@genspectrum/dashboard-components 0.6.2 → 0.6.4

package/dist/genspectrum-components.d.ts

@@ -488,6 +488,67 @@ export declare class MutationsComponent extends PreactLitAdapterWithGridJsStyles
     render(): JSX_2.Element;
 }
 
+/**
+ * ## Context
+ *
+ * This component displays mutations (substitutions and deletions) over time for a dataset selected by a LAPIS filter.
+ * The shown date range is determined by the date field in the LAPIS filter.
+ * If the date field is not set, the date range is determined by all available dates in the dataset.
+ *
+ * ## Views
+ *
+ * ### Grid View
+ *
+ * The grid view shows the proportion for each mutation over date ranges.
+ *
+ * The grid will show at max 100 rows and 200 columns for browser performance reasons.
+ * More data might make the browser unresponsive.
+ * If the numbers are exceeded, an error message will be shown.
+ * In both cases, the `lapisFilter` should be narrowed down to reduce the number of mutations or date ranges.
+ * The number of date ranges can also be reduced by selecting a larger granularity (months instead of weeks).
+ */
+export declare class MutationsOverTimeComponent extends PreactLitAdapterWithGridJsStyles {
+    /**
+     * Required.
+     *
+     * LAPIS filter to select the displayed data.
+     */
+    lapisFilter: Record<string, string | number | null | boolean>;
+    /**
+     * The type of the sequence for which the mutations should be shown.
+     */
+    sequenceType: 'nucleotide' | 'amino acid';
+    /**
+     * A list of tabs with views that this component should provide.
+     */
+    views: 'grid'[];
+    /**
+     * The width of the component.
+     *
+     * Visit https://genspectrum.github.io/dashboard-components/?path=/docs/components-size-of-components--docs for more information.
+     */
+    width: string;
+    /**
+     * The height of the component.
+     *
+     * Visit https://genspectrum.github.io/dashboard-components/?path=/docs/components-size-of-components--docs for more information.
+     */
+    height: string;
+    /**
+     * The granularity of the time axis.
+     */
+    granularity: 'day' | 'week' | 'month' | 'year';
+    /**
+     * Required.
+     *
+     * The LAPIS field that the data should be aggregated by.
+     * The values will be used for the columns of the grid.
+     * Must be a field of type `date` in LAPIS.
+     */
+    lapisDateField: string;
+    render(): JSX_2.Element;
+}
+
 /**
  * ## Context
  *
@@ -902,14 +963,14 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-mutations-component': MutationsComponent;
+        'gs-prevalence-over-time': PrevalenceOverTimeComponent;
     }
 }
 
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-prevalence-over-time': PrevalenceOverTimeComponent;
+        'gs-mutations-component': MutationsComponent;
     }
 }
 
@@ -935,6 +996,13 @@ declare global {
 }
 
 
+declare global {
+    interface HTMLElementTagNameMap {
+        'gs-mutations-over-time-component': MutationsOverTimeComponent;
+    }
+}
+
+
 declare global {
     interface HTMLElementTagNameMap {
         'gs-date-range-selector': DateRangeSelectorComponent;

