 @@ export const MultiSelect: Story = { argTypes: { size: { control: 'select', - options: ['medium', 'large'], + options: ['small', 'medium', 'large'], }, }, render: (args) => ({ @@ -62,9 +62,9 @@ export const MultiSelect: Story = { - Button - Button - Button + Button + Button + Button `, }),