@genspectrum/dashboard-components 0.6.1 → 0.6.3

package/dist/genspectrum-components.d.ts

@@ -180,6 +180,53 @@ export declare class DateRangeSelectorComponent extends PreactLitAdapter {
 
 declare type LapisFilter = Record<string, string | number | null | boolean>;
 
+/**
+ *
+ * ## Context
+ *
+ * This component provides a text input field to filter by lineages.
+ * Currently, it is designed to work well with Pango Lineages,
+ * but it may also be used for other lineage types, if suitable.
+ *
+ * It fetches all available values of the `lapisField` from the LAPIS instance
+ * and provides an autocomplete list with the available values of the lineage and sublineage queries
+ * (a `*` appended to the lineage value).
+ *
+ * @fires {CustomEvent<Record<string, string>>} gs-lineage-filter-changed
+ * Fired when the input field is changed.
+ * The `details` of this event contain an object with the `lapisField` as key and the input value as value.
+ * Example:
+ * ```
+ * {
+ *  "pangoLineage": "B.1.1.7"
+ * }
+ *  ```
+ */
+export declare class LineageFilterComponent extends PreactLitAdapter {
+    /**
+     * The initial value to use for this lineage filter.
+     */
+    initialValue: string;
+    /**
+     * Required.
+     *
+     * The LAPIS field name to use for this lineage filter.
+     * The field must exist on this LAPIS instance.
+     */
+    lapisField: string;
+    /**
+     * The placeholder text to display in the input field.
+     */
+    placeholderText: string;
+    /**
+     * The width of the component.
+     *
+     * Visit https://genspectrum.github.io/dashboard-components/?path=/docs/components-size-of-components--docs for more information.
+     */
+    width: string;
+    render(): JSX_2.Element;
+}
+
 /**
  * ## Context
  *
@@ -441,6 +488,62 @@ 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.
+ *
+ */
+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
  *
@@ -888,6 +991,13 @@ declare global {
 }
 
 
+declare global {
+    interface HTMLElementTagNameMap {
+        'gs-mutations-over-time-component': MutationsOverTimeComponent;
+    }
+}
+
+
 declare global {
     interface HTMLElementTagNameMap {
         'gs-date-range-selector': DateRangeSelectorComponent;
@@ -929,15 +1039,6 @@ declare global {
 }
 
 
-declare module 'chart.js' {
-    interface CartesianScaleTypeRegistry {
-        logit: {
-            options: CoreScaleOptions;
-        };
-    }
-}
-
-
 declare global {
     interface HTMLElementTagNameMap {
         'gs-lineage-filter': LineageFilterComponent;
@@ -947,3 +1048,12 @@ declare global {
     }
 }
 
+
+declare module 'chart.js' {
+    interface CartesianScaleTypeRegistry {
+        logit: {
+            options: CoreScaleOptions;
+        };
+    }
+}
+

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));

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@genspectrum/dashboard-components",
-    "version": "0.6.1",
+    "version": "0.6.3",
     "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/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);
 }