package/dist/style.css

@@ -376,7 +376,7 @@ input[type="range"] {
     background-color: #C6C6C6;
     pointer-events: none;
 }/*
-! tailwindcss v3.4.4 | MIT License | https://tailwindcss.com
+! tailwindcss v3.4.6 | MIT License | https://tailwindcss.com
 *//*
 1. Prevent padding and border from affecting element width. (https://github.com/mozdevs/cssremedy/issues/4)
 2. Allow adding a border to an element by just adding a border-width. (https://github.com/tailwindcss/tailwindcss/pull/116)
@@ -2825,9 +2825,6 @@ input.tab:checked + .tab-content,
 .mb-2 {
   margin-bottom: 0.5rem;
 }
-.ml-2 {
-  margin-left: 0.5rem;
-}
 .ml-2\.5 {
   margin-left: 0.625rem;
 }
@@ -3032,6 +3029,9 @@ input.tab:checked + .tab-content,
   padding-top: 1rem;
   padding-bottom: 1rem;
 }
+.text-center {
+  text-align: center;
+}
 .text-justify {
   text-align: justify;
 }
@@ -3123,6 +3123,9 @@ input.tab:checked + .tab-content,
   --tw-bg-opacity: 1;
   background-color: rgb(243 244 246 / var(--tw-bg-opacity));
 }
+.hover\:font-bold:hover {
+  font-weight: 700;
+}
 .hover\:text-blue-700:hover {
   --tw-text-opacity: 1;
   color: rgb(29 78 216 / var(--tw-text-opacity));
@@ -3147,6 +3150,9 @@ input.tab:checked + .tab-content,
   --tw-ring-offset-shadow: var(--tw-ring-inset) 0 0 0 var(--tw-ring-offset-width) var(--tw-ring-offset-color);
   --tw-ring-shadow: var(--tw-ring-inset) 0 0 0 calc(0px + var(--tw-ring-offset-width)) var(--tw-ring-color);
   box-shadow: var(--tw-ring-offset-shadow), var(--tw-ring-shadow), var(--tw-shadow, 0 0 #0000);
+}
+.peer:hover ~ .peer-hover\:block {
+  display: block;
 }.flatpickr-calendar{background:transparent;opacity:0;display:none;text-align:center;visibility:hidden;padding:0;-webkit-animation:none;animation:none;direction:ltr;border:0;font-size:14px;line-height:24px;border-radius:5px;position:absolute;width:307.875px;-webkit-box-sizing:border-box;box-sizing:border-box;-ms-touch-action:manipulation;touch-action:manipulation;background:#fff;-webkit-box-shadow:1px 0 0 #e6e6e6,-1px 0 0 #e6e6e6,0 1px 0 #e6e6e6,0 -1px 0 #e6e6e6,0 3px 13px rgba(0,0,0,0.08);box-shadow:1px 0 0 #e6e6e6,-1px 0 0 #e6e6e6,0 1px 0 #e6e6e6,0 -1px 0 #e6e6e6,0 3px 13px rgba(0,0,0,0.08)}.flatpickr-calendar.open,.flatpickr-calendar.inline{opacity:1;max-height:640px;visibility:visible}.flatpickr-calendar.open{display:inline-block;z-index:99999}.flatpickr-calendar.animate.open{-webkit-animation:fpFadeInDown 300ms cubic-bezier(.23,1,.32,1);animation:fpFadeInDown 300ms cubic-bezier(.23,1,.32,1)}.flatpickr-calendar.inline{display:block;position:relative;top:2px}.flatpickr-calendar.static{position:absolute;top:calc(100% + 2px)}.flatpickr-calendar.static.open{z-index:999;display:block}.flatpickr-calendar.multiMonth .flatpickr-days .dayContainer:nth-child(n+1) .flatpickr-day.inRange:nth-child(7n+7){-webkit-box-shadow:none !important;box-shadow:none !important}.flatpickr-calendar.multiMonth .flatpickr-days .dayContainer:nth-child(n+2) .flatpickr-day.inRange:nth-child(7n+1){-webkit-box-shadow:-2px 0 0 #e6e6e6,5px 0 0 #e6e6e6;box-shadow:-2px 0 0 #e6e6e6,5px 0 0 #e6e6e6}.flatpickr-calendar .hasWeeks .dayContainer,.flatpickr-calendar .hasTime .dayContainer{border-bottom:0;border-bottom-right-radius:0;border-bottom-left-radius:0}.flatpickr-calendar .hasWeeks .dayContainer{border-left:0}.flatpickr-calendar.hasTime .flatpickr-time{height:40px;border-top:1px solid #e6e6e6}.flatpickr-calendar.noCalendar.hasTime .flatpickr-time{height:auto}.flatpickr-calendar:before,.flatpickr-calendar:after{position:absolute;display:block;pointer-events:none;border:solid transparent;content:'';height:0;width:0;left:22px}.flatpickr-calendar.rightMost:before,.flatpickr-calendar.arrowRight:before,.flatpickr-calendar.rightMost:after,.flatpickr-calendar.arrowRight:after{left:auto;right:22px}.flatpickr-calendar.arrowCenter:before,.flatpickr-calendar.arrowCenter:after{left:50%;right:50%}.flatpickr-calendar:before{border-width:5px;margin:0 -5px}.flatpickr-calendar:after{border-width:4px;margin:0 -4px}.flatpickr-calendar.arrowTop:before,.flatpickr-calendar.arrowTop:after{bottom:100%}.flatpickr-calendar.arrowTop:before{border-bottom-color:#e6e6e6}.flatpickr-calendar.arrowTop:after{border-bottom-color:#fff}.flatpickr-calendar.arrowBottom:before,.flatpickr-calendar.arrowBottom:after{top:100%}.flatpickr-calendar.arrowBottom:before{border-top-color:#e6e6e6}.flatpickr-calendar.arrowBottom:after{border-top-color:#fff}.flatpickr-calendar:focus{outline:0}.flatpickr-wrapper{position:relative;display:inline-block}.flatpickr-months{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex}.flatpickr-months .flatpickr-month{background:transparent;color:rgba(0,0,0,0.9);fill:rgba(0,0,0,0.9);height:34px;line-height:1;text-align:center;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none;overflow:hidden;-webkit-box-flex:1;-webkit-flex:1;-ms-flex:1;flex:1}.flatpickr-months .flatpickr-prev-month,.flatpickr-months .flatpickr-next-month{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none;text-decoration:none;cursor:pointer;position:absolute;top:0;height:34px;padding:10px;z-index:3;color:rgba(0,0,0,0.9);fill:rgba(0,0,0,0.9)}.flatpickr-months .flatpickr-prev-month.flatpickr-disabled,.flatpickr-months .flatpickr-next-month.flatpickr-disabled{display:none}.flatpickr-months .flatpickr-prev-month i,.flatpickr-months .flatpickr-next-month i{position:relative}.flatpickr-months .flatpickr-prev-month.flatpickr-prev-month,.flatpickr-months .flatpickr-next-month.flatpickr-prev-month{/*
       /*rtl:begin:ignore*/left:0/*
       /*rtl:end:ignore*/}/*

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@genspectrum/dashboard-components",
-    "version": "0.6.2",
+    "version": "0.6.4",
     "description": "GenSpectrum web components for building dashboards",
     "type": "module",
     "license": "AGPL-3.0-only",
@@ -68,6 +68,7 @@
         "flatpickr": "^4.6.13",
         "gridjs": "^6.2.0",
         "lit": "^3.1.3",
+        "object-hash": "^3.0.0",
         "preact": "^10.20.1",
         "zod": "^3.23.0"
     },
@@ -87,6 +88,7 @@
         "@storybook/web-components": "^8.0.9",
         "@storybook/web-components-vite": "^8.0.9",
         "@types/node": "^20.12.7",
+        "@types/object-hash": "^3.0.6",
         "@typescript-eslint/eslint-plugin": "^7.14.1",
         "@typescript-eslint/parser": "^7.14.1",
         "autoprefixer": "^10.4.19",

package/src/constants.ts

@@ -1,4 +1,4 @@
-export const LAPIS_URL = 'https://lapis.cov-spectrum.org/open/v2/';
+export const LAPIS_URL = 'https://lapis.cov-spectrum.org/open/v2';
 
 export const AGGREGATED_ENDPOINT = `${LAPIS_URL}/sample/aggregated`;
 export const NUCLEOTIDE_MUTATIONS_ENDPOINT = `${LAPIS_URL}/sample/nucleotideMutations`;

package/src/lapisApi/lapisTypes.ts

@@ -30,6 +30,7 @@ const mutationProportionCount = z.object({
     position: z.number(),
 });
 export const mutationsResponse = makeLapisResponse(z.array(mutationProportionCount));
+export type MutationsResponse = z.infer<typeof mutationsResponse>;
 
 const insertionCount = z.object({
     insertion: z.string(),

package/src/operator/FillMissingOperator.spec.ts

@@ -10,7 +10,9 @@ describe('FillMissingOperator', () => {
         const query = new FillMissingOperator(
             child,
             'id',
-            (ids) => [Math.min(...ids), Math.max(...ids)],
+            (ids) => {
+                return { min: Math.min(...ids), max: Math.max(...ids) };
+            },
             (min, max) => {
                 const result = [];
                 for (let i = min; i <= max; i++) {

package/src/operator/FillMissingOperator.ts

@@ -5,7 +5,9 @@ export class FillMissingOperator<Data, KeyToFill extends keyof Data> implements
     constructor(
         private child: Operator<Data>,
         private keyField: KeyToFill,
-        private getMinMaxFn: (values: Iterable<Data[KeyToFill]>) => [Data[KeyToFill], Data[KeyToFill]] | null,
+        private getMinMaxFn: (
+            values: Iterable<Data[KeyToFill]>,
+        ) => { min: Data[KeyToFill]; max: Data[KeyToFill] } | null,
         private getAllRequiredKeysFn: (min: Data[KeyToFill], max: Data[KeyToFill]) => Data[KeyToFill][],
         private defaultValueFn: (key: Data[KeyToFill]) => Data,
     ) {}
@@ -17,7 +19,7 @@ export class FillMissingOperator<Data, KeyToFill extends keyof Data> implements
         if (minMax === null) {
             return childEvaluated;
         }
-        const [min, max] = minMax;
+        const { min, max } = minMax;
         const requiredKeys = this.getAllRequiredKeysFn(min, max);
         const content = childEvaluated.content;
         for (const key of requiredKeys) {

package/src/preact/components/tooltip.stories.tsx

@@ -0,0 +1,54 @@
+import { type Meta, type StoryObj } from '@storybook/preact';
+import { expect, waitFor, within } from '@storybook/test';
+
+import Tooltip, { type TooltipProps } from './tooltip';
+
+const meta: Meta<TooltipProps> = {
+    title: 'Component/Tooltip',
+    component: Tooltip,
+    parameters: { fetchMock: {} },
+};
+
+export default meta;
+
+const tooltipContent = 'This is some content.';
+
+export const TooltipStory: StoryObj<TooltipProps> = {
+    render: (args) => (
+        <div class='flex justify-center px-4 py-16'>
+            <Tooltip {...args}>
+                <div>Hover me</div>
+            </Tooltip>
+        </div>
+    ),
+    args: {
+        content: tooltipContent,
+    },
+};
+
+export const RendersStringContent: StoryObj<TooltipProps> = {
+    ...TooltipStory,
+    play: async ({ canvasElement }) => {
+        const canvas = within(canvasElement);
+        const tooltipBase = canvas.getByText('Hover me');
+
+        await waitFor(() => expect(tooltipBase).toBeInTheDocument());
+
+        await waitFor(() => expect(canvas.queryByText(tooltipContent, { exact: false })).toBeInTheDocument());
+    },
+};
+
+export const RendersComponentConent: StoryObj<TooltipProps> = {
+    ...TooltipStory,
+    args: {
+        content: <div>{tooltipContent}</div>,
+    },
+    play: async ({ canvasElement }) => {
+        const canvas = within(canvasElement);
+        const tooltipBase = canvas.getByText('Hover me');
+
+        await waitFor(() => expect(tooltipBase).toBeInTheDocument());
+
+        await waitFor(() => expect(canvas.queryByText(tooltipContent, { exact: false })).toBeInTheDocument());
+    },
+};

package/src/preact/components/tooltip.tsx

@@ -0,0 +1,31 @@
+import { flip, offset, shift } from '@floating-ui/dom';
+import { type FunctionComponent } from 'preact';
+import { useRef } from 'preact/hooks';
+import { type JSXInternal } from 'preact/src/jsx';
+
+import { dropdownClass } from './dropdown';
+import { useFloatingUi } from '../shared/floating-ui/hooks';
+
+export type TooltipProps = {
+    content: string | JSXInternal.Element;
+};
+
+const Tooltip: FunctionComponent<TooltipProps> = ({ children, content }) => {
+    const referenceRef = useRef<HTMLDivElement>(null);
+    const floatingRef = useRef<HTMLDivElement>(null);
+
+    useFloatingUi(referenceRef, floatingRef, [offset(5), shift(), flip()]);
+
+    return (
+        <div className='relative'>
+            <div className='peer' ref={referenceRef}>
+                {children}
+            </div>
+            <div ref={floatingRef} className={`${dropdownClass} hidden peer-hover:block`}>
+                {content}
+            </div>
+        </div>
+    );
+};
+
+export default Tooltip;

package/src/preact/mutationComparison/queryMutationData.ts

@@ -28,6 +28,17 @@ export function filterMutationData(
     data: MutationData[],
     displayedSegments: DisplayedSegment[],
     displayedMutationTypes: DisplayedMutationType[],
+) {
+    return data.map((mutationEntry) => ({
+        displayName: mutationEntry.displayName,
+        data: filterBySegmentAndMutationType(mutationEntry.data, displayedSegments, displayedMutationTypes),
+    }));
+}
+
+export function filterBySegmentAndMutationType(
+    data: SubstitutionOrDeletionEntry[],
+    displayedSegments: DisplayedSegment[],
+    displayedMutationTypes: DisplayedMutationType[],
 ) {
     const byDisplayedSegments = (mutationEntry: SubstitutionOrDeletionEntry) => {
         if (mutationEntry.mutation.segment === undefined) {
@@ -45,8 +56,5 @@ export function filterMutationData(
         );
     };
 
-    return data.map((mutationEntry) => ({
-        displayName: mutationEntry.displayName,
-        data: mutationEntry.data.filter(byDisplayedSegments).filter(byDisplayedMutationTypes),
-    }));
+    return data.filter(byDisplayedSegments).filter(byDisplayedMutationTypes);
 }